1PB7,1PB8,1Y1M


Conserved Protein Domain Family
PBP2_iGluR_NMDA_Nr1

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cd13719: PBP2_iGluR_NMDA_Nr1 
Click on image for an interactive view with Cn3D
The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily.
This group contains the ligand binding domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of 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. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site.
Statistics
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PSSM-Id: 270437
Aligned: 51 rows
Threshold Bit Score: 408.287
Created: 19-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:1PB8; Rattus norvegicus Nr1 ligand-binding core in complex with D-serine (agonist), contacts at 4 A.
    View structure with Cn3D
  • Structure:1PB7; Rattus norvegicus Nr1 ligand-binding core in complex with glycine (agonist), contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                         
1PB7_A          3 STRLKIVTIHQEPFVYVKPtmsdgtckeeftvngdpvkk---victgpndtspgsprhtvpQCCYGFCIDLLIKLARTMN 79   Norway rat
CAP24109      418 PKHLRVVTVADPPFVYTTPvgspsqcaelgstvvewskfdkivvpgpwyscpmtsantteyFCCAGLAIDLLSNLSLPEV 497  Caenorhabditi...
EFX71929      438 PTFLKVMTIVEQPFVYARRvsdpsgesclaadgeva---------cpwfnntadssgtdrfYCCRGYCIDLLKELARKNN 508  common water ...
1PB8_A          3 STRLKIVTIHQEPFVYVKPtmsdgtckeeftvngdpvkk---victgpndtspgsprhtvpQCCYGFCIDLLIKLARTMN 79   Norway rat
NP_495033     394 PKHLRVVTVADPPFVYTTPigspsqcaelgntvvewsifdkivvsgpwyscpltlensteyFCCAGLAIDLLSNLSLPEA 473  Caenorhabditi...
NP_001011573  411 PTHLKVLTIEEKPFVYVREiafsesclpeeilc---------------phfnvtdgettktFCCKGYCMDLLKELSKTIN 475  honey bee
XP_969654     405 PTHLKVLTIEEKPFVYVRKlvepqdvctaeeip---------------cphfnatqdlagsYCCKGYCMDLLKELSKKIN 469  red flour beetle
XP_001653302  412 PTHLKVLTIEEKPFVYVRKllddeidceddeia---------------cphfnstdgnekdYCCKGYCIDLLKALAQRIN 476  yellow fever ...
EEB11312      415 PTHLKVLTIEEKPFVYVRTikepedkcdkneip---------------cpffnateddyqlRCCRGFCMDLLMELSKIVN 479  human body louse
EEC15663       82 PKHLKVATIAERPFVWVRPvpdesdclpseif----------------cpwtnssdgiaypFCCEGYCMDLLQSLSQKLN 145  black-legged ...
Feature 1                                                                                 ###    #
1PB7_A         80 ----------------------FTYEVHLVAdgkFGTQERvnn------snkKEWNGMMGELLSGQADMIVAPLTINNER 131  Norway rat
CAP24109      498 hnlnifrkrnskiqannsidtsFTFSLHLNEs--YGVIQAaet-------tgITIGGVIGELDGDTADMAIGGITINPER 568  Caenorhabditi...
EFX71929      509 ----------------------FTYSLALSPdgqFGSLSPkng------tgkKEWNGLIGELVNDRADMIVAPLTINPER 560  common water ...
1PB8_A         80 ----------------------FTYEVHLVAdgkFGTQERvnn------snkKEWNGMMGELLSGQADMIVAPLTINTER 131  Norway rat
NP_495033     474 nnsi---------------dtsFTFSLHLNEsygVVQASEtt---------gITISGVIGELDGDTADMAIGGITINPER 529  Caenorhabditi...
NP_001011573  476 ----------------------FTYSLALSPdgqFGNYIIknns----vggkKEWTGLIGELVNERADMIVAPLTINPER 529  honey bee
XP_969654     470 ----------------------FTYSLALSPdgqFGNYIIrnss----gsgkKEWTGLIGELVGERADMIVAPLTINPER 523  red flour beetle
XP_001653302  477 ----------------------FTYDLALSPdgqFGHYQLknhttgigtsvkKEWNGLIGELVAERADLIVAPLTINPER 534  yellow fever ...
