SMTL ID : 7jvk.1

Structure of the M101A variant of the SidA ornithine hydroxylase with the FAD in the "out" conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 27 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, R.144, E.166, E.167, V.168, A.209, I.210, G.211, S.257, Y.324, G.406, Y.407, R.409, S.466, L.467, L.468 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.90, A:H.91, A:M.94 Hydrogen bonds: A:A.50, A:R.84, A:Q.85, A:W.90, A:V.168, A:V.168, A:R.409, A:R.409, A:S.466 Water bridges: A:S.51, A:R.84, A:G.211, A:G.211, A:S.257 Salt bridges: A:H.91 pi-Stacking: A:H.91, A:Y.324, A:Y.324 FAD.5: 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, R.144, E.166, E.167, V.168, A.209, I.210, G.211, S.257, N.323, Y.324, G.406, Y.407, R.409, S.466, L.467, L.468 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:W.90, B:H.91, B:M.94 Hydrogen bonds: B:A.50, B:R.84, B:Q.85, B:W.90, B:V.168, B:V.168, B:R.409, B:R.409, B:S.466 Water bridges: B:F.47, B:G.48, B:G.48, B:E.83, B:G.211, B:G.211, B:G.212, B:S.257 Salt bridges: B:H.91 pi-Stacking: B:H.91, B:Y.324, B:Y.324 FAD.8: 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, R.144, E.166, E.167, V.168, A.209, I.210, G.211, S.257, Y.324, G.406, Y.407, R.409, S.466, L.467, L.468 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:W.90, C:M.94, C:Y.324 Hydrogen bonds: C:A.50, C:R.84, C:Q.85, C:W.90, C:V.168, C:V.168, C:R.409, C:R.409, C:S.466 Water bridges: C:F.47, C:G.48, C:G.48, C:A.89, C:G.211, C:G.211, C:G.212, C:S.257, C:Y.407, C:Y.407 Salt bridges: C:H.91 pi-Stacking: C:Y.324, C:Y.324 pi-Cation interactions: C:R.84, C:H.91 FAD.11: 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, R.144, E.166, E.167, V.168, A.209, I.210, G.211, S.257, N.323, Y.324, G.406, Y.407, R.409, S.466, L.467, L.468 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:W.90, D:M.94 Hydrogen bonds: D:A.50, D:R.84, D:Q.85, D:W.90, D:V.168, D:V.168, D:R.409, D:R.409, D:S.466 Water bridges: D:G.48, D:S.51, D:G.211, D:G.211, D:N.323 Salt bridges: D:H.91 pi-Stacking: D:H.91, D:Y.324, D:Y.324

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

PGE.2: 4 residues within 4Å: Chain A: R.84, S.92, S.230, K.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.231 PGE.6: 6 residues within 4Å: Chain B: R.84, S.92, G.93, S.230, K.231, T.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.231, B:T.234 Water bridges: B:G.93

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

ACT.3: 5 residues within 4Å: Chain A: I.103, K.107, N.293, F.296, S.469 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.103, A:F.296 Hydrogen bonds: A:S.469 Salt bridges: A:K.107 ACT.7: 4 residues within 4Å: Chain B: I.103, K.107, F.296, S.469 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.103 Hydrogen bonds: B:S.469 Salt bridges: B:K.107 ACT.9: 4 residues within 4Å: Chain C: I.103, K.107, F.296, S.469 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.296 Salt bridges: C:K.107 ACT.12: 5 residues within 4Å: Chain D: I.103, K.107, N.293, F.296, S.469 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.103 Hydrogen bonds: D:N.293 Salt bridges: D:K.107

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: S.138 Chain B: D.288 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.288, A:S.138 CA.10: 2 residues within 4Å: Chain C: S.138 Chain D: D.288 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:D.288, C:S.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, A.C. et al., Structural Determinants of Flavin Dynamics in a Class B Monooxygenase. Biochemistry (2020)

Release Date

2020-12-02

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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