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(-) Description

Title :  STRUCTURE OF HUMAN TESTIS-SPECIFIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE HOLO FORM WITH NAD+
 
Authors :  L. Betts, M. Machius, P. Danshina, D. O'Brien
Date :  24 Jun 15  (Deposition) - 09 Mar 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  O,P
Biol. Unit 1:  O,P  (2x)
Keywords :  Human Sperm Gapdh Metabolic Enzyme Sperm Specific With Nad+ Cofactor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. V. Danshina, W. Qu, B. R. Temple, R. J. Rojas, M. J. Miley, M. Machius, L. Betts, D. A. O'Brien
Structural Analyses To Identify Selective Inhibitors Of Glyceraldehyde 3-Phosphate Dehydrogenase-S, A Sperm-Specifi Glycolytic Enzyme.
Mol. Hum. Reprod. V. 22 410 2016
PubMed-ID: 26921398  |  Reference-DOI: 10.1093/MOLEHR/GAW016

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, TESTIS-SPECIFIC
    Chains: O, P
    EC Number: 1.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 74-407
    Gene: GAPDHS, GAPD2, GAPDH2, GAPDS, HSD-35, HSD35
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPERMATOGENIC CELL-SPECIFIC GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 2,GAPDH-2,SPERMATOGENIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : OP
Biological Unit 1 (2x): OP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2OCS4Mod. Amino AcidCYSTEINESULFONIC ACID
3SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN O:81 , GLY O:82 , PHE O:83 , GLY O:84 , ARG O:85 , ILE O:86 , ASP O:106 , PRO O:107 , PHE O:108 , LYS O:151 , SER O:169 , THR O:170 , GLY O:171 , TYR O:173 , SER O:193 , ALA O:194 , OCS O:224 , ALA O:255 , ASN O:388 , TYR O:392 , SO4 O:502 , HOH O:611 , HOH O:651 , HOH O:666 , HOH O:685 , HOH O:697 , HOH O:737 , HOH O:743 , HOH O:768 , HOH O:771 , HOH O:772 , HOH O:778 , HOH O:785binding site for residue NAD O 501
2AC2SOFTWARETHR O:254 , THR O:256 , ARG O:306 , NAD O:501 , HOH O:611 , HOH O:625 , HOH O:685binding site for residue SO4 O 502
3AC3SOFTWAREASN P:81 , GLY P:82 , PHE P:83 , GLY P:84 , ARG P:85 , ILE P:86 , ASP P:106 , PRO P:107 , PHE P:108 , LYS P:151 , SER P:169 , THR P:170 , GLY P:171 , TYR P:173 , SER P:193 , ALA P:194 , OCS P:224 , ALA P:255 , ASN P:388 , TYR P:392 , SO4 P:502 , HOH P:603 , HOH P:631 , HOH P:638 , HOH P:657 , HOH P:671 , HOH P:677 , HOH P:710 , HOH P:720 , HOH P:730 , HOH P:767 , HOH P:775 , HOH P:783binding site for residue NAD P 501
4AC4SOFTWARETHR P:254 , THR P:256 , ARG P:306 , NAD P:501 , HOH P:603 , HOH P:654 , HOH P:678 , HOH P:775binding site for residue SO4 P 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C7O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C7O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C7O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C7O)

(-) Exons   (0, 0)

(no "Exon" information available for 5C7O)

(-) 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 O from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh......eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee..............hhhhhh......eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c7o O  74 RELTVGINGFGRIGRLVLRACMEKGVKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGSVEFRNGQLVVDNHEISVYQCKEPKQIPWRAVGSPYVVESTGVYLSIQAASDHISAGAQRVVISAPSPDAPMFVMGVNENDYNPGSMNIVSNAScTTNCLAPLAKVIHERFGIVEGLMTTVHSYTATQKTVDGPSRKAWRDGRGAHQNIIPASTGAAKAVTKVIPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPAPYSAIKEAVKAAAKGPMAGILAYTEDEVVSTDFLGDTHSSIFDAKAGIALNDNFVKLISWYDNEYGYSHRVVDLLRYMFSRDK 408
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|      233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403     
                                                                                                                                                                                224-OCS                                                                                                                                                                                    


Chain P from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh......eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee..............hhhhhh......eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c7o P  74 RELTVGINGFGRIGRLVLRACMEKGVKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGSVEFRNGQLVVDNHEISVYQCKEPKQIPWRAVGSPYVVESTGVYLSIQAASDHISAGAQRVVISAPSPDAPMFVMGVNENDYNPGSMNIVSNAScTTNCLAPLAKVIHERFGIVEGLMTTVHSYTATQKTVDGPSRKAWRDGRGAHQNIIPASTGAAKAVTKVIPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPAPYSAIKEAVKAAAKGPMAGILAYTEDEVVSTDFLGDTHSSIFDAKAGIALNDNFVKLISWYDNEYGYSHRVVDLLRYMFSRDK 408
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|      233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403     
                                                                                                                                                                                224-OCS
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5C7O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C7O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C7O)

(-) Gene Ontology  (18, 18)

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 Related Entries

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        G3PT_HUMAN | O14556: 3h9e 3pfw 5c7l

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5c7l