SMTL ID : 5muf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-12-mer

Ligands

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.126, A:A.180 Water bridges: A:Y.57 Salt bridges: A:R.53, A:H.54, A:R.101, A:H.179 PO4.2: 7 residues within 4Å: Chain B: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.180 Water bridges: B:Y.57, B:Y.57 Salt bridges: B:R.53, B:H.54, B:R.101, B:H.179 PO4.3: 6 residues within 4Å: Chain C: R.53, H.54, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.126, C:E.126, C:A.180 Salt bridges: C:R.53, C:H.54, C:R.101, C:H.179 PO4.4: 7 residues within 4Å: Chain D: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.126, D:A.180 Water bridges: D:Y.57 Salt bridges: D:R.53, D:H.54, D:R.101, D:H.179 PO4.5: 7 residues within 4Å: Chain E: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:A.180 Water bridges: E:Y.57, E:Y.57 Salt bridges: E:R.53, E:H.54, E:R.101, E:H.179 PO4.6: 6 residues within 4Å: Chain F: R.53, H.54, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:E.126, F:E.126, F:A.180 Salt bridges: F:R.53, F:H.54, F:R.101, F:H.179 PO4.7: 7 residues within 4Å: Chain G: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:E.126, G:E.126, G:A.180 Water bridges: G:Y.57, G:Y.57 Salt bridges: G:R.53, G:H.54, G:R.101, G:H.179 PO4.8: 7 residues within 4Å: Chain H: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:E.126, H:A.180 Water bridges: H:Y.57 Salt bridges: H:R.53, H:H.54, H:R.101, H:H.179 PO4.9: 6 residues within 4Å: Chain I: R.53, H.54, R.101, E.126, H.179, A.180 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:E.126, I:A.180 Salt bridges: I:R.53, I:H.54, I:R.101, I:H.179 PO4.10: 7 residues within 4Å: Chain J: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:E.126, J:E.126, J:A.180 Water bridges: J:Y.57, J:Y.57 Salt bridges: J:R.53, J:H.54, J:R.101, J:H.179 PO4.11: 7 residues within 4Å: Chain K: R.53, H.54, Y.57, R.101, E.126, H.179, A.180 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:E.126, K:A.180 Water bridges: K:Y.57 Salt bridges: K:R.53, K:H.54, K:R.101, K:H.179 PO4.12: 6 residues within 4Å: Chain L: R.53, H.54, R.101, E.126, H.179, A.180 6 PLIP interactions: 6 interactions with chain L Hydrogen bonds: L:E.126, L:A.180 Salt bridges: L:R.53, L:H.54, L:R.101, L:H.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly. Structure (2017)

Release Date

2017-07-12

Peptides

Serine/threonine-protein phosphatase PGAM5, mitochondrial: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

Serine/threonine-protein phosphatase PGAM5, mitochondrial