SMTL ID : 4g1v.2 (3 other biounits)

X-ray structure of yeast flavohemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: I.42, F.43, N.44, N.47, Q.53, A.56, L.57, T.60, Q.80, I.81, K.84, H.85, L.88, I.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133, P.392, K.393, M.394 Ligands: NO2.4 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:I.42, A:F.43, A:F.43, A:F.43, A:F.43, A:L.57, A:I.81, A:I.81, A:L.88, A:I.90, A:H.94, A:Y.95, A:Y.95, A:V.98, A:Y.126, A:I.129, A:F.133, A:F.133 Hydrogen bonds: A:N.47, A:Q.80, A:K.393, A:M.394 Water bridges: A:N.44, A:N.44, A:Q.48 Salt bridges: A:K.84, A:K.84 pi-Stacking: A:F.133 Metal complexes: A:H.85 HEM.5: 25 residues within 4Å: Chain B: I.42, F.43, N.44, N.47, Q.53, A.56, L.57, T.60, Q.80, I.81, K.84, H.85, L.88, I.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133, P.392, K.393, M.394 Ligands: NO2.8 29 PLIP interactions: 29 interactions with chain B, Hydrophobic interactions: B:I.42, B:F.43, B:F.43, B:F.43, B:F.43, B:L.57, B:I.81, B:I.81, B:L.88, B:I.90, B:H.94, B:Y.95, B:Y.95, B:V.98, B:Y.126, B:I.129, B:F.133, B:F.133 Hydrogen bonds: B:N.47, B:Q.80, B:K.393, B:M.394 Water bridges: B:N.44, B:N.44, B:Q.48 Salt bridges: B:K.84, B:K.84 pi-Stacking: B:F.133 Metal complexes: B:H.85 HEM.9: 25 residues within 4Å: Chain C: I.42, F.43, N.44, N.47, Q.53, A.56, L.57, T.60, Q.80, I.81, K.84, H.85, L.88, I.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133, P.392, K.393, M.394 Ligands: NO2.12 29 PLIP interactions: 29 interactions with chain C, Hydrophobic interactions: C:I.42, C:F.43, C:F.43, C:F.43, C:F.43, C:L.57, C:I.81, C:I.81, C:L.88, C:I.90, C:H.94, C:Y.95, C:Y.95, C:V.98, C:Y.126, C:I.129, C:F.133, C:F.133 Hydrogen bonds: C:N.47, C:Q.80, C:K.393, C:M.394 Water bridges: C:N.44, C:N.44, C:Q.48 Salt bridges: C:K.84, C:K.84 pi-Stacking: C:F.133 Metal complexes: C:H.85 HEM.13: 25 residues within 4Å: Chain D: I.42, F.43, N.44, N.47, Q.53, A.56, L.57, T.60, Q.80, I.81, K.84, H.85, L.88, I.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133, P.392, K.393, M.394 Ligands: NO2.16 29 PLIP interactions: 29 interactions with chain D, Hydrophobic interactions: D:I.42, D:F.43, D:F.43, D:F.43, D:F.43, D:L.57, D:I.81, D:I.81, D:L.88, D:I.90, D:H.94, D:Y.95, D:Y.95, D:V.98, D:Y.126, D:I.129, D:F.133, D:F.133 Hydrogen bonds: D:N.47, D:Q.80, D:K.393, D:M.394 Water bridges: D:N.44, D:N.44, D:Q.48 Salt bridges: D:K.84, D:K.84 pi-Stacking: D:F.133 Metal complexes: D:H.85 HEM.17: 25 residues within 4Å: Chain E: I.42, F.43, N.44, N.47, Q.53, A.56, L.57, T.60, Q.80, I.81, K.84, H.85, L.88, I.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133, P.392, K.393, M.394 Ligands: NO2.20 29 PLIP interactions: 29 interactions with chain E, Hydrophobic interactions: E:I.42, E:F.43, E:F.43, E:F.43, E:F.43, E:L.57, E:I.81, E:I.81, E:L.88, E:I.90, E:H.94, E:Y.95, E:Y.95, E:V.98, E:Y.126, E:I.129, E:F.133, E:F.133 Hydrogen bonds: E:N.47, E:Q.80, E:K.393, E:M.394 Water bridges: E:N.44, E:N.44, E:Q.48 Salt bridges: E:K.84, E:K.84 pi-Stacking: E:F.133 Metal complexes: E:H.85 HEM.21: 25 residues within 4Å: Chain F: I.42, F.43, N.44, N.47, Q.53, A.56, L.57, T.60, Q.80, I.81, K.84, H.85, L.88, I.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133, P.392, K.393, M.394 Ligands: NO2.24 29 PLIP interactions: 29 interactions with chain F, Hydrophobic interactions: F:I.42, F:F.43, F:F.43, F:F.43, F:F.43, F:L.57, F:I.81, F:I.81, F:L.88, F:I.90, F:H.94, F:Y.95, F:Y.95, F:V.98, F:Y.126, F:I.129, F:F.133, F:F.133 Hydrogen bonds: F:N.47, F:Q.80, F:K.393, F:M.394 Water bridges: F:N.44, F:N.44, F:Q.48 Salt bridges: F:K.84, F:K.84 pi-Stacking: F:F.133 Metal complexes: F:H.85

