SMTL ID : 7fiq.1

The crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from Thermoanaerobacter sp.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-tetramer

Ligands

4 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.1: 5 residues within 4Å: Chain A: R.54, F.73, E.108, F.126, K.159 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.54, A:R.54, A:K.159 Water bridges: A:E.108, A:E.108, A:T.124, A:K.159, A:D.298 Salt bridges: A:K.159 MAN.8: 7 residues within 4Å: Chain B: R.54, L.62, F.73, E.108, T.124, F.126, K.159 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.54, B:R.54, B:K.159 Water bridges: B:E.108, B:E.108, B:K.159, B:D.298 Salt bridges: B:K.159 MAN.14: 5 residues within 4Å: Chain C: R.54, F.73, E.108, F.126, K.159 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.54, C:R.54, C:K.159 Water bridges: C:S.75, C:K.159, C:D.298 Salt bridges: C:K.159 MAN.21: 7 residues within 4Å: Chain D: R.54, L.62, F.73, E.108, T.124, F.126, K.159 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.54, D:R.54, D:K.159 Water bridges: D:S.75, D:E.108, D:E.108, D:E.108, D:K.159, D:Y.238 Salt bridges: D:K.159

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.151, I.152, V.153, V.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.152, A:V.191

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 7 residues within 4Å: Chain A: H.50, Y.79, F.91, V.95, D.143, L.144, K.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.145 PGE.22: 8 residues within 4Å: Chain D: H.50, Y.79, F.91, K.93, V.95, D.143, L.144, K.145 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.93, D:D.143, D:K.145 Water bridges: D:K.93

17 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.160, R.177, H.230, F.279 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.160, A:D.160, A:H.230, H2O.9, H2O.11 ZN.5: 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.11 ZN.6: 2 residues within 4Å: Chain A: E.259 Chain D: H.205 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.205, A:E.259, A:E.259 ZN.7: 2 residues within 4Å: Chain A: H.30, D.92 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.30, A:D.92 ZN.9: 3 residues within 4Å: Chain A: H.205 Chain B: P.180, D.181 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.205, B:D.181, B:D.181, H2O.10, H2O.23 ZN.10: 2 residues within 4Å: Chain B: H.30, D.92 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.30, B:D.92 ZN.11: 5 residues within 4Å: Chain B: E.99, 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.24 ZN.12: 3 residues within 4Å: Chain A: P.180, D.181 Chain B: H.205 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.181, A:D.181, B:H.205, H2O.10, H2O.11 ZN.13: 4 residues within 4Å: Chain B: D.160, R.177, H.230, F.279 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.160, B:H.230, H2O.23, H2O.24 ZN.16: 4 residues within 4Å: Chain C: D.160, R.177, H.230, F.279 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.160, C:D.160, C:H.230, H2O.36, H2O.37 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.38 ZN.18: 2 residues within 4Å: Chain B: E.259 Chain C: H.205 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.205, B:E.259, B:E.259, H2O.24 ZN.19: 2 residues within 4Å: Chain C: H.30, D.92 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.30 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.23: 2 residues within 4Å: Chain D: H.30, D.92 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.30, D:D.92 ZN.24: 4 residues within 4Å: Chain D: D.160, R.177, H.230, F.279 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.160, D:D.160, D:H.230, H2O.45, H2O.49 ZN.25: 4 residues within 4Å: Chain D: E.103, Y.123, C.137, H.150 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.103, D:C.137, D:H.150, H2O.49

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

1PE.15: 8 residues within 4Å: Chain C: Y.79, F.91, K.93, P.94, V.95, D.143, L.144, K.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.145 Water bridges: C:K.93, C:K.145

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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