SMTL ID : 5guw.3 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: R.71, C.72, C.75, H.76, T.84, K.86, L.88, R.96, Y.100, L.104, I.105, T.109, L.111, G.112, M.113, P.114, W.116, M.130, I.134 Chain B: A.32, E.33, Q.36 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:R.71, A:L.88, A:L.88, A:L.104, A:I.105, A:M.113, A:P.114, A:M.130, A:I.134, B:Q.36 Hydrogen bonds: A:K.86, A:Y.100, A:T.109 Salt bridges: A:R.96 Metal complexes: A:H.76 HEC.4: 21 residues within 4Å: Chain A: E.33 Chain B: R.71, C.72, C.75, H.76, T.84, K.86, L.88, I.92, R.96, Y.100, L.101, L.104, I.105, T.109, L.111, G.112, M.113, P.114, W.116, I.134 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:R.71, B:L.88, B:L.88, B:L.101, B:L.104, B:I.105, B:I.105, B:M.113, B:P.114, B:I.134 Salt bridges: B:R.96 Metal complexes: B:H.76

2 x DHE: HEME D(Non-covalent)

DHE.2: 22 residues within 4Å: Chain A: R.181, H.207, I.208, R.210, R.223, R.250, S.251, Y.270, A.308, A.309, I.310, H.352, R.397, L.449, F.450, F.466, Q.508, W.523, G.556, F.558 Chain B: Y.35, A.38 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:I.208, A:R.250, A:R.250, A:A.308, A:L.449, A:F.450, A:F.450, A:W.523, A:W.523, A:F.558, B:Y.35, B:Y.35 Hydrogen bonds: A:S.251, A:I.310, A:Q.508 Salt bridges: A:R.181, A:H.207, A:H.207, A:R.210, A:R.223, A:R.250, A:R.397, A:K.452 Metal complexes: A:H.207 DHE.5: 22 residues within 4Å: Chain A: Y.35, Q.36, A.38 Chain B: R.181, H.207, I.208, R.210, R.223, R.250, S.251, Y.270, A.308, A.309, I.310, H.352, R.397, L.449, F.450, Q.508, W.523, G.556, F.558 28 PLIP interactions: 25 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:I.208, B:R.250, B:R.250, B:A.308, B:A.309, B:L.449, B:F.450, B:F.450, B:W.523, B:F.558, A:Y.35, A:Y.35, A:Q.36 Hydrogen bonds: B:S.251, B:Y.270, B:I.310, B:Q.508 Salt bridges: B:R.181, B:H.207, B:H.207, B:R.210, B:R.210, B:R.223, B:R.223, B:R.250, B:R.397, B:K.452 Metal complexes: B:H.207

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

CL.3: 4 residues within 4Å: Chain A: G.293, M.294 Chain B: V.289, S.290 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: S.290 Chain B: G.293, M.294 Ligand excluded by 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

Nitrite reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

Nitrite reductase