SMTL ID : 2vr0.1

Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-4-2-mer

Ligands

28 x HEC: HEME C(Non-covalent)(Covalent)

HEC.1: 19 residues within 4Å: Chain A: Y.115, R.116, A.118, F.128, I.131, R.133, L.143, C.147, C.150, K.151, C.232, H.233, V.234, Y.236, F.238, F.251, H.298, N.429 Ligands: HEC.3 15 PLIP interactions: 14 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:A.118, A:F.128, A:I.131, A:L.143, A:V.234, A:Y.236, A:Y.236, A:F.238, A:F.251 Hydrogen bonds: A:R.116, A:N.429 Salt bridges: A:R.133, A:H.298 pi-Stacking: A:H.298 Metal complexes: H2O.1 HEC.2: 22 residues within 4Å: Chain A: Y.39, F.57, Q.60, Y.61, Y.64, G.186, C.187, C.190, H.191, M.196, L.198, R.221, R.225, M.321, I.332, S.333, H.335, W.337 Chain C: E.126, V.127, A.128 Ligands: HEC.3 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:F.57, A:Q.60, A:Q.60, A:Y.61, A:Y.64, A:L.198, A:L.198, A:W.337, A:W.337 Hydrogen bonds: A:Q.60, A:R.225, A:S.333 Salt bridges: A:R.221 Metal complexes: A:H.191, A:H.335 HEC.3: 26 residues within 4Å: Chain A: G.78, S.79, A.118, R.119, G.120, H.121, Y.123, A.124, D.127, C.150, K.151, I.185, T.189, V.228, C.229, C.232, H.233, H.320, M.321, W.337, T.338, K.342 Ligands: HEC.1, HEC.2, HEC.4, CA.7 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:K.151, A:I.185, A:I.185, A:H.320 Hydrogen bonds: A:Y.123, A:W.337 Salt bridges: A:K.342 Metal complexes: A:H.121, A:H.233 HEC.4: 26 residues within 4Å: Chain A: T.74, K.77, G.78, E.117, A.118, C.229, H.233, E.300, Y.301, W.304, H.309, V.314, T.315, C.316, C.319, H.320, S.339, P.340, M.341, Q.369, N.429, S.430, F.433, H.434 Ligands: HEC.3, CA.7 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:H.233, A:E.300, A:E.300, A:W.304, A:W.304, A:H.309, A:V.314, A:P.340, A:N.429, A:F.433, A:F.433 Hydrogen bonds: A:T.74, A:G.78, A:S.339, A:S.339, A:Q.369, A:N.429 Salt bridges: A:K.77 Metal complexes: A:H.320, A:H.434 HEC.5: 18 residues within 4Å: Chain A: H.309, V.314, C.319, P.340, M.346, A.348, C.349, C.352, H.353, R.364, V.365, F.433, P.436 Chain B: H.353, K.356 Chain C: D.138, R.141 Ligands: HEC.12 11 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: A:V.314, A:V.314, A:P.340, A:R.364, A:V.365, A:F.433 Metal complexes: A:H.309, A:H.353 Salt bridges: C:R.141, B:H.353, B:K.356 HEC.8: 18 residues within 4Å: Chain B: Y.115, R.116, A.118, D.127, F.128, I.131, R.133, C.147, C.150, K.151, C.232, H.233, V.234, Y.236, F.238, H.298, N.429 Ligands: HEC.10 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:A.118, B:F.128, B:F.128, B:I.131, B:V.234, B:Y.236, B:Y.236, B:F.238 Hydrogen bonds: B:R.116, B:N.429 Water bridges: B:Y.115, B:A.118 Salt bridges: B:R.133, B:H.298 pi-Cation interactions: B:H.298 Metal complexes: H2O.3 HEC.9: 23 residues within 4Å: Chain B: Y.39, F.57, Q.60, Y.61, Y.64, I.185, G.186, C.187, C.190, H.191, M.196, L.198, R.221, R.225, V.228, M.321, Y.323, I.332, S.333, H.335, W.337 Chain C: A.157 Ligands: HEC.10 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.57, B:F.57, B:Q.60, B:Y.61, B:Y.64, B:L.198, B:V.228, B:W.337, C:A.157 