SMTL ID : 8rfk.1

Soluble glucose dehydrogenase from acinetobacter calcoaceticus - single mutant pH8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: R.228, G.247, P.248, T.348 Ligands: 01.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.247, A:P.248, H2O.4, H2O.14 CA.2: 4 residues within 4Å: Chain A: E.253, N.255, Y.263, G.270 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.253, A:Y.263, H2O.3, H2O.7, H2O.12 CA.3: 6 residues within 4Å: Chain A: V.268, A.269, Y.271, D.273, S.275, E.309 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.269, A:Y.271, A:D.273, H2O.3, H2O.6 CA.5: 5 residues within 4Å: Chain B: R.228, G.247, P.248, T.348 Ligands: 01.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.247, B:P.248, H2O.30, H2O.42 CA.6: 4 residues within 4Å: Chain B: E.253, N.255, Y.263, G.270 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.253, B:Y.263, H2O.27, H2O.33, H2O.37 CA.7: 7 residues within 4Å: Chain B: V.268, A.269, Y.271, D.273, S.275, Y.277, E.309 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.269, B:Y.271, B:E.309, H2O.28, H2O.31

2 x 01: 3-(3,5-dicarboxy-1~{H}-pyrrol-2-yl)pyridine-2,4,6-tricarboxylic acid

01.4: 18 residues within 4Å: Chain A: Q.76, H.144, R.228, N.229, Q.231, Q.246, G.247, P.248, N.249, F.343, W.346, T.348, A.350, L.376, K.377, R.406, R.408 Ligands: CA.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.231, A:Q.246, A:Q.246, A:P.248 Water bridges: A:R.228, A:R.228, A:R.228, A:R.228, A:G.247, A:A.350, A:R.406, A:R.408 Salt bridges: A:H.144, A:R.228, A:K.377, A:R.406, A:R.408 pi-Cation interactions: A:R.406 01.8: 18 residues within 4Å: Chain B: Q.76, H.144, R.228, N.229, Q.231, Q.246, G.247, P.248, N.249, F.343, W.346, T.348, A.350, L.376, K.377, R.406, R.408 Ligands: CA.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:K.377 Hydrogen bonds: B:Q.231, B:Q.246, B:Q.246, B:P.248 Water bridges: B:R.228, B:R.228, B:R.228, B:A.350, B:R.406, B:R.406, B:R.408, B:N.428 Salt bridges: B:H.144, B:R.228, B:K.377, B:R.406, B:R.408 pi-Cation interactions: B:R.406

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lublin, V. et al., Does Acinetobacter calcoaceticus glucose dehydrogenase produce self-damaging H2O2?. Biosci.Rep. (2024)

Release Date

2024-05-08

Peptides

Quinoprotein glucose dehydrogenase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Quinoprotein glucose dehydrogenase B

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