SMTL ID : 4tm0.1

Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-ox-NADP+-L-orn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: G.37, F.38, G.39, P.40, A.41, F.61, E.62, R.63, R.64, W.69, H.70, M.73, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, N.294, Y.295, Y.365, L.373, S.422, L.423, L.424 Ligands: NAP.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:M.73, A:Y.365 Hydrogen bonds: A:G.37, A:F.38, A:A.41, A:R.63, A:R.63, A:W.69, A:V.147, A:V.147, A:N.294, A:Y.295, A:Y.365 Water bridges: A:F.38, A:G.39, A:E.62, A:T.183, A:L.185, A:R.430, A:R.430 pi-Stacking: A:H.70 pi-Cation interactions: A:R.63 FAD.6: 28 residues within 4Å: Chain B: V.36, G.37, F.38, G.39, P.40, A.41, F.61, E.62, R.63, R.64, W.69, H.70, M.73, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, N.294, Y.295, Y.365, S.422, L.423, L.424 Ligands: NAP.7 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.69, B:H.70, B:M.73, B:Y.365 Hydrogen bonds: B:F.38, B:A.41, B:R.63, B:R.63, B:W.69, B:V.147, B:V.147, B:G.184, B:N.294, B:Y.295, B:Y.295, B:Y.365 Water bridges: B:F.38, B:G.39, B:G.39, B:S.68, B:S.422 pi-Stacking: B:H.70 pi-Cation interactions: B:R.63 FAD.11: 27 residues within 4Å: Chain C: G.37, F.38, G.39, P.40, A.41, F.61, E.62, R.63, R.64, W.69, H.70, M.73, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, N.294, Y.295, Y.365, S.422, L.423, L.424 Ligands: NAP.12 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:H.70, C:M.73, C:Y.365 Hydrogen bonds: C:A.41, C:R.63, C:R.63, C:H.70, C:V.147, C:V.147, C:G.184, C:N.294, C:Y.295, C:Y.295, C:S.422 Water bridges: C:F.38, C:G.39, C:E.62, C:Y.365 pi-Stacking: C:H.70 pi-Cation interactions: C:R.63 FAD.16: 27 residues within 4Å: Chain D: G.37, F.38, G.39, P.40, A.41, F.61, E.62, R.63, R.64, W.69, H.70, M.73, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, N.294, Y.295, Y.365, S.422, L.423, L.424 Ligands: NAP.17 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:H.70, D:M.73, D:Y.365 Hydrogen bonds: D:F.38, D:G.39, D:A.41, D:R.63, D:W.69, D:V.147, D:V.147, D:N.294, D:Y.295, D:Y.365, D:S.422 Water bridges: D:N.42, D:R.64 pi-Stacking: D:H.70 pi-Cation interactions: D:R.63