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

FAD.2: 26 residues within 4Å: Chain A: N.44, T.46, V.50, K.84, Y.189, R.207, H.208, Y.209, S.210, A.223, V.224, K.225, E.227, R.230, F.233, P.234, G.236, L.237, V.238, S.239, V.282, T.285, E.388, F.390, G.391 Chain D: E.108 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.189, A:H.208, A:F.390, A:F.390 Hydrogen bonds: A:N.44, A:T.46, A:H.208, A:H.208, A:S.210, A:A.223, A:K.225, A:R.230, A:L.237, A:V.238, A:S.239 Water bridges: A:R.207, A:R.207 Salt bridges: A:R.207, A:R.207 pi-Stacking: A:Y.209, A:F.390 FAD.6: 26 residues within 4Å: Chain B: N.44, T.46, V.50, K.84, Y.189, R.207, H.208, Y.209, S.210, A.223, V.224, K.225, E.227, R.230, F.233, P.234, G.236, L.237, V.238, S.239, V.282, T.285, E.388, F.390, G.391 Chain F: E.108 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.189, B:H.208, B:F.390, B:F.390 Hydrogen bonds: B:N.44, B:T.46, B:H.208, B:H.208, B:S.210, B:A.223, B:K.225, B:R.230, B:L.237, B:V.238, B:S.239 Water bridges: B:R.207, B:R.207 Salt bridges: B:R.207, B:R.207 pi-Stacking: B:Y.209, B:F.390 FAD.10: 26 residues within 4Å: Chain C: N.44, T.46, V.50, K.84, Y.189, R.207, H.208, Y.209, S.210, A.223, V.224, K.225, E.227, R.230, F.233, P.234, G.236, L.237, V.238, S.239, V.282, T.285, E.388, F.390, G.391 Chain E: E.108 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:Y.189, C:H.208, C:F.390, C:F.390 Hydrogen bonds: C:N.44, C:T.46, C:H.208, C:H.208, C:S.210, C:A.223, C:K.225, C:R.230, C:L.237, C:V.238, C:S.239 Water bridges: C:R.207, C:R.207 Salt bridges: C:R.207, C:R.207 pi-Stacking: C:Y.209, C:F.390 FAD.14: 26 residues within 4Å: Chain A: E.108 Chain D: N.44, T.46, V.50, K.84, Y.189, R.207, H.208, Y.209, S.210, A.223, V.224, K.225, E.227, R.230, F.233, P.234, G.236, L.237, V.238, S.239, V.282, T.285, E.388, F.390, G.391 28 PLIP interactions: 27 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Y.189, D:H.208, D:F.390, D:F.390 Hydrogen bonds: D:N.44, D:T.46, D:T.46, D:H.208, D:H.208, D:Y.209, D:S.210, D:A.223, D:K.225, D:R.230, D:L.237, D:V.238, D:S.239, D:T.285, A:E.108 Water bridges: D:R.207, D:R.207, D:E.227, D:E.227, D:E.227 Salt bridges: D:R.207, D:R.207 pi-Stacking: D:Y.209, D:F.390 FAD.18: 26 residues within 4Å: Chain C: E.108 Chain E: N.44, T.46, V.50, K.84, Y.189, R.207, H.208, Y.209, S.210, A.223, V.224, K.225, E.227, R.230, F.233, P.234, G.236, L.237, V.238, S.239, V.282, T.285, E.388, F.390, G.391 28 PLIP interactions: 27 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:Y.189, E:H.208, E:F.390, E:F.390 Hydrogen bonds: E:N.44, E:T.46, E:T.46, E:H.208, E:H.208, E:Y.209, E:S.210, E:A.223, E:K.225, E:R.230, E:L.237, E:V.238, E:S.239, E:T.285, C:E.108 Water bridges: E:R.207, E:R.207, E:E.227, E:E.227, E:E.227 Salt bridges: E:R.207, E:R.207 pi-Stacking: E:Y.209, E:F.390 FAD.22: 26 residues within 4Å: Chain B: E.108 Chain F: N.44, T.46, V.50, K.84, Y.189, R.207, H.208, Y.209, S.210, A.223, V.224, K.225, E.227, R.230, F.233, P.234, G.236, L.237, V.238, S.239, V.282, T.285, E.388, F.390, G.391 28 PLIP interactions: 27 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:Y.189, F:H.208, F:F.390, F:F.390 Hydrogen bonds: F:N.44, F:T.46, F:T.46, F:H.208, F:H.208, F:Y.209, F:S.210, F:A.223, F:K.225, F:R.230, F:L.237, F:V.238, F:S.239, F:T.285, B:E.108 Water bridges: F:R.207, F:R.207, F:E.227, F:E.227, F:E.227 Salt bridges: F:R.207, F:R.207 pi-Stacking: F:Y.209, F:F.390

