SMTL ID : 5cku.1

Structure of Aspergillus fumigatus ornithine hydroxylase (SidA) mutant N323A bound to NADP and ornithine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: V.45, 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, S.469 21 PLIP interactions: 21 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:R.84, A:G.211, A:G.211, A:G.212 Salt bridges: A:H.91 pi-Stacking: A:W.90, A:H.91 FAD.8: 28 residues within 4Å: Chain B: V.45, 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, S.469 21 PLIP interactions: 21 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:R.84, B:G.211, B:G.211, B:G.212 Salt bridges: B:H.91 pi-Stacking: B:W.90, B:H.91 FAD.15: 28 residues within 4Å: Chain C: V.45, 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, S.469 21 PLIP interactions: 21 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:R.84, C:G.211, C:G.211, C:G.212 Salt bridges: C:H.91 pi-Stacking: C:W.90, C:H.91 FAD.22: 28 residues within 4Å: Chain D: V.45, 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, S.469 21 PLIP interactions: 21 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:R.84, D:G.211, D:G.211, D:G.212 Salt bridges: D:H.91 pi-Stacking: D:W.90, D:H.91

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

NAP.2: 13 residues within 4Å: Chain A: P.217, G.253, S.254, G.255, Q.256, S.257, R.279, Y.324, S.325, A.404, T.405, G.406, Y.407 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.254, A:S.254, A:S.257, A:S.257, A:R.279, A:S.325, A:S.325 Water bridges: A:S.229, A:G.255, A:Q.256, A:A.258, A:R.279, A:R.279, A:D.280, A:S.325, A:V.326, A:G.406, A:Y.407 Salt bridges: A:R.279 pi-Cation interactions: A:R.279, A:R.279 NAP.9: 13 residues within 4Å: Chain B: P.217, G.253, S.254, G.255, Q.256, S.257, R.279, Y.324, S.325, A.404, T.405, G.406, Y.407 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:S.254, B:S.254, B:S.257, B:S.257, B:R.279, B:S.325, B:S.325 Water bridges: B:S.229, B:G.255, B:Q.256, B:A.258, B:R.279, B:R.279, B:D.280, B:S.325, B:V.326, B:G.406, B:Y.407 Salt bridges: B:R.279 pi-Cation interactions: B:R.279, B:R.279 NAP.16: 13 residues within 4Å: Chain C: P.217, G.253, S.254, G.255, Q.256, S.257, R.279, Y.324, S.325, A.404, T.405, G.406, Y.407 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:S.254, C:S.254, C:S.257, C:S.257, C:R.279, C:S.325, C:S.325 Water bridges: C:S.229, C:S.254, C:G.255, C:Q.256, C:A.258, C:R.279, C:R.279, C:S.325, C:V.326, C:G.406 Salt bridges: C:R.279 pi-Cation interactions: C:R.279, C:R.279 NAP.23: 13 residues within 4Å: Chain D: P.217, G.253, S.254, G.255, Q.256, S.257, R.279, Y.324, S.325, A.404, T.405, G.406, Y.407 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:S.254, D:S.254, D:S.257, D:S.257, D:R.279, D:S.325, D:S.325 Water bridges: D:S.229, D:S.254, D:G.255, D:Q.256, D:A.258, D:R.279, D:R.279, D:S.325, D:V.326, D:G.406 Salt bridges: D:R.279 pi-Cation interactions: D:R.279, D:R.279

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

ORN.3: 7 residues within 4Å: Chain A: Q.102, I.103, K.107, N.293, F.296, L.467, S.469 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.103, A:L.467 Hydrogen bonds: A:N.293, A:S.469 Water bridges: A:N.293 Salt bridges: A:K.107 ORN.10: 7 residues within 4Å: Chain B: Q.102, I.103, K.107, N.293, F.296, L.467, S.469 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.103, B:L.467 Hydrogen bonds: B:N.293, B:S.469 Water bridges: B:N.293 Salt bridges: B:K.107 ORN.17: 7 residues within 4Å: Chain C: Q.102, I.103, K.107, N.293, F.296, L.467, S.469 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.103, C:L.467 Hydrogen bonds: C:N.293, C:S.469 Water bridges: C:N.293 Salt bridges: C:K.107 ORN.24: 7 residues within 4Å: Chain D: Q.102, I.103, K.107, N.293, F.296, L.467, S.469 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.103, D:L.467 Hydrogen bonds: D:N.293, D:S.469 Water bridges: D:N.293 Salt bridges: D:K.107

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

SO4.4: 5 residues within 4Å: Chain A: R.364, V.365, E.366, H.367, H.368 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.364, A:V.365, A:H.367, A:H.368 Salt bridges: A:H.368 SO4.5: 2 residues within 4Å: Chain A: H.421, K.444 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.421, A:K.444 SO4.6: 7 residues within 4Å: Chain A: L.125, H.126, G.129, R.130, L.131, I.132 Chain B: L.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.125, A:L.131, A:I.132 Salt bridges: A:H.126 SO4.11: 5 residues within 4Å: Chain B: R.364, V.365, E.366, H.367, H.368 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.364, B:V.365, B:H.367, B:H.368 Salt bridges: B:H.368 SO4.12: 2 residues within 4Å: Chain B: H.421, K.444 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.421, B:K.444 SO4.13: 7 residues within 4Å: Chain A: L.112 Chain B: L.125, H.126, G.129, R.130, L.131, I.132 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.125, B:L.131, B:I.132 Salt bridges: B:H.126 SO4.18: 5 residues within 4Å: Chain C: R.364, V.365, E.366, H.367, H.368 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.364, C:V.365, C:H.367, C:H.368 Salt bridges: C:H.368 SO4.19: 2 residues within 4Å: Chain C: H.421, K.444 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.421, C:K.444 SO4.20: 7 residues within 4Å: Chain C: L.125, H.126, G.129, R.130, L.131, I.132 Chain D: L.112 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.125, C:L.131, C:I.132 Salt bridges: C:H.126 SO4.25: 5 residues within 4Å: Chain D: R.364, V.365, E.366, H.367, H.368 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.364, D:V.365, D:H.367, D:H.368 Salt bridges: D:H.368 SO4.26: 2 residues within 4Å: Chain D: H.421, K.444 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:H.421, D:K.444 SO4.27: 7 residues within 4Å: Chain C: L.112 Chain D: L.125, H.126, G.129, R.130, L.131, I.132 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.125, D:L.131, D:I.132 Salt bridges: D:H.126

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: F.291, E.294 Chain B: H.133 Chain D: Y.336, M.339, Y.340, R.343, W.352 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.343, D:R.343 GOL.14: 8 residues within 4Å: Chain A: H.133 Chain B: F.291, E.294 Chain C: Y.336, M.339, Y.340, R.343, W.352 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.343, C:R.343 GOL.21: 8 residues within 4Å: Chain B: Y.336, M.339, Y.340, R.343, W.352 Chain C: F.291, E.294 Chain D: H.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.343, B:R.343 GOL.28: 8 residues within 4Å: Chain A: Y.336, M.339, Y.340, R.343, W.352 Chain C: H.133 Chain D: F.291, E.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.343, A:R.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, R. et al., Contribution to catalysis of ornithine binding residues in ornithine N5-monooxygenase. Arch.Biochem.Biophys. (2015)

Release Date

2015-09-30

Peptides

L-ornithine N(5)-monooxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-ornithine N(5)-monooxygenase