SMTL ID : 3zv5.1

CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT 2,3-DIHYDROXYBIPHENYL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.12, S.15, G.16, L.17, D.36, K.37, G.58, D.59, V.60, R.61, N.86, A.87, G.88, Y.119, T.140, I.141, S.142, Y.155, K.159, P.184, G.185, G.186, M.187, T.189, D.190, L.191, I.204 Ligands: BPY.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.12, A:S.15, A:S.15, A:S.15, A:L.17, A:K.37, A:K.37, A:D.59, A:V.60, A:R.61, A:N.86, A:G.88, A:Y.119, A:Y.155, A:K.159, A:M.187, A:M.187, A:T.189, A:D.190 Water bridges: A:R.192 NAD.3: 28 residues within 4Å: Chain B: G.12, A.14, S.15, G.16, L.17, D.36, K.37, G.58, D.59, V.60, N.86, A.87, G.88, V.114, Y.119, T.140, I.141, S.142, N.143, Y.155, K.159, P.184, G.185, G.186, M.187, T.189, D.190, L.191 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.184 Hydrogen bonds: B:A.14, B:S.15, B:S.15, B:L.17, B:K.37, B:K.37, B:D.59, B:V.60, B:N.86, B:Y.119, B:Y.155, B:K.159, B:G.186, B:M.187, B:T.189, B:T.189, B:T.189, B:D.190 Water bridges: B:G.16, B:R.192 pi-Cation interactions: B:K.37 NAD.4: 28 residues within 4Å: Chain C: G.12, S.15, G.16, L.17, D.36, K.37, G.58, D.59, V.60, R.61, N.86, A.87, G.88, Y.119, T.140, I.141, S.142, Y.155, K.159, P.184, G.185, G.186, M.187, T.189, D.190, L.191, I.204 Ligands: BPY.5 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.12, C:S.15, C:S.15, C:S.15, C:L.17, C:K.37, C:K.37, C:D.59, C:V.60, C:R.61, C:N.86, C:G.88, C:K.159, C:M.187, C:M.187, C:D.190 Water bridges: C:R.192 NAD.6: 28 residues within 4Å: Chain D: G.12, A.14, S.15, G.16, L.17, D.36, K.37, G.58, D.59, V.60, N.86, A.87, G.88, V.114, Y.119, T.140, I.141, S.142, N.143, Y.155, K.159, P.184, G.185, G.186, M.187, T.189, D.190, L.191 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.184 Hydrogen bonds: D:A.14, D:S.15, D:S.15, D:L.17, D:K.37, D:K.37, D:D.59, D:V.60, D:N.86, D:K.159, D:G.186, D:M.187, D:T.189, D:T.189, D:D.190 Water bridges: D:G.16, D:R.192 pi-Cation interactions: D:K.37

2 x BPY: BIPHENYL-2,3-DIOL(Non-covalent)

BPY.2: 13 residues within 4Å: Chain A: W.90, S.142, N.143, N.149, G.150, Y.155, L.191, I.204, L.209, M.212, M.255 Chain C: F.260 Ligands: NAD.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.90, A:L.191, A:I.204, A:L.209, C:F.260 Hydrogen bonds: A:S.142, A:S.142, A:N.143, A:N.143 BPY.5: 13 residues within 4Å: Chain A: F.260 Chain C: W.90, S.142, N.143, N.149, G.150, Y.155, L.191, I.204, L.209, M.212, M.255 Ligands: NAD.4 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.90, C:L.191, C:I.204, C:L.209, A:F.260 Hydrogen bonds: C:S.142, C:S.142, C:N.143, C:N.143, C:Y.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhindwal, S. et al., Biochemical Studies and Ligand-Bound Structures of Biphenyl Dehydrogenase from Pandoraea Pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme. J.Biol.Chem. (2011)

Release Date

2011-08-31

Peptides

CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE

Related Entries With Identical Sequence