SMTL ID : 5b3v.1 (3 other biounits)

Crystal structure of biliverdin reductase in complex with biliverdin and NADP+ from Synechocystis sp. PCC 6803

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

monomer

Ligands

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 residues within 4Å: Chain A: G.20, T.21, G.22, Y.23, A.24, W.44, N.46, S.47, N.50, A.81, T.82, I.83, N.84, H.87, E.104, Y.105, E.131, I.133, R.170, W.171, Q.177, F.287 Ligands: BLA.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.133, A:F.287 Hydrogen bonds: A:T.21, A:T.21, A:G.22, A:Y.23, A:A.24, A:N.46, A:S.47, A:N.50, A:T.82, A:H.87, A:Q.177 Water bridges: A:N.46, A:N.84 Salt bridges: A:R.170 pi-Stacking: A:Y.105

2 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.2: 9 residues within 4Å: Chain A: T.160, M.162, T.172, R.188, Y.238, K.240, R.249, R.283 Ligands: BLA.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.172, A:Y.238 Salt bridges: A:R.188, A:K.240 BLA.3: 12 residues within 4Å: Chain A: Y.23, Y.105, I.133, E.134, A.184, A.185, S.187, R.188, R.191, L.286 Ligands: NAP.1, BLA.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.23, A:Y.105, A:I.133, A:L.286 Hydrogen bonds: A:S.187, A:S.187 Salt bridges: A:R.188, A:R.188, A:R.191 pi-Stacking: A:Y.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takao, H. et al., A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity. Nat Commun (2017)

Release Date

2017-02-15

Peptides

Biliverdin reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Biliverdin reductase

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