SMTL ID : 7o5z.1

Human phosphomannomutase 2 (PMM2) with mutation T237M in apo state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.125, N.130, R.136, G.177, G.178, S.181, F.182, D.183 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.125, A:R.125, A:N.130, A:R.136, A:R.136, A:G.177, A:S.181, A:D.183 Water bridges: A:S.181, A:S.181, A:S.181 GOL.2: 5 residues within 4Å: Chain A: R.38, Q.39, K.40, I.41, K.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.38, A:K.40, A:I.41 Water bridges: A:R.38, A:K.42 GOL.3: 6 residues within 4Å: Chain A: D.50, F.51, E.52, E.72, V.76, N.126 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.50, A:D.50, A:E.72, A:N.126 Water bridges: A:F.51, A:E.52, A:E.72 GOL.4: 4 residues within 4Å: Chain A: Y.108, K.111, I.112, K.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.111 GOL.8: 9 residues within 4Å: Chain A: R.118, S.137, C.138, S.139, E.142 Chain B: N.88, Q.90, F.124, N.126 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.88, B:Q.90, B:N.126, A:R.118, A:S.137, A:S.139 GOL.9: 7 residues within 4Å: Chain B: N.73, M.128, S.175, D.183, F.185, W.189, D.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.73, B:D.183, B:W.189 GOL.10: 4 residues within 4Å: Chain B: Y.104, S.107, Y.108, K.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.104, B:Y.108, B:K.111 GOL.11: 5 residues within 4Å: Chain B: L.84, C.85, R.196, H.197, N.200 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.200 Water bridges: B:L.84, B:N.200

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.14, D.16, G.17, T.18, D.211, K.212 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.1, H2O.2 MG.6: 5 residues within 4Å: Chain A: F.223, T.224, D.225, T.228, G.230 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.223, A:D.225, A:T.228, H2O.3, H2O.5 MG.12: 7 residues within 4Å: Chain B: D.14, D.16, G.17, T.18, D.211, K.212, D.219 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.14, B:D.16, B:D.211, H2O.5, H2O.6, H2O.6 MG.13: 6 residues within 4Å: Chain B: F.223, T.224, D.225, P.226, T.228, 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.9

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

NA.7: 1 residues within 4Å: Chain A: D.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.50 NA.14: 2 residues within 4Å: Chain B: R.196, E.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.196

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

CL.15: 6 residues within 4Å: Chain A: T.120, F.121, I.122 Chain B: T.120, F.121, I.122 Ligand excluded by PLIP

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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