SMTL ID : 3wfb.1

Reduced cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 27 residues within 4Å: Chain C: Q.30, I.31, G.34, L.35, M.37, Y.41, F.53, R.57, H.60, T.61, L.64, E.135, F.136, A.345, H.349, F.352, Y.353, M.397, R.440, E.441, G.444, F.447 Chain D: A.72, Y.73, F.74 Ligands: HEM.2, CA.5 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:I.31, C:M.37, C:Y.41, C:L.64, C:F.136, C:F.352, C:F.352, C:F.447, C:F.447 Salt bridges: C:R.57, C:R.57 pi-Cation interactions: C:H.349 Metal complexes: C:H.60, C:H.349 Hydrogen bonds: D:Y.73 HEM.2: 27 residues within 4Å: Chain C: E.135, F.136, W.203, V.210, E.211, H.258, H.259, S.277, E.280, F.284, A.322, G.326, F.327, H.329, T.330, N.335, H.339, G.340, T.344, H.347, G.348, A.351, F.352, Y.356 Ligands: HEM.1, CL.4, CA.5 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:W.203, C:V.210, C:H.258, C:E.280, C:F.284, C:F.284, C:A.322, C:A.351, C:F.352, C:F.352, C:Y.356 Hydrogen bonds: C:N.335, C:G.340 Water bridges: C:H.258, C:W.262 Salt bridges: C:H.339 pi-Stacking: C:H.347 Metal complexes: C:H.347

1 x FE: FE (III) ION(Non-covalent)

FE.3: 5 residues within 4Å: Chain C: H.207, E.211, H.258, H.259 Ligands: CL.4 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.207, C:E.211, C:E.211, C:H.258, C:H.259

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

CL.4: 5 residues within 4Å: Chain C: V.210, E.211, H.259 Ligands: HEM.2, FE.3 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain C: R.57, E.135 Chain D: G.71, Y.73 Ligands: HEM.1, HEM.2 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:G.71, D:Y.73, C:E.135, C:E.135, H2O.5

1 x HEC: HEME C(Covalent)

HEC.6: 23 residues within 4Å: Chain C: P.52, F.53, N.54 Chain D: N.59, C.61, C.64, H.65, A.75, P.76, L.78, V.81, R.84, R.85, W.98, M.99, L.104, R.109, R.110, A.111, M.112, P.113, F.115, L.125 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C, Hydrophobic interactions: D:N.59, D:L.78, D:V.81, D:W.98, D:R.110, D:M.112, D:F.115, D:F.115, D:L.125, C:P.52, C:N.54 Water bridges: D:R.85, D:R.85 Salt bridges: D:R.84, D:R.85, D:R.109 Metal complexes: D:H.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, N. et al., Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes. Proteins (2014)

Release Date

2014-05-28

Peptides

antibody fab fragment light chain: A
antibody fab fragment heavy chain: B
Nitric oxide reductase subunit B: C
Nitric oxide reductase subunit C: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
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antibody fab fragment light chain

antibody fab fragment heavy chain

Nitric oxide reductase subunit B

Nitric oxide reductase subunit C

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