Hydrogen bonds: B:Q.60, B:Y.323, B:S.333 Salt bridges: B:R.221, B:R.225 pi-Stacking: B:W.337 Metal complexes: B:H.191, B:H.335 HEC.10: 25 residues within 4Å: Chain B: G.78, S.79, A.118, R.119, G.120, H.121, Y.123, A.124, D.127, C.150, K.151, I.185, T.189, V.228, C.229, C.232, H.233, H.320, M.321, W.337, T.338 Ligands: HEC.8, HEC.9, HEC.11, CA.14 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:A.118, B:A.124, B:K.151, B:I.185, B:I.185, B:T.189, B:H.320 Hydrogen bonds: B:R.119, B:G.120, B:D.127, B:W.337 Water bridges: B:G.78, B:S.339 Salt bridges: B:K.342 Metal complexes: B:H.121, B:H.233 HEC.11: 27 residues within 4Å: Chain B: T.74, K.77, G.78, E.117, A.118, C.229, H.233, E.300, Y.301, W.304, H.309, V.314, T.315, C.316, C.319, H.320, S.339, P.340, M.341, Q.369, N.429, S.430, F.433, H.434 Ligands: HEC.10, HEC.12, CA.14 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:K.77, B:H.233, B:E.300, B:W.304, B:N.429, B:F.433 Hydrogen bonds: B:T.74, B:G.78, B:S.339, B:Q.369, B:Q.369 Water bridges: B:S.339 Salt bridges: B:K.77 Metal complexes: B:H.320, B:H.434 HEC.12: 22 residues within 4Å: Chain A: T.308, H.353, K.356 Chain B: H.309, V.314, D.318, C.319, P.340, A.348, C.349, C.352, H.353, R.364, V.365, F.433, P.436 Chain C: R.141, M.148, K.149, P.150 Ligands: HEC.5, HEC.11 10 PLIP interactions: 1 interactions with chain C, 7 interactions with chain B, 2 interactions with chain A, Hydrogen bonds: C:R.141 Hydrophobic interactions: B:V.314, B:P.340, B:R.364, B:V.365, B:F.433 Metal complexes: B:H.309, B:H.353 Salt bridges: A:H.353, A:K.356 HEC.15: 20 residues within 4Å: Chain C: T.37, F.42, C.43, C.46, I.48, M.49, C.66, N.67, H.70, D.89, V.90, M.92, N.93, P.98, L.103, A.104, G.105, T.108 Ligands: HEC.16, HQO.19 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:F.42, C:I.48, C:H.70, C:D.89 Hydrogen bonds: C:G.105, C:T.108 Metal complexes: C:D.89 HEC.16: 23 residues within 4Å: Chain C: R.40, C.43, M.49, V.52, G.53, H.56, H.61, I.64, S.65, C.66, C.69, H.70, I.102, L.103, A.104, K.109, V.112, T.137, V.143, Q.144, H.145 Ligands: HEC.15, HEC.17 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:R.40, C:V.52, C:V.52, C:H.56, C:H.61, C:I.64, C:I.102, C:V.112, C:T.137, C:V.143, C:Q.144 Hydrogen bonds: C:Q.144 Water bridges: C:T.137 Salt bridges: C:K.109 Metal complexes: C:H.70, C:H.145 HEC.17: 23 residues within 4Å: Chain C: G.60, H.61, I.64, D.68, C.69, V.112, N.115, C.116, C.119, H.120, C.136, T.137, H.140, V.143 Chain D: K.329 Chain F: C.119, H.120, M.122, T.123 Ligands: HEC.16, HEC.18, HEC.36, HEC.37 15 PLIP interactions: 9 interactions with chain C, 4 interactions with chain F, 2 interactions with chain D, Hydrophobic interactions: C:I.64, C:V.112, C:N.115, C:T.137, C:H.140, C:V.143, D:K.329 Salt bridges: C:H.61, F:H.120, D:K.329 Metal complexes: C:H.61, C:H.120 Hydrogen bonds: F:M.122, F:T.123, F:T.123 HEC.18: 21 residues within 4Å: Chain A: D.318, Y.323, T.324, R.325, K.331, R.347, Q.351 Chain C: C.116, H.120, T.123, N.124, S.129, K.133, C.136, C.139, H.140 Chain D: