SMTL ID : 4tm1.1

Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-NADP+-Br

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

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

FDA.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, M.80, Q.81, V.82, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, Y.365, S.422, L.423, L.424 Ligands: NAP.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:H.70, A:M.73, A:Y.365 Hydrogen bonds: A:F.38, A:G.39, A:A.41, A:R.63, A:R.63, A:W.69, A:Q.81, A:V.82, A:V.147, A:V.147, A:L.424, A:S.425 Water bridges: A:F.38, A:N.42, A:E.62, A:R.64, A:S.68, A:E.146, A:G.184, A:L.185, A:R.430 Salt bridges: A:H.70 pi-Stacking: A:H.70 pi-Cation interactions: A:R.63 FDA.12: 27 residues within 4Å: Chain B: G.37, F.38, G.39, P.40, A.41, F.61, E.62, R.63, R.64, W.69, H.70, M.73, M.80, Q.81, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, Y.365, S.422, L.423, L.424 Ligands: NAP.13 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:H.70, B:M.73, B:Y.365 Hydrogen bonds: B:F.38, B:G.39, B:A.41, B:R.63, B:R.63, B:W.69, B:Q.81, B:V.147, B:V.147, B:L.424, B:S.425 Water bridges: B:F.38, B:N.42, B:R.64, B:S.68, B:S.68, B:L.185, B:L.185, B:R.430 Salt bridges: B:H.70 pi-Stacking: B:H.70 pi-Cation interactions: B:R.63 FDA.21: 28 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, M.80, Q.81, V.82, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, Y.365, S.422, L.423, L.424 Ligands: NAP.22 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:H.70, C:M.73, C:Y.365 Hydrogen bonds: C:F.38, C:G.39, C:A.41, C:R.63, C:R.63, C:W.69, C:Q.81, C:V.147, C:V.147, C:L.424, C:S.425 Water bridges: C:F.38, C:N.42, C:R.64, C:S.68, C:L.185, C:L.185 Salt bridges: C:H.70 pi-Stacking: C:H.70 FDA.30: 30 residues within 4Å: Chain D: 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, M.80, Q.81, V.82, R.123, S.145, E.146, V.147, S.182, T.183, G.184, L.185, Y.365, Q.410, S.422, L.423, L.424 Ligands: NAP.31 26 PLIP interactions: 26 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:R.63, D:R.64, D:W.69, D:Q.81, D:V.147, D:V.147, D:L.424, D:S.425 Water bridges: D:N.42, D:S.68, D:H.70, D:H.70, D:G.184, D:L.185, D:L.185, D:R.430 Salt bridges: D:H.70 pi-Stacking: D:H.70 pi-Cation interactions: D:R.63

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

NAP.2: 28 residues within 4Å: Chain A: 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, R.291, N.294, Y.295, S.296, H.328, V.329, A.362, T.363, G.364, Y.365, L.423 Chain D: Y.289 Ligands: FDA.1, BR.8 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Q.227 Hydrogen bonds: A:K.79, A:Q.81, A:R.188, A:G.225, A:S.228, A:S.228, A:E.231, A:R.291, 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:G.226, A:G.226, A:Q.227, A:E.231, A:V.297, A:G.364, A:G.364, A:Y.365 pi-Stacking: A:H.328 NAP.13: 26 residues within 4Å: Chain B: 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, R.291, N.294, Y.295, S.296, H.328, V.329, A.362, T.363, G.364, Y.365, L.423 Chain C: Y.289 Ligands: FDA.12 26 PLIP interactions: 25 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Q.227 Hydrogen bonds: B:K.79, B:Q.81, B:G.225, B:Q.227, B:S.228, B:S.228, B:E.231, B:R.291, B:N.294, B:N.294, B:S.296, B:S.296, B:V.329, B:V.329, C:Y.289 Water bridges: B:R.188, B:G.226, B:Q.227, B:S.228, B:A.229, B:S.296, B:V.297, B:G.364, B:Y.365 pi-Cation interactions: B:H.328 NAP.22: 26 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, R.291, N.294, Y.295, S.296, H.328, V.329, A.362, T.363, G.364, Y.365, L.423 Ligands: FDA.21 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:Q.227 Hydrogen bonds: C:K.79, C:Q.81, C:R.188, C:G.225, C:S.228, C:S.228, C:E.231, C:R.291, C:N.294, C:N.294, C:S.296, C:S.296, C:V.329, C:V.329 Water bridges: C:S.202, C:G.226, C:Q.227, C:Q.227, C:Q.227, C:A.229, C:R.291, C:S.296, C:G.364, C:Y.365 NAP.31: 26 residues within 4Å: Chain A: Y.289 Chain D: 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, Y.365, L.423 Ligands: FDA.30, BR.40 28 PLIP interactions: 27 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Q.227 Hydrogen bonds: D:K.79, D:Q.81, D:G.225, D:S.228, D:S.228, D:E.231, D:N.294, D:N.294, D:S.296, D:S.296, D:S.296, D:V.329, D:V.329, A:Y.289 Water bridges: D:G.226, D:Q.227, D:Q.227, D:Q.227, D:A.229, D:R.291, D:R.291, D:N.294, D:A.362, D:G.364, D:Y.365, D:Y.365, D:Y.365

