SMTL ID : 7o58.1

Human phosphomannomutase 2 (PMM2) with mutation T237M in complex with the activator glucose 1,6-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: R.38, Q.39, K.40, I.41, K.42, D.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.41 Water bridges: A:K.42 GOL.2: 3 residues within 4Å: Chain A: C.85, R.196, H.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.196, A:R.196 Water bridges: A:R.196 GOL.3: 6 residues within 4Å: Chain A: Y.104, S.107, Y.108, K.111, D.162 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.107, A:S.107, A:S.107, A:K.111 GOL.4: 5 residues within 4Å: Chain A: Y.108, K.111, I.112, K.158 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.108, A:K.111 GOL.6: 6 residues within 4Å: Chain A: A.110, K.111 Chain B: N.103, Y.104, S.107 Ligands: GOL.14 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.110, B:S.107 Water bridges: B:N.103, B:Y.104 GOL.12: 8 residues within 4Å: Chain B: K.25, I.26, T.27, K.28, D.31, L.58, G.59, K.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.26, B:D.31, B:K.65 Water bridges: B:D.31 GOL.13: 7 residues within 4Å: Chain B: N.73, M.128, S.175, D.183, F.185, W.189, D.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.73, B:D.183, B:W.189 Water bridges: B:E.221 GOL.14: 5 residues within 4Å: Chain B: Y.104, S.107, Y.108, K.111 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.108, B:K.111 GOL.15: 5 residues within 4Å: Chain B: L.97, D.100, E.166, F.167, K.170 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.100, B:D.100, B:E.166, B:K.170

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 15 PLIP interactions: 15 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:S.181, A:D.183, A:D.183 Water bridges: A:G.177 Salt bridges: A:R.136, A:R.143

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 7 residues within 4Å: Chain A: D.14, D.16, G.17, T.18, D.211, K.212, D.219 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.14, A:D.16, A:D.211, H2O.1, H2O.2, H2O.4 MG.8: 6 residues within 4Å: Chain A: F.223, T.224, D.225, P.226, T.228, G.230 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.223, A:D.225, A:T.228, A:T.228, H2O.6 MG.16: 6 residues within 4Å: Chain B: D.14, D.16, G.17, T.18, D.211, K.212 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.14, B:D.16, B:D.211, H2O.7, H2O.7, H2O.8 MG.17: 6 residues within 4Å: Chain B: F.223, T.224, D.225, P.226, T.228, G.230 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.225, B:T.228, B:T.228, H2O.10, H2O.12

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

CL.9: 6 residues within 4Å: Chain A: T.120, F.121, I.122 Chain B: T.120, F.121, I.122 Ligand excluded by PLIP

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

NA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.11: 2 residues within 4Å: Chain A: D.50, E.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.50 NA.18: 3 residues within 4Å: Chain B: R.196, E.199, N.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.199

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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