6 x K: POTASSIUM ION(Non-covalent)

K.3: 2 residues within 4Å: Chain A: H.36, E.38 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.36, A:E.38 K.7: 2 residues within 4Å: Chain B: H.36, E.38 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.36, B:E.38 K.11: 2 residues within 4Å: Chain C: H.36, E.38 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.36, C:E.38 K.15: 2 residues within 4Å: Chain D: H.36, E.38 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.36, D:E.38 K.19: 2 residues within 4Å: Chain E: H.36, E.38 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.36, E:E.38 K.23: 2 residues within 4Å: Chain F: H.36, E.38 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.36, F:E.38

6 x NO2: NITRITE ION(Non-covalent)

NO2.4: 5 residues within 4Å: Chain A: Y.29, F.43, Q.53, L.57 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.29, A:Y.29 NO2.8: 5 residues within 4Å: Chain B: Y.29, F.43, Q.53, L.57 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.29, B:Y.29 NO2.12: 5 residues within 4Å: Chain C: Y.29, F.43, Q.53, L.57 Ligands: HEM.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.29, C:Y.29 NO2.16: 5 residues within 4Å: Chain D: Y.29, F.43, Q.53, L.57 Ligands: HEM.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.29 NO2.20: 5 residues within 4Å: Chain E: Y.29, F.43, Q.53, L.57 Ligands: HEM.17 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.29 NO2.24: 5 residues within 4Å: Chain F: Y.29, F.43, Q.53, L.57 Ligands: HEM.21 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Hammi, E. et al., Active site analysis of yeast flavohemoglobin based on its structure with a small ligand or econazole. Febs J. (2012)

Release Date

2012-11-14

Peptides

Flavohemoglobin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Flavohemoglobin

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