SMTL ID : 7fir.1

The crystal structure of beta-1,2-mannobiose phosphorylase in complex with 1,4-mannobiose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x Z2D- GUP: alpha-L-gulopyranose-(1-4)-alpha-L-allopyranose(Non-covalent)

Z2D-GUP.1: 9 residues within 4Å: Chain A: R.54, F.73, E.108, F.126, F.134, K.159, K.211, N.236, Y.238 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.54, A:R.54, A:K.159, A:K.211, A:N.236, A:Y.238, A:Y.238 Water bridges: A:T.124, A:K.159, A:K.159, A:K.159 Salt bridges: A:K.211 Z2D-GUP.2: 9 residues within 4Å: Chain B: R.54, F.73, E.108, F.126, F.134, K.159, K.211, N.236, Y.238 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.54, B:R.54, B:K.159, B:K.211, B:N.236, B:Y.238, B:Y.238 Water bridges: B:K.159 Salt bridges: B:K.211 Z2D-GUP.3: 9 residues within 4Å: Chain C: R.54, F.73, E.108, F.126, F.134, K.159, K.211, N.236, Y.238 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.54, C:R.54, C:K.159, C:K.211, C:N.236, C:Y.238 Water bridges: C:S.75, C:K.211 Salt bridges: C:K.211 Z2D-GUP.4: 9 residues within 4Å: Chain D: R.54, F.73, E.108, T.124, F.126, F.134, K.159, K.211, Y.238 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.54, D:R.54, D:K.159, D:K.211, D:Y.238, D:Y.238 Water bridges: D:E.108, D:E.108, D:K.159, D:Y.238, D:D.298, D:K.159, D:K.159 Salt bridges: D:K.211

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

PGE.5: 5 residues within 4Å: Chain A: Y.79, F.91, D.143, L.144, K.145 No protein-ligand interaction detected (PLIP)

17 x ZN: ZINC ION(Non-covalent)

ZN.6: 3 residues within 4Å: Chain A: H.205 Chain B: P.180, D.181 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.181, B:D.181, A:H.205, H2O.10, H2O.23 ZN.7: 3 residues within 4Å: Chain A: D.160, R.177, H.230 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.160, A:D.160, A:H.230, H2O.7, H2O.11 ZN.8: 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.23 ZN.9: 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.10: 3 residues within 4Å: Chain A: E.259, P.260 Chain D: H.205 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: A:E.259, D:H.205, H2O.1, H2O.1, H2O.6 ZN.11: 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.11 ZN.12: 2 residues within 4Å: Chain B: H.30, D.92 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.30, B:D.92, H2O.24 ZN.13: 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.24 ZN.14: 4 residues within 4Å: Chain B: D.160, R.177, H.230, F.279 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.160, B:D.160, B:H.230, H2O.20, H2O.24 ZN.15: 2 residues within 4Å: Chain B: E.259 Chain C: H.205 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.205, B:E.259, B:E.259 ZN.17: 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.31, H2O.36 ZN.18: 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.37 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 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.265, C:E.265, H2O.37, H2O.38 ZN.21: 2 residues within 4Å: Chain D: H.30, D.92 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.30, D:D.92, H2O.43 ZN.22: 3 residues within 4Å: Chain D: D.160, R.177, H.230 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.160, D:D.160, D:H.230, H2O.46, H2O.48 ZN.23: 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.47

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

1PE.16: 8 residues within 4Å: Chain C: Y.79, F.91, K.93, P.94, V.95, D.143, L.144, K.145 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.145 Water bridges: C:K.93

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
A

B
B

C
C

D
D

Beta-1,2-mannobiose phosphorylase

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