SMTL ID : 7o4g.1

Human phosphomannomutase 2 (PMM2) wild-type soaked with the activator glucose 1,6-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Y.147, D.150, K.151, N.154, R.156, Q.157, I.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.150, A:D.150, A:N.154

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.14, D.16, G.17, T.18, D.211, K.212, N.218, D.219 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.14, A:D.16, A:D.211, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: F.223, T.224, D.225, T.228, G.230 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.223, A:D.225, A:T.228, A:T.228 MG.7: 7 residues within 4Å: Chain B: D.14, D.16, G.17, D.211, K.212, N.218, D.219 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.14, B:D.16, B:D.211, H2O.2, H2O.3 MG.8: 5 residues within 4Å: Chain B: F.223, D.225, T.228, M.229, G.230 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.223, B:D.225, B:T.228, B:T.228, H2O.3

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

CL.4: 6 residues within 4Å: Chain A: T.120, F.121, I.122 Chain B: T.120, F.121, I.122 Ligand excluded by PLIP

1 x G16: 1,6-di-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G16.5: 10 residues within 4Å: Chain A: R.125, N.130, R.136, R.143, G.177, G.178, Q.179, I.180, S.181, D.183 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.125, A:R.125, A:N.130, A:R.136, A:R.136, A:G.178, A:Q.179, A:I.180, A:S.181, A:D.183, A:D.183 Water bridges: A:G.177 Salt bridges: A:R.136, A:R.143

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: D.50, E.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.52, A:E.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Briso-Montiano, A. et al., Insight on molecular pathogenesis and pharmacochaperoning potential in phosphomannomutase 2 deficiency, provided by novel human phosphomannomutase 2 structures. J Inherit Metab Dis (2022)

Release Date

2022-02-02

Peptides

Phosphomannomutase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphomannomutase 2

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