SMTL ID : 5o0x.1

Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

FAD.1: 18 residues within 4Å: Chain A: Y.35, H.49, P.50, F.51, T.52, H.66, I.67, R.68, V.70, G.71, S.72, W.73, T.74, I.128, T.131, W.285 Ligands: CL.6, P6G.11 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.35, A:P.50, A:W.285 Hydrogen bonds: A:H.49, A:P.50, A:T.52, A:T.52, A:H.66, A:R.68, A:S.72, A:W.73, A:T.74, A:T.131 Salt bridges: A:H.49 pi-Stacking: A:F.51, A:W.285, A:W.285

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: R.68 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: A.69 Ligands: PEG.19 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: P.57 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 2 residues within 4Å: Ligands: FAD.1, P6G.11 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: P.250 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: S.72, K.76 Ligand excluded by PLIP

5 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.9: 2 residues within 4Å: Chain A: E.254 Ligands: P6G.10 No protein-ligand interaction detected (PLIP) P6G.10: 7 residues within 4Å: Chain A: P.111, H.114, E.117, S.118, R.279 Ligands: P6G.9, PEG.20 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.111, A:R.279 Hydrogen bonds: A:R.279 P6G.11: 4 residues within 4Å: Chain A: P.284, W.285 Ligands: FAD.1, CL.6 No protein-ligand interaction detected (PLIP) P6G.12: 9 residues within 4Å: Chain A: S.15, R.68, A.126, N.162, R.163, E.164, A.167, T.194, L.286 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.163, A:E.164, A:E.164, A:T.194 Water bridges: A:R.68, A:R.68 P6G.13: 6 residues within 4Å: Chain A: K.242, A.245, K.246, A.249, Y.274 Ligands: GOL.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.246

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 6 residues within 4Å: Chain A: T.272, K.273, Y.274, G.275 Ligands: GOL.22, GOL.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.273 PEG.15: 6 residues within 4Å: Chain A: K.138, L.141, H.142, Q.145, K.177, E.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.177, A:E.181 PEG.16: 7 residues within 4Å: Chain A: K.138, E.169, W.170, F.171, V.172, E.173, L.174 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.138, A:K.138, A:V.172, A:E.173, A:L.174 Water bridges: A:W.170 PEG.17: 4 residues within 4Å: Chain A: D.105, G.106, P.107, Y.108 No protein-ligand interaction detected (PLIP) PEG.18: 5 residues within 4Å: Chain A: K.155, D.182, N.185, F.187, D.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.155, A:N.185, A:D.188 PEG.19: 6 residues within 4Å: Chain A: K.16, A.69, G.75, Y.78 Ligands: CL.3, GOL.23 No protein-ligand interaction detected (PLIP) PEG.20: 4 residues within 4Å: Chain A: D.251, N.252, E.254 Ligands: P6G.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.251, A:D.251, A:N.252, A:N.252, A:E.254, A:E.254 Water bridges: A:K.119 PEG.21: 5 residues within 4Å: Chain A: N.29, Y.30, Q.31, D.34, P.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.34 Water bridges: A:N.29, A:Y.30 PEG.28: 4 residues within 4Å: Chain A: V.172, S.176, T.224, G.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.176, A:S.176

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 6 residues within 4Å: Chain A: A.249, P.250, D.251, Y.274, G.275 Ligands: PEG.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.251, A:G.275 Water bridges: A:V.253 GOL.23: 5 residues within 4Å: Chain A: L.13, P.14, S.15, K.16 Ligands: PEG.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.13, A:S.15, A:K.16 GOL.24: 6 residues within 4Å: Chain A: A.10, S.11, G.19, Q.21, T.64, H.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.11, A:S.11 GOL.25: 8 residues within 4Å: Chain A: V.7, V.8, N.9, I.81, Q.84, R.85, L.97, G.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.8, A:R.85 Water bridges: A:G.99 GOL.26: 4 residues within 4Å: Chain A: K.273, Y.274 Ligands: P6G.13, PEG.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.274 GOL.27: 2 residues within 4Å: Chain A: I.240, D.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magnani, F. et al., Crystal structures and atomic model of NADPH oxidase. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-06-28

Peptides

Putative ferric reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative ferric reductase

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