SMTL ID : 5gux.2 (1 other biounit)

Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

HEM.1: 30 residues within 4Å: Chain A: F.27, 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, T.344, A.345, H.349, F.352, Y.353, M.397, R.440, E.441, G.444, F.447 Chain B: A.72, Y.73, F.74 Ligands: HEM.2, XE.9, CA.14 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:F.27, A:I.31, A:I.31, A:L.35, A:M.37, A:Y.41, A:F.53, A:T.61, A:L.64, A:F.136, A:F.352, A:F.352, A:Y.353, A:F.447 Salt bridges: A:R.57, A:R.57 Metal complexes: A:H.60, A:H.349 Hydrogen bonds: B:Y.73, B:Y.73 HEM.2: 31 residues within 4Å: Chain A: E.135, F.136, W.202, W.203, V.210, E.211, H.258, H.259, S.277, E.280, P.281, 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 B: Y.73 Ligands: HEM.1, O.4, CA.14 22 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.203, A:V.210, A:E.211, A:H.258, A:F.284, A:F.284, A:A.322, A:T.344, A:A.351, A:F.352, A:F.352, A:A.355, A:Y.356 Hydrogen bonds: A:N.335, A:N.335, A:G.340, B:Y.73 Salt bridges: A:H.329, A:H.339 pi-Stacking: A:H.259 Metal complexes: A:H.347, O.4

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

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

1 x O: OXYGEN ATOM(Non-covalent)

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

7 x XE: XENON(Non-covalent)(Non-functional Binders)

XE.5: 1 residues within 4Å: Chain A: L.178 No protein-ligand interaction detected (PLIP) XE.6: 2 residues within 4Å: Chain A: I.65, W.209 No protein-ligand interaction detected (PLIP) XE.7: 4 residues within 4Å: Chain A: I.147, L.181, F.185 Ligands: XE.8 No protein-ligand interaction detected (PLIP) XE.8: 4 residues within 4Å: Chain A: M.73, F.101, I.147 Ligands: XE.7 No protein-ligand interaction detected (PLIP) XE.9: 4 residues within 4Å: Chain A: L.64, F.136, F.352 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) XE.10: 2 residues within 4Å: Chain A: V.66, T.108 No protein-ligand interaction detected (PLIP) XE.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x 10M: decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside(Non-covalent)

10M.12: 11 residues within 4Å: Chain A: W.262, L.270, W.271, S.274, P.333, Y.336, Y.337 Chain B: N.138, Q.139, P.142 Ligands: 10M.13 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.271, A:W.271, A:W.271, A:P.333 Hydrogen bonds: A:Y.336, A:Y.337, B:P.142 10M.13: 7 residues within 4Å: Chain A: M.328, Y.337, T.338, L.343, M.417, A.419 Ligands: 10M.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.337, A:T.338, A:L.343 Hydrogen bonds: A:M.417

1 x CA: CALCIUM ION(Non-covalent)

CA.14: 6 residues within 4Å: Chain A: R.57, E.135 Chain B: G.71, Y.73 Ligands: HEM.1, HEM.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.135, A:E.135, B:G.71, B:Y.73

1 x HEC: HEME C(Covalent)

HEC.15: 22 residues within 4Å: Chain A: N.54, M.427 Chain B: 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, R.109, R.110, A.111, M.112, P.113, F.115, L.125 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:N.59, B:F.74, B:A.75, B:L.78, B:L.78, B:R.110, B:M.112, B:P.113, B:F.115, B:L.125, A:N.54 Salt bridges: B:R.84, B:R.85, B:R.109 pi-Stacking: B:H.65 Metal complexes: B:H.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terasaka, E. et al., Dynamics of nitric oxide controlled by protein complex in bacterial system. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-16

Peptides

Nitric oxide reductase subunit B: A
Nitric oxide reductase subunit C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Membrane

We predict this structure to be a membrane protein.
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Nitric oxide reductase subunit B

Nitric oxide reductase subunit C

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