| |
Ncbi-mime-asn1 ::= strucseq {
structure {
id {
mmdb-id 231 } ,
descr {
name "1AMC" ,
pdb-comment "remark 3: Refinement." ,
pdb-comment "remark 3: Program 1 X-Plor 3.0" ,
pdb-comment "remark 3: Program 1 Brunger" ,
pdb-comment "remark 3: Program 2
Generate,Dgsa,Accept,Average," ,
pdb-comment "remark 3: Program 2 And Refine Protocols" ,
pdb-comment "remark 3: Authors 2
Nilges,Gronenborn,Brunger," ,
pdb-comment "remark 3: Authors 2 Clore,Kuszewski" ,
pdb-comment "remark 3: Number Of Protein Atoms: 438" ,
pdb-comment "remark 3: 1.) 100 Structures Were Generated By The Dgsa
Protocol" ,
pdb-comment "remark 3: With The Following Modifications: Initial
Temp3000k," ,
pdb-comment "remark 3: Heating Steps5000k Cooling Steps5000k, 2000
Steps Powell" ,
pdb-comment "remark 3: Minimization, Time Step0.003 Ps, And Dielectric" ,
pdb-comment "remark 3: Constant30." ,
pdb-comment "remark 3: 2.) 95 Of The 100 Structures Were Accepted By
The Accept" ,
pdb-comment "remark 3: Protocol." ,
pdb-comment "remark 3: 3.) The 95 Structures Were Averaged And
Minimized With The" ,
pdb-comment "remark 3: Refine Protocol With The Following
Modifications: Cooling" ,
pdb-comment "remark 3: Steps5000 And Powell Minimization Steps10000" ,
pdb-comment "remark 3: Coordinates Below Were Produced By Minimizing
The Average" ,
pdb-comment "remark 3: Of All Acceptable Structures Which Were
Generated By A" ,
pdb-comment "remark 3: Hybrid Distance Geometry And Simulated
Annealing Protocol." ,
pdb-comment "remark 3: Statistics Indicating Agreement Of Minimized
Average" ,
pdb-comment "remark 3: Structure With Experimental Restraints And
Ideal Geometry" ,
pdb-comment "remark 3: Follow." ,
pdb-comment "remark 3: Restraint Type Number Rmsd" ,
pdb-comment "remark 3: Distance (No Violations Greater Than 3.0
Angstroms)" ,
pdb-comment "remark 3: All 297 0.050" ,
pdb-comment "remark 3: Interresidue 204 0.047" ,
pdb-comment "remark 3: Intraresidue 47 0.088" ,
pdb-comment "remark 3: Hydrogen Bond 46 0.015" ,
pdb-comment "remark 3: Torsion Angles (No Violations Greater Than 5.0
Degrees)" ,
pdb-comment "remark 3: 27 Phi, 2 Chi 29 0.004" ,
pdb-comment "remark 3: Idealized Geometry" ,
pdb-comment "remark 3: Type Rmsd" ,
pdb-comment "remark 3: Bonds 0.004 Angstroms" ,
pdb-comment "remark 3: Angles 0.387 Degrees" ,
pdb-comment "remark 3: Impropers 0.007 Degrees" ,
pdb-comment "remark 3: X-Plor Potential Energy Terms" ,
pdb-comment "remark 3: Term Type Energy (KcalMOL)" ,
pdb-comment "remark 3: Overall 70.0" ,
pdb-comment "remark 3: Noe 36.8" ,
pdb-comment "remark 3: Cdih 3.1" ,
pdb-comment "remark 3: Bonds 5.9" ,
pdb-comment "remark 3: Angles 18.0" ,
pdb-comment "remark 3: Improper 4.4" ,
pdb-comment "remark 3: Vdw (Repel) 4.8" ,
pdb-comment "remark 4: The Coordinates In This Entry Were Generated
From Solution" ,
pdb-comment "remark 4: Nmr Data. Protein Data Bank Conventions
Require That" ,
pdb-comment "remark 4: Cryst1 And Scale Records Be Included, But The
Values On" ,
pdb-comment "remark 4: These Records Are Meaningless." ,
pdb-comment "remark 5: These Coordinates Were Generated From Solution
Nmr Data" ,
pdb-comment "remark 5: Collected In H20:trifluoroethanol-D3(4:6) And
0.5" ,
pdb-comment "remark 5: Millimolar Na2edta And 0.05 Millimolar Sodium
Azide. Ph" ,
pdb-comment "remark 5: Was Set At 3.0. Nmr Data Was Collected At 25
Degrees" ,
pdb-comment "remark 5: Celsius." ,
pdb-comment "remark 6: The Protein Was Generated By Solid Phase
Synthesis." ,
