SMTL ID : 2d0v.1 (1 other biounit)

Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

hetero-2-2-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.177, N.261, D.303, A.305 Ligands: PQQ.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.177, A:E.177 CA.3: 5 residues within 4Å: Chain C: E.177, N.261, D.303, A.305 Ligands: PQQ.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.177, C:E.177

2 x PQQ: PYRROLOQUINOLINE QUINONE(Non-covalent)

PQQ.2: 21 residues within 4Å: Chain A: E.55, C.104, V.107, R.109, T.159, S.174, G.175, A.176, E.177, T.241, W.243, N.261, D.303, R.331, N.394, Q.395, W.476, G.539, W.540, P.541 Ligands: CA.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.476, A:W.540, A:W.540 Hydrogen bonds: A:R.109, A:T.159, A:S.174, A:G.175, A:A.176, A:T.241, A:R.331, A:R.331, A:N.394, A:W.540 Water bridges: A:E.177, A:E.177 Salt bridges: A:R.109 pi-Stacking: A:W.243, A:W.243, A:W.243 PQQ.4: 21 residues within 4Å: Chain C: E.55, C.104, V.107, R.109, T.159, S.174, G.175, A.176, E.177, T.241, W.243, N.261, D.303, R.331, N.394, Q.395, W.476, G.539, W.540, P.541 Ligands: CA.3 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.476, C:W.540, C:W.540 Hydrogen bonds: C:R.109, C:S.174, C:G.175, C:A.176, C:R.331, C:R.331, C:N.394, C:W.540 Water bridges: C:E.177, C:E.177 Salt bridges: C:R.109 pi-Stacking: C:W.243, C:W.243, C:W.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nojiri, M. et al., Crystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins. Biochemistry (2006)

Release Date

2006-08-09

Peptides

methanol dehydrogenase large subunit: AC
methanol dehydrogenase small subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

methanol dehydrogenase large subunit

methanol dehydrogenase small subunit

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