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

crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-oligomer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 1 residues within 4Å: Chain A: E.367 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.367, H2O.67, H2O.150, H2O.247 NI.4: 1 residues within 4Å: Chain D: E.367 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.367, H2O.524, H2O.607, H2O.704

4 x HEC: HEME C(Covalent)

HEC.2: 25 residues within 4Å: Chain A: K.32, S.40, R.43, T.99, C.100, R.102, C.103, H.104, R.108, V.109, Q.112, R.114, W.119, L.122, H.126, W.130, L.133, Q.136, W.144, L.156, N.489, P.491 Chain C: P.44, A.45 Ligands: HEC.3 31 PLIP interactions: 7 interactions with chain C, 24 interactions with chain A, Hydrophobic interactions: C:P.44, C:P.44, A:T.99, A:V.109, A:W.119, A:L.122, A:L.122, A:W.130, A:W.130, A:L.133, A:W.144, A:L.156 Water bridges: C:Y.54, C:Y.54, C:Y.54, C:Y.54, C:Y.54, A:R.108, A:R.108, A:N.489 Hydrogen bonds: A:R.114, A:N.489 Salt bridges: A:K.32, A:R.43, A:R.108 pi-Stacking: A:H.104, A:H.104, A:H.126, A:H.126 Metal complexes: A:H.104, A:H.126 HEC.3: 23 residues within 4Å: Chain A: K.11, C.12, C.15, H.16, R.26, I.27, Q.30, W.37, I.41, R.43, M.44, H.48, L.50, L.60, R.114, F.125 Chain B: L.116, N.117, D.118, H.119, Y.120 Chain E: S.85 Ligands: HEC.2 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:I.27, A:I.27, A:W.37, A:I.41, A:H.48, A:L.50, A:L.50, A:L.60, A:F.125, B:Y.120 Hydrogen bonds: A:R.26, A:Q.30 Salt bridges: A:R.26, A:K.32, A:R.43, A:R.43, A:H.48, A:R.114 pi-Stacking: A:H.16, A:H.16 pi-Cation interactions: A:H.16 Metal complexes: A:H.16 HEC.5: 25 residues within 4Å: Chain D: K.32, S.40, R.43, T.99, C.100, R.102, C.103, H.104, R.108, V.109, Q.112, R.114, W.119, L.122, H.126, W.130, L.133, Q.136, W.144, L.156, N.489, P.491 Chain F: P.44, A.45 Ligands: HEC.6 30 PLIP interactions: 24 interactions with chain D, 6 interactions with chain F, Hydrophobic interactions: D:T.99, D:V.109, D:W.119, D:L.122, D:L.122, D:W.130, D:W.130, D:L.133, D:W.144, D:L.156, F:P.44, F:P.44 Hydrogen bonds: D:R.114, D:N.489 Water bridges: D:R.108, D:R.108, D:N.489, F:Y.54, F:Y.54, F:Y.54, F:Y.54 Salt bridges: D:K.32, D:R.43, D:R.108 pi-Stacking: D:H.104, D:H.104, D:H.126, D:H.126 Metal complexes: D:H.104, D:H.126 HEC.6: 23 residues within 4Å: Chain B: S.85 Chain D: K.11, C.12, C.15, H.16, R.26, I.27, Q.30, W.37, I.41, R.43, M.44, H.48, L.50, L.60, R.114, F.125 Chain E: L.116, N.117, D.118, H.119, Y.120 Ligands: HEC.5 22 PLIP interactions: 1 interactions with chain E, 21 interactions with chain D, Hydrophobic interactions: E:Y.120, D:I.27, D:I.27, D:W.37, D:I.41, D:H.48, D:L.50, D:L.50, D:L.60, D:F.125 Hydrogen bonds: D:R.26, D:Q.30 Salt bridges: D:R.26, D:K.32, D:R.43, D:R.43, D:H.48, D:R.114 pi-Stacking: D:H.16, D:H.16 pi-Cation interactions: D:H.16 Metal complexes: D:H.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Satoh, A. et al., Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges. J.Biol.Chem. (2002)

Release Date

2002-01-16

Peptides

Amine Dehydrogenase: AD
Amine Dehydrogenase: BE
Amine Dehydrogenase: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
G

F
G

Amine Dehydrogenase

Amine Dehydrogenase

Amine Dehydrogenase

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