SMTL ID : 5guw.2 (2 other biounits)

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x HEC: HEME C(Covalent)

HEC.1: 25 residues within 4Å: Chain A: N.59, C.61, C.64, H.65, A.75, P.76, L.78, V.81, R.84, R.85, L.95, W.98, M.99, L.104, R.109, R.110, A.111, M.112, P.113, F.115, L.125 Chain B: P.52, F.53, N.54, M.427 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:N.59, A:L.78, A:L.78, A:V.81, A:L.95, A:R.110, A:M.112, A:F.115, A:F.115, A:L.125, B:P.52, B:F.53 Salt bridges: A:R.84, A:R.85, A:R.109 Metal complexes: A:H.65

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: G.71, Y.73 Chain B: R.57, E.135 Ligands: HEM.4, HEM.5 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:G.71, A:Y.73, B:E.135, B:E.135

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

10M.3: 12 residues within 4Å: Chain A: N.138, Q.139, P.142 Chain B: W.262, L.270, W.271, S.274, L.331, P.333, Y.336, Y.337 Ligands: 10M.8 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.270, B:W.271, B:L.331 Hydrogen bonds: B:Y.337, A:Q.139 Water bridges: B:Y.336, A:P.142 10M.8: 6 residues within 4Å: Chain B: M.328, Y.337, M.417, P.418, A.419 Ligands: 10M.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.417, B:A.419

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

HEM.4: 27 residues within 4Å: Chain A: G.71, A.72, Y.73, F.74 Chain B: Q.30, I.31, G.34, L.35, M.37, G.38, Y.41, F.53, R.57, H.60, T.61, L.64, E.135, H.349, F.352, Y.353, M.397, I.400, E.441, G.444, F.447 Ligands: CA.2, HEM.5 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:I.31, B:M.37, B:F.53, B:T.61, B:L.64, B:L.64, B:F.352, B:F.352, B:I.400, B:F.447, B:F.447 Hydrogen bonds: B:Y.41, B:E.135, A:Y.73 Salt bridges: B:R.57, B:R.57 pi-Stacking: B:H.60 Metal complexes: B:H.60, B:H.349 HEM.5: 31 residues within 4Å: Chain A: Y.73 Chain B: E.135, F.136, W.203, V.210, E.211, H.258, H.259, S.277, E.280, P.281, F.284, A.322, G.323, 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 Ligands: CA.2, HEM.4, O.7 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.203, B:V.210, B:V.210, B:E.211, B:E.280, B:F.284, B:A.322, B:A.351, B:F.352, B:F.352, B:A.355, B:Y.356 Hydrogen bonds: B:N.335, B:N.335, B:G.340, B:T.344 Salt bridges: B:H.339 pi-Stacking: B:H.259, B:H.329 Metal complexes: B:H.347, O.7

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

FE.6: 5 residues within 4Å: Chain B: H.207, E.211, H.258, H.259 Ligands: O.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.207, B:E.211, B:H.258, B:H.259, O.7

1 x O: OXYGEN ATOM(Non-covalent)

O.7: 5 residues within 4Å: Chain B: E.211, H.258, H.259 Ligands: HEM.5, FE.6 No protein-ligand interaction detected (PLIP)

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 C: A
Nitric oxide reductase subunit B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Membrane

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

Nitric oxide reductase subunit B

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