SMTL ID : 1pby.1

Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: A.10, C.11, C.14, H.15, R.25, I.26, W.36, T.39, R.42, M.43, H.47, V.49, L.51, I.59, R.114, L.122, F.125 Chain B: L.107, T.108, H.109, F.110 Ligands: HEC.2 22 PLIP interactions: 1 interactions with chain B, 21 interactions with chain A, Hydrophobic interactions: B:F.110, A:I.26, A:I.26, A:W.36, A:T.39, A:H.47, A:V.49, A:L.51, A:I.59 Water bridges: A:R.25, A:K.31, A:H.121 Salt bridges: A:R.25, A:K.31, A:R.42, A:R.42, A:H.47, A:R.114 pi-Stacking: A:H.15, A:H.15 pi-Cation interactions: A:H.15 Metal complexes: A:H.15 HEC.2: 21 residues within 4Å: Chain A: K.31, T.39, R.42, R.45, T.99, C.100, R.102, C.103, H.104, R.108, V.109, Q.112, R.114, L.122, H.126, F.130, L.133, Q.136, L.156 Chain C: P.44 Ligands: HEC.1 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:T.99, A:R.102, A:V.109, A:L.122, A:F.130, A:F.130, A:L.133, A:L.133, A:L.156, C:P.44, C:P.44 Hydrogen bonds: A:Q.112 Water bridges: A:T.39, A:T.39, A:R.42, A:R.45, A:R.45, A:N.46, C:T.53 Salt bridges: A:K.31, A:R.42, A:R.42, A:R.45, A:R.114 pi-Stacking: A:H.104, A:H.104, A:H.126, A:H.126 Metal complexes: A:H.104, A:H.126

4 x TBU: TERTIARY-BUTYL ALCOHOL(Non-functional Binders)

TBU.3: 2 residues within 4Å: Chain A: G.236, T.237 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.237 TBU.4: 4 residues within 4Å: Chain A: F.217, V.238, I.240, I.263 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.217, A:I.240, A:I.263 Water bridges: A:Q.183, A:Q.183, A:Q.183, A:R.186, A:R.215 TBU.5: 3 residues within 4Å: Chain B: I.209, D.213, T.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.213, B:T.215 TBU.6: 4 residues within 4Å: Chain B: E.132, A.133, P.134, L.166 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Datta, S. et al., Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution. Acta Crystallogr.,Sect.D (2003)

Release Date

2003-09-02

Peptides

quinohemoprotein amine dehydrogenase 60 kDa subunit: A
quinohemoprotein amine dehydrogenase 40 kDa subunit: B
quinohemoprotein amine dehydrogenase 9 kDa subunit: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

quinohemoprotein amine dehydrogenase 60 kDa subunit

quinohemoprotein amine dehydrogenase 40 kDa subunit

quinohemoprotein amine dehydrogenase 9 kDa subunit

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