SMTL ID : 3mxo.2 (1 other biounit)

Crystal structure oh human phosphoglycerate mutase family member 5 (PGAM5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Y.149, C.152, R.153, F.157, P.158, P.159, G.161, W.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.157, A:P.159, A:G.161, A:W.162 EDO.2: 5 residues within 4Å: Chain A: H.60, I.67, T.70, D.71, K.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.70, A:D.71 EDO.3: 6 residues within 4Å: Chain A: H.4, Y.5, K.6, H.126, R.127, A.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.4, A:K.6, A:A.128, A:A.128 EDO.4: 5 residues within 4Å: Chain A: R.47, L.51, D.190 Ligands: EDO.7, PGE.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.47 Water bridges: A:D.190, A:D.190 EDO.5: 2 residues within 4Å: Chain A: G.192, F.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.192 Water bridges: A:F.193 EDO.6: 1 residues within 4Å: Chain A: D.135 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.10 EDO.7: 5 residues within 4Å: Chain A: H.174, R.186, T.187 Ligands: EDO.4, PGE.9 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: K.6, A.7, K.8, A.128, A.130 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: H.174, R.186, T.187 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.186, B:R.186 EDO.13: 4 residues within 4Å: Chain B: R.47, L.51, D.190 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.47, B:D.190 EDO.14: 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:T.70, B:D.71 EDO.15: 7 residues within 4Å: Chain B: R.17, A.144, R.148, L.165, S.166, L.167, R.201 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.148, B:L.167 EDO.16: 5 residues within 4Å: Chain B: G.192, F.193, M.194, P.195, P.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.192 EDO.17: 5 residues within 4Å: Chain A: E.118, R.153 Chain B: E.112, R.116, A.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.153 Water bridges: A:Y.149 EDO.18: 5 residues within 4Å: Chain B: M.2, D.3, R.122, H.126, R.153 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.3, B:R.153, B:R.153 Water bridges: B:S.1, B:Q.156

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 7 residues within 4Å: Chain A: H.12, L.53, Y.137, H.174, R.186 Ligands: EDO.4, EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.137, A:R.186

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 2 residues within 4Å: Chain A: H.4, R.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.153, A:R.153 Water bridges: A:H.4, A:H.4

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 5 residues within 4Å: Chain A: S.61, R.65, A.66, C.142, H.143 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain B: S.61, M.63, R.65, A.66, C.142, H.143 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.19: 8 residues within 4Å: Chain B: H.12, L.53, Y.137, H.174, V.176, R.178, A.184, R.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.178 Water bridges: B:R.186

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

2010-09-15

Peptides

Serine/threonine-protein phosphatase PGAM5, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Serine/threonine-protein phosphatase PGAM5, mitochondrial

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