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(-) Description

Title :  CRYSTAL STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE COMPLEXED WITH 3-PHOSPHOGLYCERIC ACID
 
Authors :  C. He, L. Zhou, L. Zhang
Date :  03 Sep 12  (Deposition) - 28 Nov 12  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  6-Phosphogluconate Dehydrogenase, 3-Phosphoglycerate, Dehydrogenase, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hitosugi, L. Zhou, S. Elf, J. Fan, H. B. Kang, J. H. Seo, C. Shan, Q. Dai L. Zhang, J. Xie, T. L. Gu, P. Jin, M. Aleckovic, G. Leroy, Y. Kang, J. A. Sudderth, R. J. Deberardinis, C. H. Luan, G. Z. Chen, S. Muller, D. M. Shin, T. K. Owonikoko, S. Lonial, M. L. Arellano, H. J. Khoury, F. R. Khuri, B. H. Lee, K. Ye, T. J. Boggon, S. Kang, C. He, J. Chen
Phosphoglycerate Mutase 1 Coordinates Glycolysis And Biosynthesis To Promote Tumor Growth.
Cancer Cell V. 22 585 2012
PubMed-ID: 23153533  |  Reference-DOI: 10.1016/J.CCR.2012.09.020

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
    Chains: A
    EC Number: 1.1.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PGD, PGDH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
13PG2Ligand/Ion3-PHOSPHOGLYCERIC ACID
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
13PG2Ligand/Ion3-PHOSPHOGLYCERIC ACID
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
13PG4Ligand/Ion3-PHOSPHOGLYCERIC ACID
2MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:212 , GLN A:213 , LYS A:248 , HIS A:249 , PRO A:252 , HOH A:682 , HOH A:757 , HOH A:895BINDING SITE FOR RESIDUE 3PG A 501
2AC2SOFTWAREGLU A:105 , ARG A:107 , MET A:185 , TRP A:266 , HOH A:625 , HOH A:639 , HOH A:689BINDING SITE FOR RESIDUE MES A 502
3AC3SOFTWAREGLY A:131 , GLU A:132 , GLY A:167 , GLU A:168 , GLY A:451 , ALA A:452BINDING SITE FOR RESIDUE MES A 503
4AC4SOFTWAREGLU A:191 , TYR A:192 , LYS A:261 , GLY A:262 , THR A:263 , ARG A:288 , ARG A:447 , HOH A:628 , HOH A:651 , HOH A:793 , HOH A:817BINDING SITE FOR RESIDUE 3PG A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GWK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GWK)

(-) 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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4gwka1 A:2-177 automated matches                                                                                                                                               d4gwka2 A:178-470 automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee...hhhhhhhhhh.......ee..hhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh.eeeeee...hhhhhhhhhhhhh.............ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gwk A   2 AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVVGAQSLKEMVSKLKKPRRIILLVKAGQAVDDFIEKLVPLLDTGDIIIDGGNSEYRDTTRRCRDLKAKGILFVGSGVSGGEEGARYGPSLMPGGNKEAWPHIKTIFQGIAAKVGTGEPCCDWVGDEGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVLGMAQDEMAQAFEDWNKTELDSFLIEITANILKFQDTDGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQASKKLKGPFQFDGDKKSFLEDIRKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPELQNLLLDDFFKSAVENCQDSWRRAVSTGVQAGIPMPCFTTALSFYDGYRHEMLPASLIQAQRDYFGAHTYELLAKPGQFIHTNWT 470
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     ||313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       
                                                                                                                                                                                                                                                                                                                                           307|                                                                                                                                                                
                                                                                                                                                                                                                                                                                                                                            310
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  4gwk
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  6PGD_HUMAN | P52209
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  1.1.1.44
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 Related Entries

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

UniProtKB/Swiss-Prot
        6PGD_HUMAN | P52209: 2jkv 4gwg

(-) Related Entries Specified in the PDB File

2jkv SAME PROTEIN WITHOUT COFACTOR
4gwg SAME PROTEIN WITHOUT COFACTOR