SMTL ID : 5vg7.1 (1 other biounit)

Crystal Structure of the R503Q missense variant of human PGM1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.119, D.290, D.292, D.294 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.290, A:D.292, A:D.294, H2O.2, H2O.8

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

SO4.2: 4 residues within 4Å: Chain A: R.219, R.223, P.246, N.248 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:R.219, A:R.219, A:N.248 Salt bridges: A:R.219, A:R.223 SO4.3: 2 residues within 4Å: Chain A: K.472, R.493 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.356, A:K.472, A:R.493, A:R.493 Salt bridges: A:K.472, A:R.493 SO4.4: 1 residues within 4Å: Chain A: Q.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.326 SO4.5: 3 residues within 4Å: Chain A: T.21, G.360, W.361 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.21, A:W.361 Water bridges: A:K.362 SO4.6: 3 residues within 4Å: Chain A: R.87, I.108, V.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.87 Water bridges: A:R.87, A:E.195 SO4.7: 1 residues within 4Å: Chain A: H.262 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.262 SO4.8: 3 residues within 4Å: Chain A: S.507, G.508, R.517 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.508 Water bridges: A:Q.505, A:Q.505, A:R.517, A:R.517 Salt bridges: A:R.517 SO4.9: 4 residues within 4Å: Chain A: E.434, V.435, E.436, R.557 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.434, A:E.436 Water bridges: A:T.555, A:R.557, A:R.557 Salt bridges: A:R.557 SO4.10: 2 residues within 4Å: Chain A: K.301, H.302 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.301, A:K.301 Salt bridges: A:K.301, A:H.302 SO4.11: 7 residues within 4Å: Chain A: R.66, F.67, Y.68, M.69, K.70, E.71, E.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.68, A:M.69, A:K.70, A:E.71, A:E.257 Water bridges: A:K.70 Salt bridges: A:K.70 SO4.12: 2 residues within 4Å: Chain A: P.246, A.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.247 Water bridges: A:N.248

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: R.345, D.498, G.499 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.345, A:R.345, A:D.498 GOL.14: 3 residues within 4Å: Chain A: T.328, R.331, S.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.331, A:S.371 GOL.15: 7 residues within 4Å: Chain A: F.305, N.307, R.424, N.425, F.426, F.427, P.534 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.307, A:R.424, A:F.427 Water bridges: A:F.305, A:N.307

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

2018-06-20

Peptides

Phosphoglucomutase-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglucomutase-1

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