SMTL ID : 3o0t.1 (1 other biounit)

Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in complex with phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: R.17, H.18, R.65, E.90, H.143, A.144 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.144 Water bridges: A:R.17, A:R.17, A:Y.21, A:N.169 Salt bridges: A:R.17, A:H.18, A:R.65, A:H.143 PO4.9: 7 residues within 4Å: Chain B: R.17, H.18, Y.21, R.65, E.90, H.143, A.144 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.90, B:A.144 Water bridges: B:E.90, B:H.143, B:N.169 Salt bridges: B:R.17, B:H.18, B:R.65 PO4.10: 3 residues within 4Å: Chain A: R.164 Chain B: S.1, R.182 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:R.164 Salt bridges: A:R.164, B:R.182 Hydrogen bonds: B:S.1, B:S.1 PO4.11: 4 residues within 4Å: Chain A: R.201 Chain B: H.12, R.178, R.186 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:H.12, A:R.201 Salt bridges: B:H.12, B:R.178, B:R.186, A:R.201

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: R.17, A.144, R.148, L.165, S.166, L.167, R.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.148, A:L.167 EDO.3: 6 residues within 4Å: Chain A: G.192, F.193, M.194, P.195 Chain B: R.47, F.193 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.47, A:G.192 EDO.4: 4 residues within 4Å: Chain A: M.2, D.3, H.126, R.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.3, A:H.126 EDO.5: 5 residues within 4Å: Chain A: R.47, I.172, T.187, D.190 Chain B: G.192 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.47, A:D.190 Water bridges: A:H.174, B:T.191, B:T.191 EDO.6: 3 residues within 4Å: Chain A: R.178, P.179, N.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180, A:N.180 Water bridges: A:N.180 EDO.7: 3 residues within 4Å: Chain A: R.38, I.72, R.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.75, A:R.75 Water bridges: A:R.38 EDO.8: 6 residues within 4Å: Chain A: H.60, I.67, T.70, D.71, S.74, K.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.70, A:D.71, A:S.74 EDO.12: 5 residues within 4Å: Chain B: R.47, L.51, I.172, D.190 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.47, B:D.190 EDO.13: 5 residues within 4Å: Chain A: N.168 Chain B: H.174, R.186, T.187 Ligands: EDO.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.174, A:N.168 Water bridges: A:N.168 EDO.14: 6 residues within 4Å: Chain B: R.17, A.144, R.148, S.166, L.167, R.201 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.148, B:R.148, B:L.167, B:L.167 Water bridges: B:N.145 EDO.15: 5 residues within 4Å: Chain B: H.60, I.67, T.70, D.71, K.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.71, B:K.82

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

2010-10-06

Peptides

Serine/threonine-protein phosphatase PGAM5, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine/threonine-protein phosphatase PGAM5, mitochondrial

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