SMTL ID : 6x0j.1

Structure of reduced SidA ornithine hydroxylase with the FAD "in" and complexed with NADP and L-ornithine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 22 residues within 4Å: Chain A: K.93, Q.95, R.137, K.208, P.210, G.246, S.247, G.248, Q.249, S.250, E.253, R.272, N.316, Y.317, S.318, A.397, T.398, G.399, Y.400, L.460 Ligands: ORN.2, FDA.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Q.249 Hydrogen bonds: A:Q.95, A:Q.95, A:K.208, A:K.208, A:S.247, A:G.248, A:S.250, A:S.250, A:E.253, A:R.272, A:N.316, A:S.318, A:S.318 Water bridges: A:S.92, A:Q.249, A:Q.249, A:A.251, A:R.272, A:R.272, A:V.319, A:Y.400 Salt bridges: A:R.272 pi-Cation interactions: A:R.272, A:R.272 NAP.4: 21 residues within 4Å: Chain B: K.93, Q.95, R.137, K.208, P.210, G.246, S.247, G.248, Q.249, S.250, E.253, R.272, N.316, Y.317, S.318, A.397, T.398, G.399, Y.400 Ligands: ORN.5, FDA.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Q.249 Hydrogen bonds: B:Q.95, B:Q.95, B:S.247, B:G.248, B:S.250, B:S.250, B:E.253, B:R.272, B:N.316, B:S.318, B:S.318 Water bridges: B:Q.249, B:A.251, B:E.253, B:D.273, B:S.318, B:S.318, B:V.319, B:Y.400, B:Y.400, B:R.402 Salt bridges: B:R.272 pi-Cation interactions: B:R.272, B:R.272 NAP.7: 21 residues within 4Å: Chain C: K.93, Q.95, R.137, K.208, P.210, G.246, S.247, G.248, Q.249, S.250, E.253, R.272, N.316, Y.317, S.318, A.397, T.398, G.399, Y.400 Ligands: ORN.8, FDA.9 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:Q.249 Hydrogen bonds: C:Q.95, C:Q.95, C:K.208, C:S.247, C:G.248, C:S.250, C:S.250, C:E.253, C:R.272, C:N.316, C:N.316, C:S.318, C:S.318, C:S.318 Water bridges: C:S.92, C:K.93, C:S.211, C:Q.249, C:Q.249, C:A.251, C:N.316, C:S.318, C:G.399, C:G.399, C:Y.400, C:Y.400 Salt bridges: C:R.272 pi-Cation interactions: C:R.272, C:R.272 NAP.10: 22 residues within 4Å: Chain D: S.92, K.93, Q.95, R.137, K.208, P.210, G.246, S.247, G.248, Q.249, S.250, E.253, R.272, N.316, Y.317, S.318, A.397, T.398, G.399, Y.400 Ligands: ORN.11, FDA.12 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Q.249 Hydrogen bonds: D:K.208, D:S.247, D:G.248, D:S.250, D:E.253, D:R.272, D:N.316, D:S.318, D:S.318 Water bridges: D:S.211, D:Q.249, D:S.250, D:S.250, D:V.319, D:Y.400, D:R.402 Salt bridges: D:R.272 pi-Cation interactions: D:R.272, D:R.272

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

ORN.2: 9 residues within 4Å: Chain A: Q.95, I.96, K.100, N.286, F.289, N.316, L.460, S.462 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.96, A:L.460 Hydrogen bonds: A:N.286, A:T.315, A:S.462 Water bridges: A:Q.95, A:N.286 Salt bridges: A:K.100 ORN.5: 10 residues within 4Å: Chain B: Q.95, I.96, K.100, N.286, F.289, T.315, N.316, L.460, S.462 Ligands: NAP.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.96, B:L.460 Hydrogen bonds: B:N.286, B:S.462 Water bridges: B:N.286 Salt bridges: B:K.100 ORN.8: 9 residues within 4Å: Chain C: Q.95, I.96, K.100, N.286, F.289, N.316, L.460, S.462 Ligands: NAP.7 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.96, C:L.460 Hydrogen bonds: C:N.286, C:N.286 Water bridges: C:N.286, C:T.315 Salt bridges: C:K.100 ORN.11: 10 residues within 4Å: Chain D: Q.95, I.96, K.100, N.286, F.289, T.315, N.316, L.460, S.462 Ligands: NAP.10 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.96, D:L.460 Hydrogen bonds: D:N.286, D:N.286, D:T.315 Water bridges: D:N.286 Salt bridges: D:K.100

4 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.3: 28 residues within 4Å: Chain A: G.39, G.41, P.42, A.43, L.75, E.76, R.77, Q.78, W.83, H.84, M.87, M.94, Q.95, I.96, R.137, E.159, E.160, V.161, A.202, I.203, G.204, Y.400, R.402, S.459, L.460, L.461, S.462 Ligands: NAP.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:H.84, A:M.87, A:Y.400 Hydrogen bonds: A:A.43, A:R.77, A:Q.78, A:W.83, A:Q.95, A:V.161, A:V.161, A:R.402, A:L.461, A:S.462 Water bridges: A:G.41 Salt bridges: A:H.84 pi-Stacking: A:H.84 pi-Cation interactions: A:R.77 FDA.6: 29 residues within 4Å: Chain B: V.38, G.39, G.41, P.42, A.43, L.75, E.76, R.77, Q.78, W.83, H.84, M.87, M.94, Q.95, I.96, R.137, E.159, E.160, V.161, A.202, I.203, G.204, Y.400, R.402, S.459, L.460, L.461, S.462 Ligands: NAP.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:H.84, B:M.87, B:Y.400 Hydrogen bonds: B:A.43, B:R.77, B:R.77, B:Q.78, B:W.83, B:Q.95, B:V.161, B:V.161, B:R.402, B:L.461, B:S.462 Water bridges: B:G.41, B:G.41, B:E.76, B:A.82 Salt bridges: B:H.84 pi-Stacking: B:H.84 pi-Cation interactions: B:R.77 FDA.9: 28 residues within 4Å: Chain C: G.39, G.41, P.42, A.43, L.75, E.76, R.77, Q.78, W.83, H.84, M.87, M.94, Q.95, I.96, R.137, E.159, E.160, V.161, A.202, I.203, G.204, Y.400, R.402, S.459, L.460, L.461, S.462 Ligands: NAP.7 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:H.84, C:M.87, C:Y.400 Hydrogen bonds: C:A.43, C:R.77, C:Q.78, C:W.83, C:Q.95, C:V.161, C:V.161, C:R.402, C:L.461, C:S.462 Water bridges: C:G.41, C:H.84, C:R.467 Salt bridges: C:H.84 pi-Stacking: C:H.84 pi-Cation interactions: C:R.77 FDA.12: 28 residues within 4Å: Chain D: G.39, G.41, P.42, A.43, L.75, E.76, R.77, Q.78, W.83, H.84, M.87, M.94, Q.95, I.96, R.137, E.159, E.160, V.161, A.202, I.203, G.204, Y.400, R.402, S.459, L.460, L.461, S.462 Ligands: NAP.10 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:H.84, D:M.87, D:Y.400 Hydrogen bonds: D:A.43, D:R.77, D:R.77, D:Q.78, D:W.83, D:Q.95, D:V.161, D:V.161, D:R.402, D:L.461, D:S.462 Water bridges: D:G.41, D:G.41, D:A.82 Salt bridges: D:H.84 pi-Cation interactions: D:R.77

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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