SMTL ID : 3o0r.1

Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-oligomer

Ligands

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

HEM.1: 28 residues within 4Å: Chain C: Q.30, I.31, G.34, L.35, M.37, Y.41, F.53, R.57, H.60, L.64, E.135, F.136, A.345, G.348, H.349, F.352, Y.353, M.397, I.400, R.440, E.441, G.444, F.447 Chain D: A.72, Y.73, F.74 Ligands: HEM.2, CA.5 22 PLIP interactions: 3 interactions with chain D, 19 interactions with chain C, Hydrophobic interactions: D:Y.73, C:I.31, C:L.35, C:M.37, C:L.64, C:L.64, C:F.136, C:F.352, C:F.352, C:Y.353, C:I.400, C:F.447, C:F.447 Hydrogen bonds: D:Y.73, D:Y.73, C:E.135 Water bridges: C:R.440 Salt bridges: C:R.57, C:R.57 pi-Stacking: C:H.60 Metal complexes: C:H.60, C:H.349 HEM.2: 31 residues within 4Å: Chain C: E.135, F.136, W.202, 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, A.355, Y.356 Chain D: Y.73 Ligands: HEM.1, FE.3, O.4, CA.5 19 PLIP interactions: 1 interactions with chain D, 17 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: D:Y.73, C:N.335, C:G.340 Hydrophobic interactions: C:W.203, C:V.210, C:V.210, C:E.211, C:E.280, C:F.284, C:A.322, C:A.351, C:F.352, C:A.355 Water bridges: C:H.258, C:N.335 Salt bridges: C:H.339 pi-Stacking: C:H.259 Metal complexes: C:H.347, O.4

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

FE.3: 6 residues within 4Å: Chain C: H.207, E.211, H.258, H.259 Ligands: HEM.2, O.4 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.207, C:E.211, C:H.258, C:H.259, O.4

1 x O: OXYGEN ATOM(Non-covalent)

O.4: 5 residues within 4Å: Chain C: E.211, H.258, H.259 Ligands: HEM.2, FE.3 No protein-ligand interaction detected (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.4

1 x HEC: HEME C(Covalent)

HEC.6: 24 residues within 4Å: Chain C: N.54, M.427 Chain D: N.59, N.60, C.61, C.64, H.65, F.74, 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 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:N.59, D:F.74, D:L.78, D:L.78, D:V.81, D:W.98, D:R.110, D:M.112, D:P.113, D:F.115, D:F.115, D:F.115, D:L.125, C:N.54 Water bridges: D:R.84, D:R.85, 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

Hino, T. et al., Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science (2010)

Release Date

2010-12-29

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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