2A5S,2RCA,1PB8,1PB7,2RC7


Conserved Protein Domain Family
PBP2_iGluR_NMDA

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cd13687: PBP2_iGluR_NMDA 
Click on image for an interactive view with Cn3D
The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily.
The ligand-binding domain of the ionotropic NMDA subtype is structurally homologous to the periplasmic-binding fold type II superfamily, while the N-terminal domain belongs to the periplasmic-binding fold type I. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.
Statistics
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PSSM-Id: 270405
Aligned: 92 rows
Threshold Bit Score: 259.877
Created: 27-Sep-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
peptide bindingdimer interface
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:peptide binding site [polypeptide binding site]
Evidence:
  • Structure:2A5S; Rattus norvegicus Nr2a ligand-binding core in complex with glutamate, contacts at 4 A.
  • Structure:1PB8; Rattus norvegicus Nr1 ligand-binding core in complex with D-serine (agonist), contacts at 4 A.
  • Structure:1PB7; Rattus norvegicus Nr1 ligand-binding core in complex with glycine (agonist), contacts at 4 A.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                      
2A5S_A       4 DNHLSIVTLEEAPFVIVedidpltetcvrntvpc-------------------rkfvkinnstnegmnvkKCCKGFCIDI 64   Norway rat
2RC7_A       4 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtnds--------smldrlfsslhssndtvpikfkKCCYGYCIDL 75   Norway rat
CAF95890   416 GHRLRVVTLVEHPFVFTrevdedgmcpagqlcldprtnrsdviqglfnqlrnpnstapdwdgtdlpedlrKCCYGYCIDL 495  Tetraodon nigrov...
AAL40734   512 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtnds--------stldslfnslhssndtvpikfkKCCYGYCIDL 583  human
BAB85559   573 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtnds--------stldslfsslhssndtvpikfkKCCYGYCIDL 644  human
Q9R1M7     512 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtnds--------smldrlfsslhssndtvpikfkKCCYGYCIDL 583  Norway rat
Q8TCU5     512 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtnds--------stldslfsslhssndtvpikfkKCCYGYCIDL 583  human
EAW58958   512 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtnds--------stldslfsslhssndtvpikfkKCCYGYCIDL 583  human
EAW58959   361 KLHLRVVTLIEHPFVFTrevddeglcpagqlcldpmtnds--------stldslfsslhssndtvpikfkKCCYGYCIDL 432  human
CAF93757   488 RRHMRVVTLVEHPFVFTrevdgdglcpagqlcldpltnes--------svleklfhslgapnaslprdhrKCCYGYCIDL 559  spotted green pu...
Feature 1                                                      ###    #                        
2A5S_A      65 LKKLSRTVKFTYDLYLVTngkhg-kkvnNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGT- 142  Norway rat
2RC7_A      76 LEQLAEDMNFDFDLYIVGdgkyg-awknGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRGt 154  Norway rat
CAF95890   496 LEKLAEDMGFTFDLYIVGdgkygalsgtGRWTGLVGDLLSGTADMAVTSFSINSARSRVIDFTSPFYSTSLGILVRSKDt 575  Tetraodon nigrov...
AAL40734   584 LEKIAEDMNFDFDLYIVGdgkyg-awknGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDt 662  human
BAB85559   645 LEKIAEDMNFDFDLYIVGdgkyg-awknGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDt 723  human
Q9R1M7     584 LEQLAEDMNFDFDLYIVGdgkyg-awknGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDt 662  Norway rat
Q8TCU5     584 LEKIAEDMNFDFDLYIVGdgkyg-awknGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDt 662  human
EAW58958   584 LEKIAEDMNFDFDLYIVGdgkyg-awknGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDt 662  human
EAW58959   433 LEKIAEDMNFDFDLYIVGdgkyg-awknGHWTGLVGDLLRGTAHMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDt 511  human
CAF93757   560 LEKLAEDMGFTFDLYIVGdgkyg-glknGRWTGLVGDLLSGSAHLAVTSFSINSARSQVIDFTSPFFSTSLGILVRTRDt 638  spotted green pu...
Feature 1                                                                                      
2A5S_A         --------------------------------------------------------------------------------      Norway rat
2RC7_A         --------------------------------------------------------------------------------      Norway rat
CAF95890   576 aapigafmwplhwsmwvgifvtlhltalfltlyewnspfgmtphgrnrlrvfsyssalnlcyailfgrtvatktpkcwtg 655  Tetraodon nigrov...
AAL40734   663 aapigafmwplhwtmwlgifvalhitavfltlyewkspfgltpkgrnrskvfsfssalnicyallfgrtvaikppkcwtg 742  human