R.325, K.329 Ligands: HEC.17, HEC.36, HEC.37 18 PLIP interactions: 12 interactions with chain A, 4 interactions with chain C, 2 interactions with chain D, Hydrophobic interactions: A:Y.323, A:Y.323, A:R.325, A:Q.351, C:H.120, C:T.123, C:K.133 Hydrogen bonds: A:Y.323, A:R.325, A:Q.351, A:Q.351 Salt bridges: A:R.325, A:R.325, A:R.347, D:R.325, D:K.329 pi-Stacking: A:Y.323 Metal complexes: C:H.140 HEC.20: 17 residues within 4Å: Chain D: Y.115, R.116, A.118, D.127, F.128, I.131, R.133, L.143, C.147, C.150, K.151, C.232, H.233, Y.236, H.298, N.429 Ligands: HEC.22 15 PLIP interactions: 14 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: D:A.118, D:F.128, D:F.128, D:I.131, D:L.143, D:Y.236, D:Y.236, D:Y.236 Hydrogen bonds: D:R.116, D:N.429 Water bridges: D:A.118, D:A.118 Salt bridges: D:R.133, D:H.298 Metal complexes: H2O.4 HEC.21: 23 residues within 4Å: Chain D: Y.39, F.53, F.57, Q.60, Y.61, Y.64, G.186, C.187, C.190, H.191, M.196, L.198, R.221, R.225, M.321, Y.323, I.332, S.333, H.335, W.337 Chain F: E.126, V.127 Ligands: HEC.22 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:Y.39, D:F.53, D:F.57, D:F.57, D:Y.61, D:Y.64, D:L.198, D:W.337, D:W.337 Hydrogen bonds: D:Q.60, D:Y.323, D:S.333 Salt bridges: D:R.221, D:R.225 Metal complexes: D:H.191, D:H.335 HEC.22: 25 residues within 4Å: Chain D: G.78, S.79, A.118, R.119, G.120, H.121, Y.123, A.124, D.127, C.150, K.151, I.185, T.189, V.228, C.229, C.232, H.233, H.320, M.321, W.337, T.338 Ligands: HEC.20, HEC.21, HEC.23, CA.26 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:K.151, D:I.185, D:I.185, D:H.320 Hydrogen bonds: D:Y.123, D:W.337 Salt bridges: D:K.342 Metal complexes: D:H.121, D:H.233 HEC.23: 27 residues within 4Å: Chain D: T.74, K.77, G.78, E.117, A.118, C.229, H.233, E.300, Y.301, W.304, H.309, V.314, T.315, C.316, C.319, H.320, S.339, P.340, M.341, Q.369, N.429, S.430, F.433, H.434 Ligands: HEC.22, HEC.24, CA.26 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:H.233, D:E.300, D:E.300, D:W.304, D:H.309, D:N.429, D:F.433 Hydrogen bonds: D:T.74, D:G.78, D:S.339, D:Q.369 Salt bridges: D:K.77 Metal complexes: D:H.320, D:H.434 HEC.24: 17 residues within 4Å: Chain D: H.309, V.314, C.319, M.346, A.348, C.349, C.352, H.353, R.364, V.365, F.433, P.436 Chain E: H.353, K.356 Chain F: R.141 Ligands: HEC.23, HEC.31 9 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 6 interactions with chain D, Salt bridges: E:H.353, E:K.356, F:R.141 Hydrophobic interactions: D:V.314, D:R.364, D:V.365, D:F.433 Metal complexes: D:H.309, D:H.353 HEC.27: 18 residues within 4Å: Chain E: Y.115, R.116, A.118, D.127, F.128, I.131, R.133, C.147, C.150, K.151, C.232, H.233, V.234, Y.236, F.238, H.298, N.429 Ligands: HEC.29 13 PLIP interactions: 12 interactions with chain E, 1 Ligand-Water interactions, Hydrophobic interactions: E:A.118, E:F.128, E:I.131, E:V.234, E:Y.236, E:Y.236, E:F.238 Hydrogen bonds: E:R.116, E:N.429 Salt bridges: E:R.133, E:H.298 pi-Stacking: E:H.298 Metal complexes: H2O.4 HEC.28: 23 residues within 4Å: Chain E: