SMTL ID : 7er6.1

Crystal structure of human Biliverdin IX-beta reductase B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 25 residues within 4Å: Chain A: G.10, A.11, T.12, G.13, Q.14, T.15, R.35, S.38, D.54, V.55, L.74, L.75, G.76, T.77, R.78, V.86, M.87, C.109, T.110, S.111, H.132, P.151, P.152, H.153, I.154 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:P.151, A:I.154, A:I.154 Hydrogen bonds: A:G.10, A:T.12, A:T.12, A:Q.14, A:T.15, A:S.38, A:D.54, A:V.55, A:L.75, A:G.76, A:R.78, A:I.154 Water bridges: A:G.10, A:A.11, A:G.13, A:Q.14, A:G.16, A:R.35, A:R.35, A:R.35, A:T.77, A:T.77, A:R.78, A:N.79, A:N.79, A:N.79 Salt bridges: A:R.35, A:R.78, A:R.78 pi-Cation interactions: A:R.35 NAP.3: 24 residues within 4Å: Chain B: G.10, A.11, T.12, G.13, Q.14, T.15, R.35, R.39, D.54, V.55, L.74, L.75, G.76, R.78, V.86, M.87, C.109, T.110, S.111, H.132, P.151, P.152, H.153, I.154 41 PLIP interactions: 40 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.154, B:I.154 Hydrogen bonds: B:G.10, B:T.12, B:T.12, B:T.12, B:Q.14, B:Q.14, B:T.15, B:T.15, B:D.54, B:V.55, B:L.75, B:G.76, B:I.154 Water bridges: B:G.10, B:A.11, B:T.12, B:G.13, B:G.16, B:R.35, B:R.35, B:R.35, B:R.35, B:R.39, B:T.77, B:T.77, B:T.77, B:R.78, B:R.78, B:R.78, B:R.78, B:R.78, B:R.78, B:R.78, A:R.92 Salt bridges: B:R.35, B:R.39, B:R.78, B:R.78 pi-Cation interactions: B:R.35

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: H.136, R.140 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.198, A:S.198 Salt bridges: A:H.136, A:R.140 SO4.4: 7 residues within 4Å: Chain A: K.137, R.140 Chain B: H.153, G.155, D.156, Q.157, V.175 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.156, B:Q.157, B:Q.157 Salt bridges: B:H.153, A:R.140 Water bridges: A:K.137 SO4.5: 1 residues within 4Å: Chain B: R.134 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.134, B:R.134, B:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M. et al., Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IX beta Reductase B as a Novel Thrombocytopenia Therapeutic Target. J.Med.Chem. (2022)

Release Date

2022-01-19

Peptides

Flavin reductase (NADPH): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Flavin reductase (NADPH)

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