SMTL ID : 6x0h.1

Structure of oxidized SidA ornithine hydroxylase with the FAD in the "out" conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 25 residues within 4Å: Chain A: V.38, G.39, G.41, P.42, A.43, L.75, E.76, R.77, Q.78, W.83, H.84, M.87, R.137, E.159, E.160, V.161, A.202, I.203, G.204, Y.317, Y.400, R.402, S.459, L.460, L.461 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.83, A:H.84, A:M.87 Hydrogen bonds: A:A.43, A:R.77, A:Q.78, A:W.83, A:V.161, A:V.161, A:R.402, A:R.402, A:S.459 Water bridges: A:F.40, A:G.41, A:S.44, A:E.76, A:R.77, A:S.250 Salt bridges: A:H.84 pi-Stacking: A:Y.317, A:Y.317 pi-Cation interactions: A:H.84 FAD.5: 27 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, R.137, E.159, E.160, V.161, A.202, I.203, G.204, N.316, Y.317, G.399, Y.400, R.402, S.459, L.460, L.461 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:W.83, B:H.84, B:M.87 Hydrogen bonds: B:A.43, B:R.77, B:Q.78, B:W.83, B:V.161, B:V.161, B:N.316, B:R.402, B:R.402, B:S.459 Water bridges: B:F.40, B:G.41, B:G.41, B:E.76, B:A.82, B:H.84, B:H.84, B:G.204, B:G.204, B:G.205, B:G.205, B:G.205, B:S.250 Salt bridges: B:H.84 pi-Stacking: B:H.84, B:Y.317, B:Y.317 FAD.7: 25 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, R.137, E.159, E.160, V.161, A.202, I.203, G.204, Y.317, G.399, Y.400, R.402, S.459, L.460, L.461 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:W.83, C:M.87, C:Y.317 Hydrogen bonds: C:A.43, C:R.77, C:R.77, C:Q.78, C:W.83, C:V.161, C:V.161, C:R.402, C:R.402, C:S.459 Water bridges: C:G.41, C:G.41, C:E.76, C:R.77, C:A.82, C:A.82, C:G.204, C:S.250, C:Y.400 Salt bridges: C:H.84 pi-Stacking: C:H.84, C:Y.317 pi-Cation interactions: C:R.77 FAD.10: 27 residues within 4Å: Chain D: V.38, G.39, G.41, P.42, A.43, L.75, E.76, R.77, Q.78, W.83, H.84, M.87, R.137, E.159, E.160, V.161, A.202, I.203, G.204, N.316, Y.317, G.399, Y.400, R.402, S.459, L.460, L.461 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:W.83, D:H.84, D:M.87, D:Y.317 Hydrogen bonds: D:A.43, D:R.77, D:Q.78, D:W.83, D:V.161, D:V.161, D:N.316, D:R.402, D:R.402, D:S.459 Water bridges: D:G.41, D:S.44, D:G.204 Salt bridges: D:H.84 pi-Stacking: D:Y.317 pi-Cation interactions: D:H.84

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

ACT.2: 5 residues within 4Å: Chain A: I.96, K.100, N.286, F.289, S.462 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.289 Hydrogen bonds: A:S.462 Salt bridges: A:K.100 ACT.6: 4 residues within 4Å: Chain B: I.96, K.100, F.289, S.462 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.96 Hydrogen bonds: B:S.462 Salt bridges: B:K.100 ACT.8: 5 residues within 4Å: Chain C: I.96, K.100, N.286, F.289, S.462 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.96, C:F.289 Hydrogen bonds: C:N.286 Salt bridges: C:K.100 ACT.11: 4 residues within 4Å: Chain D: I.96, K.100, F.289, S.462 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.289 Hydrogen bonds: D:N.286 Salt bridges: D:K.100

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 5 residues within 4Å: Chain A: R.77, S.85, S.223, K.224, T.227 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.224 Water bridges: A:R.77, A:S.85, A:S.223, A:K.224, A:T.227

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: N.129, S.131 Chain B: D.281 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.281, A:S.131 CA.9: 2 residues within 4Å: Chain C: S.131 Chain D: D.281 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.281, C:S.131, H2O.17

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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