pdb-comment "remark 7: Columns 61 - 66 Of Atom Records Contain The
Rmsd Of The" ,
pdb-comment "remark 7: Atom In The Family Of The 95 Accepted
Structures. In" ,
pdb-comment "remark 7: Entries Generated Using Crystallographic
Techniques, These" ,
pdb-comment "remark 7: Columns Contain The B Value." ,
pdb-comment "remark 8: The Entire Structure Is Essentially
Alpha-Helical." ,
pdb-comment "remark 9: Residue 4 - 25 Have The Most Experimental
Restraints (Noe" ,
pdb-comment "remark 9: Cross Peaks) And Are The Most Defined." ,
pdb-comment "remark 10: Original Deposition Revised Prior To Release" ,
pdb-comment "remark 10: Tracking Number: T5569, Date Revised: 04-Dec-94" ,
pdb-comment "remark 11: Cross Reference To Sequence Database" ,
pdb-comment "remark 11: Swiss-Prot Entry Name Pdb Entry Chain
Name" ,
pdb-comment "remark 11: A4_human" ,
history {
data-source {
name-of-database "Protein Data Bank" ,
version-of-database
release-date
std {
year 1995 ,
month 2 ,
day 3 } ,
database-entry-id
other-database {
db "PDB" ,
tag
str "1AMC" } ,
database-entry-date
std {
year 1994 ,
month 11 ,
day 14 } } } ,
attribution
sub {
authors {
names
std {
{
name
name {
last "Talafous" ,
full "J.Talafous" ,
initials "J." } } ,
{
name
name {
last "Marcinowski" ,
full "K.J.Marcinowski" ,
initials "K.J." } } ,
{
name
name {
last "Klopman" ,
full "G.Klopman" ,
initials "G." } } ,
{
name
name {
last "Zagorski" ,
full "M.G.Zagorski" ,
initials "M.G." } } } } ,
imp {
date
std {
year 1994 ,
month 11 ,
day 14 } } } ,
attribution
equiv {
muid 94281210 ,
article {
title {
name "Solution structure of residues 1-28 of the amyloid
beta-peptide." } ,
authors {
names
std {
{
name
name {
last "Talafous" ,
initials "J." } } ,
{
name
name {
last "Marcinowski" ,
initials "K.J." } } ,
{
name
name {
last "Klopman" ,
initials "G." } } ,
{
name
name {
last "Zagorski" ,
initials "M.G." } } } ,
affil
str "Department of Chemistry, Case Western Reserve University,
Cleveland, Ohio 44106." } ,
from
journal {
title {
iso-jta "Biochemistry" ,
ml-jta "Biochemistry" ,
issn "0006-2960" ,
jta "A0G" } ,
imp {
date
std {
year 1994 ,
month 6 ,
day 28 } ,
volume "33" ,
issue "25" ,
pages "7788-7796" } } } } ,
attribution
equiv {
muid 92304938 ,
article {
title {
name "NMR studies of amyloid beta-peptides: proton assignments,
secondary structure, and mechanism of an alpha-helix----beta-sheet conversion
for a homologous, 28-residue, N-terminal fragment." } ,
authors {
names
std {
{
name
name {
last "Zagorski" ,
initials "M.G." } } ,
{
name
name {
last "Barrow" ,
initials "C.J." } } } ,
affil
str "Suntory Institute for Bioorganic Research, Osaka, Japan." } ,
from
journal {
title {
iso-jta "Biochemistry" ,
ml-jta "Biochemistry" ,
issn "0006-2960" ,
jta "A0G" } ,
imp {
date
std {
year 1992 ,
month 6 ,
day 23 } ,
volume "31" ,
issue "24" ,
pages "5621-5631" } } } } ,
attribution
equiv {
muid 91305935 ,
article {
title {
name "Solution structures of beta peptide and its constituent
fragments: relation to amyloid deposition." } ,
authors {
names
std {
{
name
name {
last "Barrow" ,
initials "C.J." } } ,
{
name
name {
last "Zagorski" ,
initials "M.G." } } } ,
affil
str "Suntory Institute for Bioorganic Research, Osaka, Japan." } ,
from
journal {
title {
iso-jta "Science" ,
ml-jta "Science" ,
issn "0036-8075" ,
jta "UJ7" } ,
imp {
date
std {
year 1991 ,
month 7 ,
day 12 } ,
volume "253" ,
issue "5016" ,
pages "179-182" } } } } } ,
chemical-graph {
descr {
name "Alzheimer's Disease Amyloid Beta-Peptide (Residues 1 - 28) (E.C.
