SMTL ID : 7jvl.1

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

Coordinates

PDB Format Compare

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, R.144, E.166, E.167, V.168, A.209, I.210, G.211, Y.324, Y.407, R.409, L.415, S.466, L.467, L.468 Ligands: NAP.2, ACT.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:M.94, A:Y.407 Hydrogen bonds: A:G.48, A:A.50, A:R.84, A:R.84, A:Q.85, A:W.90, A:V.168, A:V.168, A:Y.324, A:Y.407, A:R.409, A:R.409, A:S.466 Water bridges: A:G.48, A:S.51, A:E.83, A:A.89, A:G.211, A:G.212, A:G.212 Salt bridges: A:H.91 pi-Stacking: A:H.91 pi-Cation interactions: A:R.84, A:R.409 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, Y.324, Y.407, R.409, L.415, S.466, L.467, L.468 Ligands: NAP.6, ACT.7 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:M.94, B:Y.407 Hydrogen bonds: B:G.48, B:A.50, B:R.84, B:Q.85, B:W.90, B:V.168, B:V.168, B:Y.324, B:Y.324, B:Y.407, 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 Salt bridges: B:H.91 pi-Stacking: B:H.91 pi-Cation interactions: B:R.409 FAD.10: 25 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, Y.324, Y.407, R.409, S.466, L.468 Ligands: NAP.11, ACT.12 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:M.94, C:Y.407 Hydrogen bonds: C:G.48, C:A.50, C:R.84, C:Q.85, C:W.90, C:V.168, C:V.168, C:Y.324, C:Y.407, C:R.409, C:R.409, C:S.466 Water bridges: C:F.47, C:G.48, C:S.51, C:E.83, C:G.211, C:G.212, C:G.212 Salt bridges: C:H.91 pi-Stacking: C:H.91 pi-Cation interactions: C:R.84, C:R.409 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, R.144, E.166, E.167, V.168, A.209, I.210, G.211, Y.324, Y.407, R.409, S.466, L.467, L.468 Ligands: NAP.15, ACT.16 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:M.94 Hydrogen bonds: D:G.48, D:A.50, D:R.84, D:R.84, D:Q.85, D:W.90, D:V.168, D:V.168, D:Y.324, D:Y.324, D:Y.407, D:R.409, D:R.409, D:S.466 Water bridges: D:F.47, D:G.48, D:G.48, D:A.89, D:G.211, D:G.212 Salt bridges: D:H.91 pi-Stacking: D:H.91 pi-Cation interactions: D:R.84, D:R.409

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

NAP.2: 21 residues within 4Å: Chain A: K.100, Q.102, R.144, P.217, L.252, 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.1 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:Q.102, A:Q.102, A:S.254, A:S.254, A:S.257, A:S.257, A:E.260, A:R.279, A:N.323, A:S.325, A:S.325, A:R.328 Water bridges: A:S.99, A:K.100, A:S.218, A:G.253, A:G.255, A:Q.256, A:A.258, A:R.279, A:R.279, A:R.279, A:R.279, A:R.279, A:V.326, A:G.406, A:G.406, A:Y.407, A:Y.407, A:Y.407 Salt bridges: A:R.279 pi-Cation interactions: A:R.279, A:R.279 NAP.6: 21 residues within 4Å: Chain B: K.100, Q.102, R.144, K.215, 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.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:Q.256 Hydrogen bonds: B:K.100, B:Q.102, B:Q.102, B:S.254, B:G.255, B:S.257, B:R.279, B:N.323, B:S.325, B:S.325, B:R.328 Water bridges: B:S.99, B:K.100, B:Q.256, B:S.257, B:A.258, B:E.260, B:R.279, B:R.279, 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 24 PLIP interactions: 24 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 Water bridges: C:S.99, C:K.100, C:Q.256, C:A.258, C:D.280, C:V.326, C:A.404, C:G.406, C:Y.407 Salt bridges: C:R.279 pi-Cation interactions: C:R.279, C:R.279 NAP.15: 20 residues within 4Å: Chain D: K.100, Q.102, R.144, K.215, P.217, L.252, 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 Ligands: FAD.14 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:Q.256 Hydrogen bonds: D:K.100, D:Q.102, D:Q.102, D:K.215, D:S.254, D:G.255, D:S.257, D:S.257, D:N.323, D:S.325, D:S.325 Water bridges: D:K.100, D:S.229, D:Q.256, D:A.258, D:R.279, D:R.279, D:R.279, D:V.326, D:R.328, D:G.406, D:Y.407 Salt bridges: D:R.279 pi-Cation interactions: D:R.279, D:R.279

8 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.4: 6 residues within 4Å: Chain A: W.90, Q.102, I.103, L.467, L.468 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.103 Hydrogen bonds: A:L.468 ACT.7: 6 residues within 4Å: Chain B: W.90, Q.102, I.103, L.467, L.468 Ligands: FAD.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.103 Hydrogen bonds: B:L.468 ACT.8: 4 residues within 4Å: Chain B: I.103, K.107, F.296, S.469 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.103, B:F.296 Hydrogen bonds: B:S.469 Salt bridges: B:K.107 ACT.12: 6 residues within 4Å: Chain C: W.90, Q.102, I.103, L.467, L.468 Ligands: FAD.10 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.103 Hydrogen bonds: C:L.468 ACT.13: 5 residues within 4Å: Chain C: Q.102, 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.16: 5 residues within 4Å: Chain D: W.90, I.103, L.467, L.468 Ligands: FAD.14 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.103 Hydrogen bonds: D:L.468 ACT.17: 6 residues within 4Å: Chain D: I.103, K.107, N.293, F.296, L.467, S.469 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.103, D:F.296, D:L.467 Hydrogen bonds: D:N.293 Salt bridges: D:K.107

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 2 residues within 4Å: Chain A: S.138 Chain B: D.288 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.288, B:D.288 CA.18: 2 residues within 4Å: Chain C: S.138 Chain D: D.288 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.288

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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