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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NMDA RECEPTOR GLUN3A LIGAND BINDING DOMAIN APO STATE
 
Authors :  Y. Yao, A. Y. Lau, M. L. Mayer
Date :  24 Apr 13  (Deposition) - 31 Jul 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yao, J. Belcher, A. J. Berger, M. L. Mayer, A. Y. Lau
Conformational Analysis Of Nmda Receptor Glun1, Glun2, And Glun3 Ligand-Binding Domains Reveals Subtype-Specific Characteristics.
Structure V. 21 1788 2013
PubMed-ID: 23972471  |  Reference-DOI: 10.1016/J.STR.2013.07.011

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 3A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22 MODIFIED
    Expression System Strain: ORIGAMI B(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN (UNP RESIDUES 511-660, 776-915)
    Gene: GRIN3A
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUN3A, GLUTAMATE RECEPTOR CHI-1, N-METHYL-D-ASPARTATE RECEPTOR, N-METHYL-D-ASPARTATE RECEPTOR SUBTYPE 3A, NMDAR3A, NR3A, NMDAR-L, NMDAR-L1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:141 , ALA A:226 , ASP A:229 , HIS A:283 , TYR A:287 , HOH A:628 , HOH A:636BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWAREASP B:74 , VAL B:281 , LYS B:285 , HOH B:604 , HOH B:638 , HOH B:639BINDING SITE FOR RESIDUE GOL B 301

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:29 -A:67
2A:35 -A:68
3A:238 -A:292
4B:29 -B:67
5B:35 -B:68
6B:238 -B:292

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:15 -Pro A:16
2Asp A:214 -Pro A:215
3His B:15 -Pro B:16
4Asp B:214 -Pro B:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KCD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KCD)

(-) Exons   (0, 0)

(no "Exon" information available for 4KCD)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4kcda_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eee...........eeee.....hhhhhhhhhhhhh......hhh.eeeeehhhhhhhhhhhhhhheeeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee..........hhhhhh......ee....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh......eeeeehhhhhhhhhhh....eeeeeeeeeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kcd A   3 NKLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRGTELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYKVVPC 292
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4kcdb_ B: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eee...........eeee.....hhhhhhhhhhhhh......hhh.eeeeehhhhhhhhhhhhhhheeeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee..........hhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh......eeeeehhhhhhhhhh.....eeeeeeeeeeeee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kcd B   4 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRGTELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYKVVPCGK 294
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KCD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KCD)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NMD3A_RAT | Q9R1M7: 2rc7 2rc8 2rc9

(-) Related Entries Specified in the PDB File

2rc7 GLUN3A LBD GLYCINE COMPLEX
2rc8 GLUN3A LBD D-SERINE COMPLEX
2rc9 GLUN3A LBD ACPC COMPLEX
4kcc