EEB11312      480 ----------------------FTYSLALSPdgqFGSYVVrnt------gnkKEWTGLIGELVTERADMIVAPLTINPER 531  human body louse
EEC15663      146 ----------------------FTYTLYQVQdgqYGTFDFvng------sthKRWSGMVGDLVRGVADMIIAPLTITPER 197  black-legged ...
Feature 1                                                                                         
1PB7_A        132 AQYIEFSKPFKYQGLTILVKKGT--------------------------------------------------------- 154  Norway rat
CAP24109      569 ERIVDFSEPWLYHGIRILEKNIPrdspmqsflqplqsslwtalfisvilvglaiffldfkspferfyqadremdqdlkke 648  Caenorhabditi...
EFX71929      561 AQVIEFSKPFKYQGITILEKKQPksstlvsflqpfrdtlwilvmvsvhvvalvlylldrfspfgrfrlanaenteedaln 640  common water ...
1PB8_A        132 AQYIEFSKPFKYQGLTILVKKGT--------------------------------------------------------- 154  Norway rat
NP_495033     530 ERIVDFTEPWLYHGIRILEKNIPrdspmqsflqplqsslwtalfisvilvglaiycldfkspferfyqadkemeqdlkke 609  Caenorhabditi...
NP_001011573  530 AEFIEFSKPFKYQGITILEKKPSrsstlvsflqpfsntlwilvmvsvhvvalvlylldrfspfgrfklantdgteedaln 609  honey bee
XP_969654     524 AEFIEFSKPFKYQGITILEKKPSrsstlvsflqpfsntlwilvmvsvhvvalvlylldrfspfgrfklantdgteedaln 603  red flour beetle
XP_001653302  535 AEFIEFSKPFKYQGITILEKKPSrsstlvsflqpfsntlwilvmvsvhvvalvlylldrfspfgrfklttndgteedaln 614  yellow fever ...
EEB11312      532 AEFIEFSKPFKYQGITILEKKPSrsstlvsflqpfsntlwilvmvsvhvvalvlylldrfspfgrfkignaegteedaln 611  human body louse
EEC15663      198 SMEIEFTKPFKYQGITILAKKANksstlasflqpfqktlwilvmvsvhvvalalylldrfspfgryklpnsdateedaln 277  black-legged ...
Feature 1                                                                                         
1PB7_A        155 --------------------------------------------------------------------------RITGIN 160  Norway rat
CAP24109      649 felwvgndvdenvnfgeamwfvwgvllnsgvsektprscsarvlgivwcgfcmimvasytanlaaflvldqpekGLTGVT 728  Caenorhabditi...
EFX71929      641 ls--------------saiwfawgvllnsgigegtprsfsarvlgmvwagfamiivasytanlaaflvldrpktSLSGIN 706  common water ...
1PB8_A        155 --------------------------------------------------------------------------RITGIN 160  Norway rat
NP_495033     610 felwigkdadenvnfgeamwfvwgvllnsgvsektprscsarvlgivwcgfcmimvasytanlaaflvldqpekGLTGVT 689  Caenorhabditi...
NP_001011573  610 ls--------------savwfawgvllnsgigegtprsfsarvlgmvwagfamiivasytanlaaflvlerpktKLTGIN 675  honey bee
XP_969654     604 ls--------------saiwfawgvllnsgigegtprsfsarvlgmvwagfamiivasytanlaaflvlerpktKLTGIN 669  red flour beetle
XP_001653302  615 ls--------------saiwfawgvllnsgigegtprsfsarvlgmvwagfamiivasytanlaaflvlerpktKLSGIN 680  yellow fever ...
EEB11312      612 ls--------------saiwfawgvllnsgigegtprsfsarvlgmvwagfamiivasytanlaaflvlerpktKLSGIN 677  human body louse
EEC15663      278 ls--------------saiwfawgvllnsgiaegtprsfsgrvlgmvwagfamivvasytanlaaflvlekpesSLSGIN 343  black-legged ...
