SMTL ID : 3ozw.1

The Crystal Structure of flavohemoglobin from R. eutrophus in complex with ketoconazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 18 residues within 4Å: Chain A: V.42, F.43, N.44, I.81, K.84, H.85, L.88, V.90, Q.94, Y.95, V.98, Y.126, L.129, A.130, L.133, P.398, D.399 Ligands: KKK.3 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:V.42, A:F.43, A:F.43, A:F.43, A:F.43, A:I.81, A:L.88, A:V.90, A:V.90, A:Q.94, A:Y.95, A:V.98, A:Y.126, A:L.129, A:L.133 Hydrogen bonds: A:N.44, A:D.399 Water bridges: A:K.84, A:K.84, A:D.399, A:D.399, A:D.399 Salt bridges: A:K.84 Metal complexes: A:H.85 HEM.7: 17 residues within 4Å: Chain B: V.42, F.43, N.44, I.81, K.84, H.85, L.88, V.90, Q.94, Y.95, V.98, Y.126, L.129, A.130, L.133, D.399 Ligands: KKK.8 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:V.42, B:F.43, B:F.43, B:F.43, B:F.43, B:I.81, B:I.81, B:L.88, B:V.90, B:V.90, B:Q.94, B:Y.95, B:V.98, B:Y.126, B:L.129, B:L.133 Hydrogen bonds: B:N.44, B:D.399 Water bridges: B:N.44, B:Q.53 Salt bridges: B:K.84 Metal complexes: B:H.85

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 27 residues within 4Å: Chain A: N.44, A.46, Q.48, E.49, Q.50, Y.190, R.206, Q.207, Y.208, S.209, S.222, V.223, K.224, E.226, Q.231, P.232, G.234, Y.235, V.236, S.237, V.276, T.279, E.394, V.395, F.396, G.397 Ligands: KKK.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.190, A:Q.207, A:F.396, A:F.396 Hydrogen bonds: A:N.44, A:E.49, A:E.49, A:Q.50, A:Q.207, A:Q.207, A:S.209, A:S.222, A:K.224, A:Y.235, A:V.236, A:S.237, A:T.279 Water bridges: A:S.222, A:E.226, A:E.226 Salt bridges: A:R.206, A:R.206 pi-Stacking: A:Y.208, A:F.396 FAD.6: 26 residues within 4Å: Chain B: N.44, A.46, E.49, Q.50, K.84, Y.190, R.206, Q.207, Y.208, S.209, S.222, V.223, K.224, E.226, Q.231, P.232, G.234, Y.235, V.236, S.237, V.276, T.279, E.394, V.395, F.396, G.397 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.190, B:Q.207, B:E.394, B:F.396, B:F.396, B:F.396 Hydrogen bonds: B:N.44, B:E.49, B:Q.207, B:Q.207, B:Y.208, B:S.209, B:S.222, B:K.224, B:Y.235, B:V.236, B:S.237, B:T.279 Water bridges: B:S.222, B:E.226, B:E.226, B:Q.231 Salt bridges: B:R.206, B:R.206 pi-Stacking: B:Y.208, B:F.396

2 x KKK: 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine(Non-covalent)

KKK.3: 13 residues within 4Å: Chain A: I.25, F.28, Y.29, F.43, Q.50, Q.53, A.56, L.57, L.102, P.398 Ligands: HEM.1, FAD.2, DGG.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.53, A:A.56, A:L.102, A:P.398 Hydrogen bonds: A:Q.53 KKK.8: 14 residues within 4Å: Chain B: I.25, F.28, Y.29, H.47, Q.52, Q.53, A.56, L.57, H.85, L.102, I.371, G.397, P.398 Ligands: HEM.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.47, B:Q.53, B:Q.53, B:A.56, B:L.57, B:L.102, B:I.371, B:P.398, B:P.398 Hydrogen bonds: B:Y.29, B:Q.53

1 x DGG: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL(Non-covalent)

DGG.4: 10 residues within 4Å: Chain A: A.60, A.63, Y.64, N.67, S.73, L.74, V.77, W.122, L.129 Ligands: KKK.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.60, A:Y.64, A:N.67, A:V.77, A:V.77, A:W.122, A:W.122 Hydrogen bonds: A:N.67

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: E.165, M.310, R.311, D.312, R.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.310, A:D.312, A:R.313 Salt bridges: A:R.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Hammi, E. et al., Structure of Ralstonia eutropha Flavohemoglobin in Complex with Three Antibiotic Azole Compounds. Biochemistry (2011)

Release Date

2011-03-16

Peptides

Flavohemoglobin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Flavohemoglobin

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