SMTL ID : 4b69.1

A. fumigatus ornithine hydroxylase (SidA) bound to ornithine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 26 residues within 4Å: Chain A: G.46, G.48, P.49, A.50, L.82, E.83, R.84, Q.85, W.90, H.91, M.94, M.101, Q.102, I.103, R.144, E.166, E.167, V.168, A.209, I.210, G.211, Y.407, R.409, S.466, L.467, L.468 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:M.94, A:Y.407 Hydrogen bonds: A:A.50, A:R.84, A:Q.85, A:W.90, A:Q.102, A:V.168, A:V.168, A:R.409, A:L.468, A:S.469 Water bridges: A:G.48, A:S.51, A:H.91, A:G.211, A:G.211, A:G.212, A:G.212, A:G.212 Salt bridges: A:H.91 pi-Stacking: A:W.90 FAD.7: 26 residues within 4Å: Chain B: G.46, G.48, P.49, A.50, L.82, E.83, R.84, Q.85, W.90, H.91, M.94, M.101, Q.102, I.103, R.144, E.166, E.167, V.168, A.209, I.210, G.211, Y.407, R.409, S.466, L.467, L.468 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:M.94, B:Y.407 Hydrogen bonds: B:A.50, B:R.84, B:Q.85, B:W.90, B:Q.102, B:V.168, B:V.168, B:R.409, B:L.468, B:S.469 Water bridges: B:G.48, B:S.51, B:H.91, B:G.211, B:G.211, B:G.212, B:G.212, B:G.212 Salt bridges: B:H.91 pi-Stacking: B:W.90 FAD.13: 26 residues within 4Å: Chain C: G.46, G.48, P.49, A.50, L.82, E.83, R.84, Q.85, W.90, H.91, M.94, M.101, Q.102, I.103, R.144, E.166, E.167, V.168, A.209, I.210, G.211, Y.407, R.409, S.466, L.467, L.468 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:M.94, C:Y.407 Hydrogen bonds: C:A.50, C:R.84, C:Q.85, C:W.90, C:Q.102, C:V.168, C:V.168, C:R.409, C:L.468, C:S.469 Water bridges: C:G.48, C:S.51, C:H.91, C:G.211, C:G.211, C:G.212, C:G.212, C:G.212 Salt bridges: C:H.91 pi-Stacking: C:W.90 FAD.19: 26 residues within 4Å: Chain D: G.46, G.48, P.49, A.50, L.82, E.83, R.84, Q.85, W.90, H.91, M.94, M.101, Q.102, I.103, R.144, E.166, E.167, V.168, A.209, I.210, G.211, Y.407, R.409, S.466, L.467, L.468 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:M.94, D:Y.407 Hydrogen bonds: D:A.50, D:R.84, D:Q.85, D:W.90, D:Q.102, D:V.168, D:V.168, D:R.409, D:L.468, D:S.469 Water bridges: D:G.48, D:S.51, D:H.91, D:G.211, D:G.211, D:G.212, D:G.212, D:G.212 Salt bridges: D:H.91 pi-Stacking: D:W.90

4 x ORN: L-ornithine(Non-covalent)

ORN.2: 8 residues within 4Å: Chain A: Q.102, I.103, K.107, N.293, F.296, N.323, L.467, S.469 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.103, A:L.467 Hydrogen bonds: A:Q.102, A:N.293, A:N.323, A:S.469 Water bridges: A:N.293, A:T.322 Salt bridges: A:K.107 ORN.8: 8 residues within 4Å: Chain B: Q.102, I.103, K.107, N.293, F.296, N.323, L.467, S.469 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.103, B:L.467 Hydrogen bonds: B:Q.102, B:N.293, B:N.323, B:S.469 Water bridges: B:N.293, B:T.322 Salt bridges: B:K.107 ORN.14: 8 residues within 4Å: Chain C: Q.102, I.103, K.107, N.293, F.296, N.323, L.467, S.469 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.103, C:L.467 Hydrogen bonds: C:Q.102, C:N.293, C:N.323, C:S.469 Water bridges: C:N.293, C:T.322 Salt bridges: C:K.107 ORN.20: 8 residues within 4Å: Chain D: Q.102, I.103, K.107, N.293, F.296, N.323, L.467, S.469 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.103, D:L.467 Hydrogen bonds: D:Q.102, D:N.293, D:N.323, D:S.469 Water bridges: D:N.293, D:T.322 Salt bridges: D:K.107

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

SO4.3: 6 residues within 4Å: Chain A: R.364, V.365, E.366, H.367, H.368, G.369 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.364, A:E.366, A:H.367, A:H.368, A:G.369 Salt bridges: A:H.368 SO4.9: 6 residues within 4Å: Chain B: R.364, V.365, E.366, H.367, H.368, G.369 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.364, B:H.367, B:H.367, B:H.368, B:G.369 Salt bridges: B:H.368 SO4.15: 6 residues within 4Å: Chain C: R.364, V.365, E.366, H.367, H.368, G.369 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.364, C:E.366, C:H.367, C:H.368, C:G.369 Salt bridges: C:H.368 SO4.21: 6 residues within 4Å: Chain D: R.364, V.365, E.366, H.367, H.368, G.369 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.364, D:H.367, D:H.367, D:H.368, D:G.369 Salt bridges: D:H.368

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.125, H.126, G.129, R.130, L.131, I.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.126, A:L.131, A:I.132 GOL.5: 8 residues within 4Å: Chain A: Y.336, M.339, Y.340, R.343, W.352 Chain B: F.291, E.294 Chain D: H.133 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:H.133, B:E.294, A:R.343 GOL.6: 3 residues within 4Å: Chain A: M.216, P.217, S.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.218 Water bridges: A:S.218 GOL.10: 6 residues within 4Å: Chain B: L.125, H.126, G.129, R.130, L.131, I.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.126, B:L.131, B:I.132 GOL.11: 8 residues within 4Å: Chain A: F.291, E.294 Chain B: Y.336, M.339, Y.340, R.343, W.352 Chain C: H.133 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.343, A:E.294 GOL.12: 3 residues within 4Å: Chain B: M.216, P.217, S.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.218 Water bridges: B:S.218 GOL.16: 6 residues within 4Å: Chain C: L.125, H.126, G.129, R.130, L.131, I.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.126, C:L.131, C:I.132 GOL.17: 8 residues within 4Å: Chain B: H.133 Chain C: Y.336, M.339, Y.340, R.343, W.352 Chain D: F.291, E.294 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:E.294, C:R.343, B:H.133 GOL.18: 3 residues within 4Å: Chain C: M.216, P.217, S.218 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.218 Water bridges: C:S.218 GOL.22: 6 residues within 4Å: Chain D: L.125, H.126, G.129, R.130, L.131, I.132 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.126, D:L.131, D:I.132 GOL.23: 8 residues within 4Å: Chain A: H.133 Chain C: F.291, E.294 Chain D: Y.336, M.339, Y.340, R.343, W.352 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.294, D:R.343 GOL.24: 3 residues within 4Å: Chain D: M.216, P.217, S.218 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.218 Water bridges: D:S.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Franceschini, S. et al., Structural Insight Into the Mechanism of Oxygen Activation and Substrate Selectivity of Flavin-Dependent N-Hydroxylating Monooxygenases. Biochemistry (2012)

Release Date

2012-10-03

Peptides

L-ORNITHINE N5 MONOOXYGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-ORNITHINE N5 MONOOXYGENASE

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