SMTL ID : 6x0i.1

Structure of oxidized SidA ornithine hydroxylase with the FAD "in" and complexed with NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: I.103, K.107, F.296, S.469 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.296 Hydrogen bonds: A:S.469 Salt bridges: A:K.107 ACT.5: 5 residues within 4Å: Chain B: I.103, K.107, N.293, F.296, S.469 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.296 Hydrogen bonds: B:N.293, B:S.469 Salt bridges: B:K.107 ACT.9: 6 residues within 4Å: Chain C: I.103, K.107, N.293, F.296, L.467, S.469 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.103, C:F.296, C:L.467 Hydrogen bonds: C:N.293 Salt bridges: C:K.107 ACT.13: 6 residues within 4Å: Chain D: I.103, K.107, N.293, F.296, L.467, S.469 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.296, D:L.467 Hydrogen bonds: D:N.293 Salt bridges: D:K.107

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

FAD.2: 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 Ligands: NAP.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:H.91, A:M.94, A:Y.407 Hydrogen bonds: A:A.50, A:R.84, 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:F.47, A:G.48, A:Q.85, A:A.89, A:G.211, A:S.466 Salt bridges: A:H.91 pi-Stacking: A:H.91 pi-Cation interactions: A:R.84 FAD.6: 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, E.166, E.167, V.168, A.209, I.210, G.211, Y.407, R.409, L.415, S.466, L.467, L.468 Ligands: NAP.7 27 PLIP interactions: 27 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 Water bridges: B:F.47, B:G.48, B:G.48, B:E.83, B:R.84, B:R.84, B:Q.85, B:A.89, B:H.91, B:G.211, B:G.212, B:G.212, B:S.466 Salt bridges: B:H.91 pi-Stacking: B:H.91 pi-Cation interactions: B:R.84 FAD.10: 27 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 Ligands: NAP.11 24 PLIP interactions: 24 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:F.47, C:G.48, C:G.48, C:R.84, C:R.84, C:R.84, C:A.89, C:A.89, C:G.211 Salt bridges: C:H.91 pi-Stacking: C:H.91 pi-Cation interactions: C:R.84 FAD.14: 27 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, E.166, E.167, V.168, A.209, I.210, G.211, Y.407, R.409, S.466, L.467, L.468 Ligands: NAP.15 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:M.94, D:Y.407 Hydrogen bonds: D:A.50, D:R.84, D:R.84, D:Q.85, D:W.90, D:Q.102, D:V.168, D:V.168, D:R.409, D:L.468 Water bridges: D:F.47, D:G.48, D:E.83, D:G.211 Salt bridges: D:H.91 pi-Stacking: D:H.91 pi-Cation interactions: D:R.84

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

NAP.3: 19 residues within 4Å: Chain A: K.100, Q.102, R.144, P.217, G.253, S.254, G.255, Q.256, S.257, E.260, R.279, N.323, Y.324, S.325, A.404, T.405, G.406, Y.407 Ligands: FAD.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:Q.102, A:Q.102, A:S.254, A:G.255, A:S.257, A:S.257, A:E.260, A:R.279, A:N.323, A:N.323, A:S.325, A:S.325 Water bridges: A:K.100, A:S.229, A:Q.256, A:A.258, A:R.279, A:V.326, A:R.328, A:G.406, A:Y.407, A:Y.407 Salt bridges: A:R.279 pi-Cation interactions: A:R.279, A:R.279 NAP.7: 19 residues within 4Å: Chain B: K.100, Q.102, R.144, P.217, G.253, S.254, G.255, Q.256, S.257, E.260, R.279, N.323, Y.324, S.325, A.404, T.405, G.406, Y.407 Ligands: FAD.6 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:Q.256 Hydrogen bonds: B:Q.102, B:Q.102, B:S.254, B:G.255, B:S.257, B:S.257, B:E.260, B:R.279, B:N.323, B:S.325, B:S.325 Water bridges: B:S.99, B:K.100, B:K.215, B:S.218, B:S.218, B:S.229, B:G.253, B:Q.256, B:A.258, B:E.260, B:R.279, B:K.320, B:K.320, B:S.325, B:V.326, B:R.328, B:G.406, B:Y.407, B:Y.407 Salt bridges: B:R.279 pi-Cation interactions: B:R.279, B:R.279 NAP.11: 20 residues within 4Å: Chain C: K.100, Q.102, R.144, P.217, G.253, S.254, G.255, Q.256, S.257, E.260, R.279, N.323, Y.324, S.325, R.328, A.404, T.405, G.406, Y.407 Ligands: FAD.10 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Q.256 Hydrogen bonds: C:Q.102, C:Q.102, C:S.254, C:G.255, C:S.257, C:S.257, C:E.260, C:R.279, C:N.323, C:S.325, C:S.325, C:R.328 Water bridges: C:K.100, C:Q.256, C:A.258, C:D.280, C:S.325, C:S.325, C:V.326, C:G.406, C:G.406, C:Y.407 Salt bridges: C:R.279 pi-Cation interactions: C:R.279, C:R.279 NAP.15: 19 residues within 4Å: Chain D: K.100, Q.102, R.144, P.217, G.253, S.254, G.255, Q.256, S.257, E.260, R.279, N.323, Y.324, S.325, A.404, T.405, G.406, Y.407 Ligands: FAD.14 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:Q.256 Hydrogen bonds: D:Q.102, D:Q.102, D:S.254, D:G.255, D:S.257, D:S.257, D:E.260, D:R.279, D:N.323, D:N.323, D:S.325, D:S.325 Water bridges: D:K.100, D:Q.256, D:A.258, D:E.260, D:R.279, D:R.279, D:R.279, D:V.326, D:G.406, D:G.406, D:Y.407 Salt bridges: D:R.279 pi-Cation interactions: D:R.279, D:R.279

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: D.288 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.288 CA.8: 2 residues within 4Å: Chain A: S.138 Chain B: D.288 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.288, H2O.3, H2O.19, H2O.26 CA.12: 2 residues within 4Å: Chain C: D.288 Chain D: S.138 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.288 CA.16: 2 residues within 4Å: Chain C: S.138 Chain D: D.288 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.288, H2O.24, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, A.C. et al., Trapping conformational states of a flavin-dependent N -monooxygenase in crystallo reveals protein and flavin dynamics. J.Biol.Chem. (2020)

Release Date

2020-08-05

Peptides

L-ornithine N(5)-monooxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-ornithine N(5)-monooxygenase

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