SMTL ID : 8rg1.1

Soluble glucose dehydrogenase from acinetobacter calcoaceticus - wild type pH8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-dimer

Ligands

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

01.1: 18 residues within 4Å: Chain A: Q.76, H.144, R.228, N.229, Q.231, Q.246, G.247, P.248, N.249, Y.343, W.346, T.348, A.350, L.376, K.377, R.406, R.408 Ligands: CA.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.343, A:A.350 Hydrogen bonds: A:N.229, A:Q.231, A:Q.246, A:Q.246, A:Q.246, A:G.247, A:P.248, A:Y.343, A:Y.343, A:T.348 Water bridges: A:R.228, A:R.228, A:R.228, A:G.247, A:A.350, A:R.406, A:R.406 Salt bridges: A:H.144, A:R.228, A:K.377, A:R.406, A:R.408 pi-Cation interactions: A:R.406 01.6: 18 residues within 4Å: Chain B: Q.76, H.144, R.228, N.229, Q.231, Q.246, G.247, P.248, N.249, Y.343, W.346, T.348, A.350, L.376, K.377, R.406, R.408 Ligands: CA.9 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.350, B:K.377 Hydrogen bonds: B:N.229, B:Q.231, B:Q.246, B:Q.246 Water bridges: B:Q.76, B:Q.76, B:R.228, B:R.228, B:R.228, B:G.247, B:Y.343, B:A.350, B:R.406 Salt bridges: B:H.144, B:R.228, B:K.377, B:R.406, B:R.408 pi-Cation interactions: B:R.406

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: V.268, A.269, Y.271, D.273, S.275, Y.277, 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.5, H2O.8 CA.3: 6 residues within 4Å: Chain A: R.228, Q.246, G.247, P.248, T.348 Ligands: 01.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.247, A:P.248, H2O.5, H2O.17 CA.4: 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.9, H2O.9, H2O.15 CA.7: 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.30, H2O.35, H2O.41 CA.8: 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:D.273, H2O.31, H2O.35 CA.9: 6 residues within 4Å: Chain B: R.228, Q.246, G.247, P.248, T.348 Ligands: 01.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.247, B:P.248, H2O.33, H2O.44

2 x LI: LITHIUM ION(Non-covalent)

LI.5: 4 residues within 4Å: Chain A: Q.177, H.180, H.193, T.194 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.193 LI.10: 4 residues within 4Å: Chain B: Q.177, H.180, H.193, T.194 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.193

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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