Number Not Assigned) (Nmr, 5 Structures)" ,
pdb-class "Proteinase Inhibitor(Trypsin)" ,
pdb-source "Human (Homo Sapiens)" ,
assembly-type other } ,
molecule-graphs {
{
id 1 ,
descr {
name " " ,
pdb-comment "SEQRES" ,
molecule-type protein ,
organism {
org {
taxname "Homo sapiens" ,
common "human" ,
db {
{
db "taxon" ,
tag
id 9606 } } ,
orgname {
name
binomial {
genus "Homo" ,
species "sapiens" } ,
lineage "Eukaryotae; mitochondrial eukaryotes; Metazoa;
Chordata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae;
Homo" ,
gcode 1 ,
mgcode 2 ,
div "PRI" } } } } ,
seq-id
gi 999978 ,
residue-sequence {
{
id 1 ,
name " 1 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 12 } } ,
{
id 2 ,
name " 2 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 1 } } ,
{
id 3 ,
name " 3 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 19 } } ,
{
id 4 ,
name " 4 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 40 } } ,
{
id 5 ,
name " 5 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 4 } } ,
{
id 6 ,
name " 6 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 25 } } ,
{
id 7 ,
name " 7 " ,
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standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 10 } } ,
{
id 8 ,
name " 8 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 46 } } ,
{
id 9 ,
name " 9 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 22 } } ,
{
id 10 ,
name " 10 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 55 } } ,
{
id 11 ,
name " 11 " ,
residue-graph
standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 19 } } ,
{
id 12 ,
name " 12 " ,
residue-graph
standard {
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other-database {
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tag
id 1 } ,
residue-graph-id 58 } } ,
{
id 13 ,
name " 13 " ,
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standard {
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other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 25 } } ,
{
id 14 ,
name " 14 " ,
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standard {
biostruc-residue-graph-set-id
other-database {
db "Standard residue dictionary" ,
tag
id 1 } ,
residue-graph-id 25 } } ,
{
id 15 ,
name " 15 " ,
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standard {
biostruc-residue-graph-set-id
other-database {
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tag
id 1 } ,
residue-graph-id 16 } } ,
{
id 16 ,
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standard {
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other-database {
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id 1 } ,
residue-graph-id 34 } } ,
{
id 17 ,
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standard {
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id 1 } ,
residue-graph-id 31 } } ,
{
id 18 ,
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standard {
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id 19 ,
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standard {
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id 20 ,
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standard {
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id 21 ,
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standard {
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id 22 ,
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id 1 } ,
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id 23 ,
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standard {
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id 1 } ,
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{
id 24 ,
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standard {
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standard {
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id 1 } ,
residue-graph-id 35 } } } ,
inter-residue-bonds {
{
atom-id-1 {
molecule-id 1 ,
residue-id 1 ,
atom-id 1 } ,
atom-id-2 {
molecule-id 1 ,
residue-id 2 ,
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{
atom-id-1 {
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residue-id 2 ,
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atom-id-2 {
molecule-id 1 ,
residue-id 3 ,
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{
atom-id-1 {
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atom-id-2 {
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{
atom-id-1 {
