SMTL ID : 8hdd.1

Complex structure of catalytic, small, and a partial electron transfer subunits from Burkholderia cepacia FAD glucose dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 36 residues within 4Å: Chain A: V.14, G.15, S.16, G.17, V.18, A.19, L.37, E.38, A.39, Q.94, I.96, R.97, A.98, G.101, T.102, T.103, H.105, W.106, A.107, A.108, S.109, M.219, A.248, V.249, V.250, A.284, A.285, N.286, E.289, I.293, N.475, H.476, S.508, N.519, V.520, T.521 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Q.94, A:T.102, A:N.475 Hydrogen bonds: A:S.16, A:S.16, A:A.19, A:A.39, A:G.40, A:R.97, A:A.98, A:G.101, A:T.102, A:T.102, A:A.107, A:A.108, A:S.109, A:S.109, A:V.250, A:V.250, A:N.286, A:E.289, A:T.521, A:T.521 pi-Stacking: A:W.106, A:H.476 pi-Cation interactions: A:H.476

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 11 residues within 4Å: Chain A: C.212, C.213, N.215, N.216, N.217, C.218, I.221, C.222, I.224, A.226, P.339 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.212, A:C.218, A:C.222

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 20 residues within 4Å: Chain A: I.224 Chain B: N.333, C.334, C.337, H.338, Y.349, Y.350, P.351, N.356, T.358, V.359, L.367, V.370, I.371, R.377, I.384, M.386, P.387, F.389, L.401 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:P.351, B:V.359, B:L.367, B:V.370, B:I.371, B:F.389, B:L.401, A:I.224 Salt bridges: B:R.377 pi-Cation interactions: B:H.338 Metal complexes: B:H.338

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okuda-Shimazaki, J. et al., Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase. Commun Biol (2022)

Release Date

2022-12-14

Peptides

Glucose dehydrogenase: A
Glucose dehydrogenase beta subunit: B
Twin-arginine translocation pathway signal: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Glucose dehydrogenase

Glucose dehydrogenase beta subunit

Twin-arginine translocation pathway signal

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