BAB85559   724 aapigafmwplhwtmwlgifvalhitavfltlyewkspfgltpkgrnrskvfsfssalnicyallfgrtvaikppkcwtg 803  human
Q9R1M7     663 aapigafmwplhwtmwlgifvalhitaifltlyewkspfgmtpkgrnrnkvfsfssalnvcyallfgrtaaikppkcwtg 742  Norway rat
Q8TCU5     663 aapigafmwplhwtmwlgifvalhitavfltlyewkspfgltpkgrnrskvfsfssalnicyallfgrtvaikppkcwtg 742  human
EAW58958   663 aapigafmwplhwtmwlgifvalhitavfltlyewkspfgltpkgrnrskvfsfssalnicyallfgrtvaikppkcwtg 742  human
EAW58959   512 aapigafmwplhwtmwlgifvalhitavfltlyewkspfgltpkgrnrskvfsfssalnicyallfgrtvaikppkcwtg 591  human
CAF93757   639 aapigafmrplhwsmwlgifvslhltavfltlyewhspfgltprgrnrervfslssalsvcyailfgrtvavktpkcwtg 718  spotted green pu...
Feature 1                                                                                      
2A5S_A     143 ---------------------------------QVTGLSDKkfqrph--------------------------------- 156  Norway rat
2RC7_A     155 ---------------------------------ELSGIHDPklhh----------------------------------- 166  Norway rat
CAF95890   656 rflmnlwaifcllvlssytanlaavmvgektfeQVSGIHDDkvrlkscrahtmhthageshtqtssfardyekadppspl 735  Tetraodon nigrov...
AAL40734   743 rflmnlwaifcmfclstytanlaavmvgekiyeELSGIHDPklhh----------------------------------- 787  human
BAB85559   804 rflmnlwaifcmfclstytanlaavmvgekiyeELSGIHDPklhh----------------------------------- 848  human
Q9R1M7     743 rflmnlwaifcmfclstytanlaavmvgekiyeELSGIHDPklhh----------------------------------- 787  Norway rat
Q8TCU5     743 rflmnlwaifcmfclstytanlaavmvgekiyeELSGIHDPklhh----------------------------------- 787  human
EAW58958   743 rflmnlwaifcmfclstytanlaavmvgekiyeELSGIHDPklhh----------------------------------- 787  human
EAW58959   592 rflmnlwaifcmfclstytanlaavmvgekiyeELSGIHDPklhh----------------------------------- 636  human
CAF93757   719 rllmnlwaifclfclstytanlaavmvgektyeQLTGIHDPkra------------------------------------ 762  spotted green pu...
Feature 1                                                ###                                   
2A5S_A     157 -----------------------------dysppFRFGTVPNGSTERNIRnnypymhqymtRFNQRGVEDALVSLKTGk- 206  Norway rat
2RC7_A     167 ------------------------------psqgFRFGTVRESSAEDYVRqsfpemheymrRYNVPATPDGVQYLKNDpe 216  Norway rat
CAF95890   736 gvwsedvwsrtstvnpsslfrpvslpqlhhpslgFRFGTVRESSAEDYMKksfpemhdymrRYNQPTTPEGVHMLKTDpp 815  Tetraodon nigrov...
AAL40734   788 ------------------------------psqgFRFGTVRESSAEDYVRqsfpemheymrRYNVPATPDGVEYLKNDpe 837  human
BAB85559   849 ------------------------------psqgFRFGTVRESSAEDYVRqsfpemheymrRYNVPATPDGVEYLKNDpe 898  human
Q9R1M7     788 ------------------------------psqgFRFGTVRESSAEDYVRqsfpemheymrRYNVPATPDGVQYLKNDpe 837  Norway rat
Q8TCU5     788 ------------------------------psqgFRFGTVRESSAEDYVRqsfpemheymrRYNVPATPDGVEYLKNDpe 837  human
EAW58958   788 ------------------------------psqgFRFGTVRESSAEDYVRqsfpemheymrRYNVPATPDGVEYLKNDpe 837  human
EAW58959   637 ------------------------------psqgFRFGTVRESSAEDYVRqsfpemheymrRYNVPATPDGVEYLKNDpe 686  human
CAF93757   763 --------------------------------vaEDYVKKSFPEMHEYMR-----------RYNVPATPDGIHQLKGDpq 799  spotted green pu...
Feature 1            ##                                                                 
2A5S_A     207 -lDAFIYDAAVLNYKAGRdegCKLVTIGsgyiFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWL 278  Norway rat
2RC7_A     217 klDAFIMDKALLDYEVSIdadCKLLTVGk--pFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 287  Norway rat
CAF95890   816 tlDAFIMDKALLDFEVSIdadCKLLTVGk--pFAIEGYGIGLPQGSPLTRNVSEFVSRYKSDGFMDMLHDKWY 886  Tetraodon nigroviridis
AAL40734   838 klDAFIMDKALLDYEVSIdadCKLLTVGk--pFAIEGYGIGLPPNSPLTANISELISQYKSHGFMDMLHDKWY 908  human
BAB85559   899 klDAFIMDKALLDYEVSIdadCKLLTVGk--pFAIEGYGIGLPPNSPLTANISELISQYKSHGFMDMLHDKWY 969  human
Q9R1M7     838 klDAFIMDKALLDYEVSIdadCKLLTVGk--pFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 908  Norway rat
Q8TCU5     838 klDAFIMDKALLDYEVSIdadCKLLTVGk--pFAIEGYGIGLPPNSPLTANISELISQYKSHGFMDMLHDKWY 908  human
EAW58958   838 klDAFIMDKALLDYEVSIdadCKLLTVGk--pFAIEGYGIGLPPNSPLTANISELISQYKSHGFMDMLHDKWY 908  human
EAW58959   687 klDAFIMDKALLDYEVSIdadCKLLTVGk--pFAIEGYGIGLPPNSPLTANISELISQYKSHGFMDMLHDKWY 757  human
CAF93757   800 rlDAFIMDKALLDYEVSIdadCKMLTVGk--pFAIEGYGIGLPQNSPLTSNLSALVSQYKSDGFMDLLHDKWY 870  spotted green pufferfish

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