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atom-id-1 {
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atom-id-1 {
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atom-id-1 {
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atom-id-1 {
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{
atom-id-1 {
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{
atom-id-1 {
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{
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{
atom-id-1 {
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{
atom-id-1 {
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atom-id-2 {
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{
atom-id-1 {
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atom-id-2 {
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{
atom-id-1 {
molecule-id 1 ,
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atom-id-2 {
molecule-id 1 ,
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{
atom-id-1 {
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atom-id-2 {
molecule-id 1 ,
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atom-id 17 } } ,
{
atom-id-1 {
molecule-id 1 ,
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atom-id-2 {
molecule-id 1 ,
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{
atom-id-1 {
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atom-id-2 {
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{
atom-id-1 {
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atom-id-2 {
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{
atom-id-1 {
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atom-id-2 {
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{
atom-id-1 {
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atom-id-2 {
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{
atom-id-1 {
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residue-id 24 ,
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atom-id-2 {
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residue-id 25 ,
atom-id 4 } } ,
{
atom-id-1 {
molecule-id 1 ,
residue-id 25 ,
atom-id 1 } ,
atom-id-2 {
molecule-id 1 ,
residue-id 26 ,
atom-id 7 } } ,
{
atom-id-1 {
molecule-id 1 ,
residue-id 26 ,
atom-id 1 } ,
atom-id-2 {
molecule-id 1 ,
residue-id 27 ,
atom-id 7 } } ,
{
atom-id-1 {
molecule-id 1 ,
residue-id 27 ,
atom-id 1 } ,
atom-id-2 {
molecule-id 1 ,
residue-id 28 ,
atom-id 9 } } } } } } ,
features {
{
id 1 ,
descr {
name "PDB secondary structure" } ,
features {
{
id 1 ,
name " H1" ,
type helix ,
location
subgraph
residues
interval {
{
molecule-id 1 ,
from 4 ,
to 25 } } } } } ,
{
id 2 ,
descr {
name "NCBI assigned secondary structure" } ,
features {
{
id 1 ,
name "helix 1" ,
type helix ,
location
subgraph
residues
interval {
{
molecule-id 1 ,
from 2 ,
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model {
{
id 3 ,
type ncbi-all-atom ,
descr {
name "Single-coordinate-per-atom model from PDB entry 1AMC with a
vector model attached" ,
pdb-method "Nmr" ,
pdb-comment "JAN 26 95 Initial Entry" } ,
model-space {
coordinate-units angstroms } ,
model-coordinates {
{
id 1 ,
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{
id 2 ,
descr {
other-comment "helix" } ,
coordinates
literal
surface {
contents
residues
interval {
{
molecule-id 1 ,
from 2 ,
to 23 } } ,
surface
cylinder {
axis-top {
scale-factor 1000000 ,
x -13856000 ,
y 711000 ,
z -372000 } ,
axis-bottom {
scale-factor 1000000 ,
x 16998000 ,
y -2862000 ,
z 587000 } ,
radius {
scale-factor 1 ,
scaled-integer-value 2 } } } } } } } } ,
sequences {
seq {
id {
pdb {
mol "1AMC" ,
rel
std {
year 1994 ,
month 11 ,
day 14 } } ,
gi 999978 } ,
descr {
pdb {
deposition
std {
year 1994 ,
month 11 ,
day 14 } ,
class "Proteinase Inhibitor(Trypsin)" ,
compound {
"Alzheimer's Disease Amyloid Beta-Peptide (Residues 1 - 28) (E.C.
Number Not Assigned) (Nmr, 5 Structures)" } ,
source {
"Human (Homo Sapiens)" } } ,
source {
org {
taxname "Homo sapiens" ,
common "human" ,
db {
{
db "taxon" ,
tag
id 9606 } } ,
orgname {
name
binomial {
genus "Homo" ,
species "sapiens" } ,
lineage "Eukaryotae; mitochondrial eukaryotes; Metazoa;
Chordata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae;
Homo" ,
gcode 1 ,
mgcode 2 ,
div "PRI" } } } } ,
inst {
repr raw ,
mol aa ,
length 28 ,
seq-data
iupacaa "DAEFRHDSGYEVHHQKLVFFAEDVGSNK" } } } }
|
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