SMTL ID : 2c12.1 (1 other biounit)

Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 31 residues within 4Å: Chain A: L.99, L.131, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, T.240, L.400, F.401, D.402, G.403, G.404, I.406, G.407, L.408, R.411 Chain B: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Chain C: Q.314 32 PLIP interactions: 22 interactions with chain A, 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:W.169, A:T.240 Hydrogen bonds: A:L.131, A:H.133, A:S.134, A:S.134, A:S.134, A:T.139, A:A.140, A:N.141, A:S.171, A:D.402, A:G.403, A:G.404, A:G.407, B:K.375, B:M.379, C:Q.314 Water bridges: A:Q.144, A:L.400, A:D.402, A:I.406, A:I.406, A:L.408, B:R.304, B:R.304, B:R.304, B:R.304, C:Q.314 pi-Stacking: A:F.401, B:H.313 Salt bridges: B:R.304 FAD.3: 32 residues within 4Å: Chain A: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Chain B: L.99, L.131, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, T.240, L.400, F.401, D.402, G.403, G.404, I.406, G.407, L.408, R.411 Chain D: Q.314 Ligands: SPM.4 31 PLIP interactions: 20 interactions with chain B, 9 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:W.169, B:W.169, B:T.240 Hydrogen bonds: B:L.131, B:H.133, B:S.134, B:S.134, B:S.134, B:T.139, B:A.140, B:N.141, B:S.171, B:L.400, B:F.401, B:D.402, B:G.403, B:G.404, A:K.375, A:M.379, D:Q.314 Water bridges: B:I.406, B:G.407, B:L.408, A:R.304, A:R.304, A:R.304, A:R.304, D:Q.314 Salt bridges: A:R.304 pi-Stacking: A:H.313, A:H.313 FAD.9: 32 residues within 4Å: Chain A: Q.314 Chain C: L.99, L.131, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, T.240, L.400, F.401, D.402, G.403, G.404, I.406, G.407, L.408, R.411 Chain D: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Ligands: SPM.10 30 PLIP interactions: 7 interactions with chain D, 21 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:K.375, D:M.379, C:L.131, C:H.133, C:S.134, C:S.134, C:S.134, C:T.139, C:A.140, C:N.141, C:S.171, C:F.401, C:D.402, C:G.403, C:G.404, A:Q.314 Water bridges: D:R.304, D:R.304, D:K.380, C:Q.144, C:L.400, C:I.406, C:G.407, C:L.408, A:Q.314 Salt bridges: D:R.304 pi-Stacking: D:H.313, C:F.401 Hydrophobic interactions: C:W.169, C:F.401 FAD.15: 32 residues within 4Å: Chain B: Q.314 Chain C: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Chain D: L.99, L.131, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, T.240, L.400, F.401, D.402, G.403, G.404, I.406, G.407, L.408, R.411 Ligands: SPM.16 28 PLIP interactions: 19 interactions with chain D, 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:W.169, D:T.240 Hydrogen bonds: D:L.131, D:H.133, D:S.134, D:S.134, D:S.134, D:T.139, D:A.140, D:N.141, D:S.171, D:D.402, D:G.403, D:G.404, C:K.375, C:M.379, B:Q.314 Water bridges: D:L.400, D:I.406, D:L.408, D:L.408, C:R.304, C:R.304, C:R.304, C:R.304 pi-Stacking: D:F.401, C:H.313 Salt bridges: C:R.304

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.71, S.72, E.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.342, A:E.342 GOL.5: 8 residues within 4Å: Chain B: I.360, Y.361, D.364, V.365, R.410 Chain D: D.322, I.325 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.364, B:R.410 Water bridges: B:N.405 GOL.6: 4 residues within 4Å: Chain A: K.375 Chain B: D.364, E.368 Ligands: GOL.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.375, A:K.375, B:E.368 GOL.8: 7 residues within 4Å: Chain A: I.360, Y.361, D.364, R.410 Chain C: D.322, I.325, R.326 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.364, A:R.410, C:D.322, C:D.322 Water bridges: A:N.405 GOL.11: 6 residues within 4Å: Chain A: D.322, I.325, R.326 Chain C: I.360, D.364, R.410 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.364, C:R.410, A:R.326 Water bridges: C:D.364, C:E.368, C:E.368, C:N.405 GOL.12: 7 residues within 4Å: Chain A: V.2 Chain C: Q.10, S.72, L.73, V.74, H.75, E.342 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.10, C:S.72, C:S.72, C:L.73, C:V.74, C:H.75, C:E.342, A:V.2, A:V.2 GOL.13: 7 residues within 4Å: Chain C: I.371, D.372, K.375 Chain D: D.364, V.367, E.368 Ligands: GOL.14 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.364, C:D.372, C:K.375 GOL.14: 5 residues within 4Å: Chain C: E.368 Chain D: I.371, D.372, K.375 Ligands: GOL.13 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:E.368, D:K.375 Hydrogen bonds: D:D.372 GOL.17: 4 residues within 4Å: Chain D: T.26, S.29, V.86, R.390 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.29, D:R.390 Water bridges: D:T.26, D:T.26, D:S.29, D:A.30 GOL.18: 4 residues within 4Å: Chain B: D.322 Chain D: I.360, D.364, R.410 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.364, D:R.410, B:D.322 Water bridges: D:E.368, D:E.368, D:N.405 GOL.19: 7 residues within 4Å: Chain D: A.13, H.16, A.17, L.57, A.60, E.71, I.79 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.17, D:E.71

3 x SPM: SPERMINE(Non-covalent)

SPM.4: 12 residues within 4Å: Chain B: Q.61, M.70, E.76, V.95, A.98, S.276, L.279, V.280, M.283, F.401, D.402 Ligands: FAD.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.95, B:A.98, B:L.279, B:V.280, B:F.401, B:D.402 Hydrogen bonds: B:V.95, B:D.402, B:D.402, B:D.402 SPM.10: 15 residues within 4Å: Chain C: Q.61, M.70, L.73, E.76, V.95, A.98, L.99, M.102, F.273, S.276, L.279, V.280, F.401, D.402 Ligands: FAD.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.95, C:A.98, C:L.279, C:F.401, C:D.402 Hydrogen bonds: C:D.402 SPM.16: 12 residues within 4Å: Chain D: Q.61, M.70, E.76, V.95, A.98, M.102, S.276, L.279, V.280, F.401, D.402 Ligands: FAD.15 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.95, D:A.98, D:L.279, D:F.401 Hydrogen bonds: D:D.402

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.7: 5 residues within 4Å: Chain B: L.106, L.341, E.342, D.343, K.351 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagpal, A. et al., Crystal Structures of Nitroalkane Oxidase: Insights Into the Reaction Mechanism from a Covalent Complex of the Flavoenzyme Trapped During Turnover. Biochemistry (2006)

Release Date

2006-02-01

Peptides

NITROALKANE OXIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NITROALKANE OXIDASE

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