SMTL ID : 7fis.1

The crystal structure of beta-1,2-mannobiose phosphorylase in complex with mannose 1-phosphate (M1P)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

5 x M1P: 1-O-phosphono-alpha-D-mannopyranose(Non-covalent)

M1P.1: 14 residues within 4Å: Chain A: F.38, N.39, R.54, D.109, K.159, D.160, K.211, H.230, Y.238, V.274, V.277, F.279, D.298 Ligands: ZN.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.39, A:R.54, A:D.109, A:K.159, A:K.159, A:Y.238, A:D.298 Water bridges: A:R.54, A:R.177, A:R.177, A:R.177, A:R.177, A:K.211, A:Y.238, A:D.298 Salt bridges: A:K.159, A:K.159, A:R.177, A:K.211 M1P.7: 7 residues within 4Å: Chain A: P.180, D.181 Chain B: S.204, H.205, S.209, N.234 Ligands: ZN.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.204, B:H.205, B:S.209, B:N.234 Water bridges: B:T.206, B:S.209 Salt bridges: B:H.205, B:H.205 M1P.9: 13 residues within 4Å: Chain B: N.39, R.54, D.109, K.159, D.160, K.211, H.230, Y.238, V.274, V.277, F.279, D.298 Ligands: ZN.14 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.39, B:R.54, B:D.109, B:K.159, B:K.159, B:Y.238, B:D.298 Water bridges: B:R.54, B:R.177, B:R.177, B:R.177, B:K.211 Salt bridges: B:K.159, B:K.159, B:R.177, B:K.211, B:K.211, B:H.230 M1P.15: 14 residues within 4Å: Chain C: N.39, R.54, D.109, K.159, D.160, R.177, K.211, H.230, Y.238, V.274, V.277, F.279, D.298 Ligands: ZN.16 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.39, C:R.54, C:D.109, C:K.159, C:K.159, C:Y.238, C:D.298 Water bridges: C:R.54, C:R.177, C:R.177, C:R.177, C:K.211, C:D.298 Salt bridges: C:K.159, C:K.159, C:R.177, C:K.211, C:K.211 M1P.21: 14 residues within 4Å: Chain D: N.39, R.54, D.109, K.159, D.160, R.177, K.211, H.230, Y.238, V.274, V.277, F.279, D.298 Ligands: ZN.25 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:N.39, D:R.54, D:D.109, D:K.159, D:D.298 Water bridges: D:R.54, D:K.159, D:K.159, D:R.177, D:R.177, D:R.177, D:R.177, D:K.211, D:K.211, D:Y.238, D:D.298 Salt bridges: D:K.159, D:K.159, D:R.177, D:K.211

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 7 residues within 4Å: Chain A: H.50, Y.79, F.91, K.93, V.95, L.144, K.145 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.50, A:K.93 Water bridges: A:H.50, A:K.93, A:K.145 PG4.8: 5 residues within 4Å: Chain B: R.17, L.18, S.19, N.20, L.266 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.20, B:N.20, B:N.20

17 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.160, R.177, H.230 Ligands: M1P.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.160, A:D.160, A:H.230, M1P.1, H2O.2 ZN.4: 4 residues within 4Å: Chain A: E.103, Y.123, C.137, H.150 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.103, A:C.137, A:H.150, H2O.10 ZN.5: 2 residues within 4Å: Chain A: E.259 Chain D: H.205 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.259, H2O.9 ZN.6: 2 residues within 4Å: Chain A: H.30, D.92 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.30, A:D.92, H2O.10 ZN.10: 3 residues within 4Å: Chain A: H.205 Chain B: P.180, D.181 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.205, B:D.181, B:D.181, H2O.21 ZN.11: 2 residues within 4Å: Chain B: H.30, D.92 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.30, B:D.92, H2O.21, H2O.21 ZN.12: 4 residues within 4Å: Chain B: E.103, Y.123, C.137, H.150 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.103, B:C.137, B:H.150, H2O.22 ZN.13: 4 residues within 4Å: Chain A: P.180, D.181 Chain B: H.205 Ligands: M1P.7 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.205, A:D.181, A:D.181, M1P.7, H2O.8 ZN.14: 5 residues within 4Å: Chain B: D.160, R.177, H.230, F.279 Ligands: M1P.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.160, B:D.160, B:H.230, H2O.13 ZN.16: 4 residues within 4Å: Chain C: D.160, R.177, H.230 Ligands: M1P.15 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.160, C:D.160, C:H.230, H2O.31 ZN.17: 4 residues within 4Å: Chain C: E.103, Y.123, C.137, H.150 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.103, C:C.137, C:H.150, H2O.34 ZN.18: 2 residues within 4Å: Chain B: E.259 Chain C: H.205 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.259, B:E.259, C:H.205, H2O.14 ZN.19: 1 residues within 4Å: Chain C: H.30 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.30, H2O.33 ZN.20: 1 residues within 4Å: Chain C: E.265 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.265, C:E.265 ZN.24: 2 residues within 4Å: Chain D: H.30, D.92 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.30, H2O.41, H2O.45 ZN.25: 4 residues within 4Å: Chain D: D.160, R.177, H.230 Ligands: M1P.21 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.160, D:H.230, H2O.43 ZN.26: 5 residues within 4Å: Chain D: I.100, E.103, Y.123, C.137, H.150 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.103, D:C.137, D:H.150

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.22: 8 residues within 4Å: Chain D: H.50, Y.79, F.91, K.93, P.94, V.95, L.144, K.145 1 PLIP interactions: 1 interactions with chain D Water bridges: D:K.145

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 3 residues within 4Å: Chain A: N.63 Chain D: E.156, R.178 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.63, D:R.178 Water bridges: D:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, L. et al., Structural investigation of a thermostable 1,2-beta-mannobiose phosphorylase from Thermoanaerobacter sp. X-514. Biochem.Biophys.Res.Commun. (2021)

Release Date

2022-01-05

Peptides

Beta-1,2-mannobiose phosphorylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

D
D

Beta-1,2-mannobiose phosphorylase

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