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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5 (PGAM5) IN ITS ENZYMATICALLY ACTIVE DODECAMERIC FORM INDUCED BY THE PRESENCE OF THE N-TERMINAL WDPNWD MOTIF
 
Authors :  A. Chaikuad, I. Alfano, S. Picaud, P. Filippakopoulos, F. Von Delft, C C. H. Arrowsmith, A. M. Edwards, S. Knapp, Structural Genomics Cons (Sgc)
Date :  13 Jan 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (4x)
Keywords :  Phosphoglycerate Mutase Family Member 5, Pgam5, Serine/Threonine Phosphatase, Mitochondrial Protein, Hydrolase, Wdpnwd Motif, Wdxnwd Motif, Dimer, Dodecamer, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, P. Filippakopoulos, S. R. Marcsisin, S. Picaud, M. Schroder, S. Sekine, H. Ichijo, J. R. Engen, K. Takeda, S. Knapp
Structures Of Pgam5 Provide Insight Into Active Site Plasticity And Multimeric Assembly.
Structure 2017
PubMed-ID: 28648608  |  Reference-DOI: 10.1016/J.STR.2017.05.020

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN PHOSPHATASE PGAM5, MITOCHONDRIAL
    Chains: A, B, C
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28-BSA4
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Expression System Vector Type: PLASMID
    Gene: PGAM5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCL-XL-BINDING PROTEIN V68,PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (4x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1PO412Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:104 , HIS A:105 , ARG A:152 , GLU A:177 , HIS A:230 , ALA A:231 , HOH A:411binding site for residue PO4 A 301
2AC2SOFTWAREARG B:104 , HIS B:105 , ARG B:152 , GLU B:177 , HIS B:230 , ALA B:231 , HOH B:411binding site for residue PO4 B 301
3AC3SOFTWAREARG C:104 , HIS C:105 , ARG C:152 , GLU C:177 , HIS C:230 , ALA C:231binding site for residue PO4 C 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:184 -Pro A:185
2Asp B:184 -Pro B:185
3Asp C:184 -Pro C:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MUF)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeeeee.........hhhhh..hhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh...eeeee....................hhhhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhh..hhhhhhhh......eeeeee.....eeeeeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5muf A  56 GVWDPNWDRREHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS 289
                                    65||      99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
                                     66|                                                                                                                                                                                                      
                                      91                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeeeee.........hhhhh..hhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh...eeeee....................hhhhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhh..hhhhhhhh......eeeeee.....eeeeeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5muf B  56 GVWDPNWDRREHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS 289
                                    65||      99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
                                     66|                                                                                                                                                                                                      
                                      91                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee.........hhhhh..hhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh...eeeee....................hhhhhhhhhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhh..hhhhhhhh......eeeeee.....eeeeeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5muf C  56 GVWDPNWDRREYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS 289
                                    65||     100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         
                                     66|                                                                                                                                                                                                     
                                      92
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5MUF)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        PGAM5_HUMAN | Q96HS1: 3mxo 3o0t

(-) Related Entries Specified in the PDB File

3mxo 3o0t