Feature 1                            ###                                           ##             
1PB7_A        161 DPrlrn-psdkFIYATVKQSSVDIYFR-RQVELSTMYRhmeKHNYESAAEAIQAVRDN-KLHAFIWDSAVLEFEASQkCD 237  Norway rat
CAP24109      729 DPrlrn-psanFSFGTVLNSNVYQYFK-RHVELSSMFRkmePHNVHRASEAVHSLLNG-SLDAFIWDSTRLEFEAARhCE 805  Caenorhabditi...
EFX71929      707 DPrlrn-pmenFTYATVRGSAVDMYFR-RQVELSNMYRtmeGNNYPTAEEAIEAVKEG-KLKAFIWDSSRLEFEAAQdCD 783  common water ...
1PB8_A        161 DPrlrn-psdkFIYATVKQSSVDIYFR-RQVELSTMYRhmeKHNYESAAEAIQAVRDN-KLHAFIWDSAVLEFEASQkCD 237  Norway rat
NP_495033     690 DPrlrn-psanFSFGTVLNSNVYQYFK-RHVELSSMFRkmePHNVRRASEAVHSLLNG-SLDAFIWDSTRLEFEAARhCE 766  Caenorhabditi...
NP_001011573  676 DArlrn-tmenLTCATVKGSAVDMYFR-RQVELSNMYRtmeANNYDTAEEAIRDIKIG-KLMAFIWDSSRLEFEAAQdCE 752  honey bee
XP_969654     670 DArlrn-tmenLTCATVKGSAVDMYFR-RQVELSNMYRtmeANNYNTAEDAIEDVKVG-KLMAFIWDSSRLEFEAAQdCE 746  red flour beetle
XP_001653302  681 DArlrn-tmenLTCATVKGSAVDMYFR-RQVELSNMYRtmeANNYDTAEQAIQDVKDG-KLMAFIWDSSRLEYEAAKdCE 757  yellow fever ...
EEB11312      678 DArlrn-tmenLTCATVKGSAVDMYFR-RQVELSNMYRtmeANNYDTAEEAINDVKNG-KLMAFIWDSSRLEYEAAQdCE 754  human body louse
EEC15663      344 DPrvggvfseyFTRVSSPGDETTRGRPqREMALASATRi-lPHTKTFSSGGAPNIVNDlQLDAFIWDSSRLEFEAAQhCE 422  black-legged ...
Feature 1                                                                  
1PB7_A        238 LVTTGelFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRY---QECD 291  Norway rat
CAP24109      806 LRTRGslFGRSAYGIGLQKNSPWTPHITSAILRMSESGVMENLDQKWIDRg-gPNCV 861  Caenorhabditis briggsae AF16
EFX71929      784 LVTAGelFGRSGYGIGLRKGSPWTDVITLSVLDFHERGFMEDLDERWIKLgsgQQCE 840  common water flea
1PB8_A        238 LVTTGelFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRY---QECD 291  Norway rat
NP_495033     767 LRTRGslFGRSAYGIGLQKNSPWTPHITSAILRMSESGVMEKLDQKWIDRg-gPNCV 822  Caenorhabditis elegans
NP_001011573  753 LVTAGelFGRSGYGIGLQKGSLWADAVTLAILDFHESGFMESLDNHWILRsnvQQCE 809  honey bee
XP_969654     747 LVTAGelFGRSGYGIGLQKGSPWADDITLAILDFHESGFMESLDNKWILQgnvQQCE 803  red flour beetle
XP_001653302  758 LVTAGelFGRSGYGIGLQKGSPWTDAVTLAILDFHESGFMESLDKEWIFHgniQQCE 814  yellow fever mosquito
EEB11312      755 LVTAGelFGRSGYGIGLQKGSPWADAVTLAILDFHESGFMESLDNRWILQgsiQHCE 811  human body louse
EEC15663      423 LVTAGeqFGRSGYGIGLQRNSFWVDKVTLTLLEMHESESPLSVSFIILSS---RQGE 476  black-legged tick

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