35 x BR: BROMIDE ION(Non-covalent)

BR.3: 4 residues within 4Å: Chain A: R.92, T.429, G.432, E.433 Ligand excluded by PLIP BR.4: 4 residues within 4Å: Chain A: R.393, Y.395, N.426, T.429 Ligand excluded by PLIP BR.5: 3 residues within 4Å: Chain A: P.76, A.77, F.235 Ligand excluded by PLIP BR.6: 5 residues within 4Å: Chain A: V.82, S.83, K.86, N.264 Chain B: H.117 Ligand excluded by PLIP BR.7: 4 residues within 4Å: Chain A: G.108, R.109, L.110, V.111 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain A: P.190, A.191 Ligands: NAP.2 Ligand excluded by PLIP BR.9: 4 residues within 4Å: Chain A: S.195, W.200, H.201, H.208 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain A: D.196, F.198, R.334 Ligand excluded by PLIP BR.11: 2 residues within 4Å: Chain A: N.322, Y.352 Ligand excluded by PLIP BR.14: 4 residues within 4Å: Chain B: G.108, R.109, L.110, V.111 Ligand excluded by PLIP BR.15: 5 residues within 4Å: Chain A: H.117 Chain B: V.82, S.83, K.86, N.264 Ligand excluded by PLIP BR.16: 4 residues within 4Å: Chain B: L.75, P.76, A.77, F.235 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain B: R.92, T.429, G.432 Ligand excluded by PLIP BR.18: 5 residues within 4Å: Chain B: S.195, W.200, H.201, R.204, H.208 Ligand excluded by PLIP BR.19: 2 residues within 4Å: Chain B: D.274 Chain C: L.326 Ligand excluded by PLIP BR.20: 5 residues within 4Å: Chain B: R.393, Y.395, N.426, T.429, E.433 Ligand excluded by PLIP BR.23: 4 residues within 4Å: Chain C: L.75, P.76, A.77, F.235 Ligand excluded by PLIP BR.24: 5 residues within 4Å: Chain C: V.82, S.83, K.86, N.264 Chain D: H.117 Ligand excluded by PLIP BR.25: 4 residues within 4Å: Chain C: R.92, T.429, G.432, E.433 Ligand excluded by PLIP BR.26: 4 residues within 4Å: Chain C: G.108, R.109, L.110, V.111 Ligand excluded by PLIP BR.27: 5 residues within 4Å: Chain C: S.195, W.200, H.201, R.204, H.208 Ligand excluded by PLIP BR.28: 5 residues within 4Å: Chain C: R.393, Y.395, N.426, T.429, E.433 Ligand excluded by PLIP BR.29: 2 residues within 4Å: Chain C: E.314, P.319 Ligand excluded by PLIP BR.32: 3 residues within 4Å: Chain A: D.274 Chain D: L.326, A.347 Ligand excluded by PLIP BR.33: 3 residues within 4Å: Chain A: L.326, A.347 Chain D: D.274 Ligand excluded by PLIP BR.34: 4 residues within 4Å: Chain D: G.108, R.109, L.110, V.111 Ligand excluded by PLIP BR.35: 5 residues within 4Å: Chain C: H.117 Chain D: V.82, S.83, K.86, N.264 Ligand excluded by PLIP BR.36: 4 residues within 4Å: Chain D: L.75, P.76, A.77, F.235 Ligand excluded by PLIP BR.37: 3 residues within 4Å: Chain D: R.92, T.429, G.432 Ligand excluded by PLIP BR.38: 4 residues within 4Å: Chain D: S.195, W.200, H.201, H.208 Ligand excluded by PLIP BR.39: 2 residues within 4Å: Chain D: Q.194, S.195 Ligand excluded by PLIP BR.40: 3 residues within 4Å: Chain D: P.190, A.191 Ligands: NAP.31 Ligand excluded by PLIP BR.41: 3 residues within 4Å: Chain D: D.196, F.198, R.334 Ligand excluded by PLIP BR.42: 5 residues within 4Å: Chain D: R.393, Y.395, N.426, T.429, E.433 Ligand excluded by PLIP BR.43: 1 residues within 4Å: Chain D: A.336 Ligand excluded by PLIP

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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