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

NAP.2: 24 residues within 4Å: Chain A: K.79, Q.81, R.123, P.190, G.224, G.225, G.226, Q.227, S.228, E.231, I.248, P.250, N.294, Y.295, S.296, A.327, H.328, V.329, A.362, T.363, G.364 Chain D: Y.289 Ligands: FAD.1, ORN.3 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Q.81, A:Q.227 Hydrogen bonds: A:Q.81, A:R.188, A:G.225, A:S.228, A:S.228, A:E.231, A:N.294, A:N.294, A:S.296, A:S.296, A:S.296, A:V.329, A:V.329, D:Y.289 Water bridges: A:S.202, A:G.226, A:Q.227, A:Q.227, A:A.229, A:S.296, A:Y.365, A:Y.365 pi-Cation interactions: A:H.328 NAP.7: 26 residues within 4Å: Chain B: K.79, Q.81, R.123, R.188, P.190, A.223, G.224, G.225, G.226, Q.227, S.228, E.231, I.248, P.250, N.294, Y.295, S.296, H.328, V.329, A.362, T.363, G.364, Y.365 Chain C: Y.289 Ligands: FAD.6, ORN.8 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Q.227 Hydrogen bonds: B:Q.81, B:R.188, B:G.225, B:S.228, B:S.228, B:E.231, B:N.294, B:N.294, B:S.296, B:S.296, B:S.296, B:V.329, B:V.329 Water bridges: B:G.226, B:Q.227, B:Q.227, B:A.229, B:Y.365, B:Y.365 pi-Cation interactions: B:H.328 NAP.12: 24 residues within 4Å: Chain B: Y.289 Chain C: K.79, Q.81, R.123, P.190, A.223, G.224, G.225, G.226, Q.227, S.228, E.231, I.248, P.250, N.294, Y.295, S.296, H.328, V.329, A.362, T.363, G.364 Ligands: FAD.11, ORN.13 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.227 Hydrogen bonds: C:Q.81, C:G.225, C:S.228, C:S.228, C:E.231, C:N.294, C:S.296, C:S.296, C:V.329, C:V.329, B:Y.289, B:Y.289 Water bridges: C:R.188, C:S.202, C:Q.227, C:Q.227, C:G.364 pi-Cation interactions: C:H.328 NAP.17: 24 residues within 4Å: Chain A: Y.289 Chain D: K.79, Q.81, R.123, P.190, G.224, G.225, G.226, Q.227, S.228, E.231, I.248, P.250, N.294, Y.295, S.296, H.328, V.329, A.362, T.363, G.364, Y.365 Ligands: FAD.16, ORN.18 22 PLIP interactions: 20 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Q.227 Hydrogen bonds: D:K.79, D:Q.81, D:G.225, D:G.225, D:S.228, D:S.228, D:N.294, D:S.296, D:S.296, D:V.329, D:V.329, A:Y.289, A:Y.289 Water bridges: D:S.202, D:G.226, D:Q.227, D:Q.227, D:A.229, D:G.364, D:Y.365 pi-Cation interactions: D:H.328

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

ORN.3: 8 residues within 4Å: Chain A: Q.81, V.82, K.86, N.264, F.267, N.294, S.425 Ligands: NAP.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.82 Hydrogen bonds: A:N.264, A:T.293, A:S.425 Salt bridges: A:K.86 ORN.8: 9 residues within 4Å: Chain B: Q.81, V.82, K.86, N.264, F.267, T.293, N.294, S.425 Ligands: NAP.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.81, B:N.264, B:S.425 Salt bridges: B:K.86 ORN.13: 10 residues within 4Å: Chain C: Q.81, V.82, K.86, N.264, F.267, T.293, N.294, L.423, S.425 Ligands: NAP.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.82 Hydrogen bonds: C:N.264, C:N.264, C:T.293 Salt bridges: C:K.86 ORN.18: 8 residues within 4Å: Chain D: Q.81, V.82, K.86, N.264, F.267, N.294, S.425 Ligands: NAP.17 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.82 Hydrogen bonds: D:Q.81, D:N.264, D:N.264 Water bridges: D:N.264 Salt bridges: D:K.86

8 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: L.49, E.50, S.52, A.54 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.49, A:S.52 K.5: 5 residues within 4Å: Chain A: E.134, S.135, L.137, H.139, E.140 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.137 K.9: 4 residues within 4Å: Chain B: L.49, E.50, S.52, A.54 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:L.49, B:S.52 K.10: 5 residues within 4Å: Chain B: E.134, S.135, L.137, H.139, E.140 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.134, B:L.137 K.14: 4 residues within 4Å: Chain C: L.49, E.50, S.52, A.54 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.52 K.15: 4 residues within 4Å: Chain C: E.134, S.135, L.137, H.139 No protein-ligand interaction detected (PLIP) K.19: 4 residues within 4Å: Chain D: L.49, E.50, S.52, A.54 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:L.49, D:S.52 K.20: 4 residues within 4Å: Chain D: E.134, S.135, L.137, H.139 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.134, D:L.137, D:H.139, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Setser, J.W. et al., Crystallographic Evidence of Drastic Conformational Changes in the Active Site of a Flavin-Dependent N-Hydroxylase. Biochemistry (2014)

Release Date

2014-09-17

Peptides

KtzI: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

KtzI

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