SMTL ID : 5vin.1 (1 other biounit)

Crystal Structure of the R515Q missense variant of human PGM1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: T.42, S.43, G.381, W.382, K.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.42, A:W.382 Salt bridges: A:K.412 SO4.2: 5 residues within 4Å: Chain A: H.141, R.316, S.401, R.450, Q.538 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.538 Salt bridges: A:H.141, A:R.316, A:R.450 SO4.3: 6 residues within 4Å: Chain A: F.88, Y.89, M.90, K.91, E.92, E.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.89, A:M.90, A:K.91, A:E.92, A:E.278 SO4.4: 4 residues within 4Å: Chain A: G.282, H.283, H.284, Y.291 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.282, A:H.284 Salt bridges: A:H.283, A:H.284 SO4.5: 4 residues within 4Å: Chain A: Y.35, S.54, S.55, A.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.35, A:A.56 SO4.6: 4 residues within 4Å: Chain A: E.455, V.456, E.457, R.578 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.455, A:E.457 Salt bridges: A:R.578 SO4.7: 4 residues within 4Å: Chain A: G.144, P.146, N.147, G.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.144, A:N.147, A:N.147 SO4.8: 2 residues within 4Å: Chain A: P.267, A.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.268 SO4.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: R.240, R.244, P.267, N.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.240, A:R.240, A:R.244, A:N.269 GOL.11: 2 residues within 4Å: Chain A: R.108, I.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.108, A:R.108 GOL.12: 1 residues within 4Å: Chain A: H.283 No protein-ligand interaction detected (PLIP) GOL.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x CO: COBALT (II) ION(Non-covalent)

CO.14: 4 residues within 4Å: Chain A: S.140, D.311, D.313, D.315 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.140, A:D.311, A:D.313, A:D.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stiers, K.M. et al., A Hotspot for Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics. Structure (2018)

Release Date

2018-06-27

Peptides

Phosphoglucomutase-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglucomutase-1

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