Y.39, F.57, Q.60, Y.61, Y.64, I.185, G.186, C.187, C.190, H.191, M.196, L.198, R.221, R.225, V.228, M.321, Y.323, I.332, S.333, H.335, W.337 Chain F: A.157 Ligands: HEC.29 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: E:F.57, E:F.57, E:Y.61, E:Y.64, E:V.228, E:W.337, F:A.157 Hydrogen bonds: E:Q.60, E:S.333 Salt bridges: E:R.221, E:R.225 Metal complexes: E:H.191, E:H.335 HEC.29: 25 residues within 4Å: Chain E: G.78, S.79, A.118, R.119, G.120, H.121, Y.123, A.124, D.127, C.150, K.151, I.185, T.189, V.228, C.229, C.232, H.233, H.320, M.321, W.337, T.338 Ligands: HEC.27, HEC.28, HEC.30, CA.33 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:A.124, E:K.151, E:I.185, E:I.185, E:I.185, E:T.189, E:H.320 Hydrogen bonds: E:A.118, E:R.119 Salt bridges: E:K.342 Metal complexes: E:H.121, E:H.233 HEC.30: 27 residues within 4Å: Chain E: T.74, K.77, G.78, E.117, A.118, C.229, H.233, E.300, Y.301, W.304, H.309, V.314, T.315, C.316, C.319, H.320, S.339, P.340, M.341, Q.369, N.429, S.430, F.433, H.434 Ligands: HEC.29, HEC.31, CA.33 18 PLIP interactions: 18 interactions with chain E, Hydrophobic interactions: E:H.233, E:E.300, E:W.304, E:W.304, E:H.309, E:N.429, E:F.433 Hydrogen bonds: E:T.74, E:K.77, E:G.78, E:S.339, E:S.339, E:Q.369 Water bridges: E:Y.76, E:Y.76 Salt bridges: E:K.77 Metal complexes: E:H.320, E:H.434 HEC.31: 23 residues within 4Å: Chain D: H.353, K.356 Chain E: T.308, H.309, V.314, D.318, C.319, P.340, M.346, A.348, C.349, C.352, H.353, R.364, V.365, F.433, P.436 Chain F: M.148, K.149, P.150, I.151 Ligands: HEC.24, HEC.30 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain D, Hydrophobic interactions: E:V.314, E:V.314, E:P.340, E:R.364, E:V.365, E:F.433 Metal complexes: E:H.309, E:H.353 Salt bridges: D:H.353, D:K.356 HEC.34: 17 residues within 4Å: Chain F: T.37, C.43, C.46, I.48, M.49, C.66, N.67, H.70, D.89, M.92, N.93, L.103, A.104, G.105, T.108 Ligands: HEC.35, HQO.38 5 PLIP interactions: 5 interactions with chain F, Hydrophobic interactions: F:H.70, F:D.89, F:M.92 Hydrogen bonds: F:G.105, F:T.108 HEC.35: 22 residues within 4Å: Chain F: R.40, C.43, M.49, V.52, G.53, H.56, H.61, I.64, S.65, C.66, C.69, H.70, I.102, A.104, K.109, V.112, T.137, V.143, Q.144, H.145 Ligands: HEC.34, HEC.36 16 PLIP interactions: 16 interactions with chain F, Hydrophobic interactions: F:R.40, F:V.52, F:H.56, F:H.61, F:I.64, F:I.102, F:A.104, F:V.112, F:T.137, F:V.143, F:Q.144, F:Q.144 Hydrogen bonds: F:Q.144 Salt bridges: F:K.109 Metal complexes: F:H.70, F:H.145 HEC.36: 23 residues within 4Å: Chain A: K.329 Chain C: C.119, H.120, T.121, M.122, T.123 Chain F: G.60, H.61, I.64, D.68, C.69, V.112, N.115, C.116, C.119, H.120, C.136, H.140, V.143 Ligands: HEC.17, HEC.18, HEC.35, HEC.37 14 PLIP interactions: 4 interactions with chain C, 7 interactions with chain F, 2 interactions with chain A, 1 interactions with chain D, Hydrogen bonds: C:M.122, C:T.123, C:T.123 Salt bridges: C:H.120, F:H.61, A:K.329 Hydrophobic interactions: F:I.64, F:V.112, F:N.115, F:V.143, A:K.329 Metal complexes: F:H.61, F:H.120 Water bridges: D:S.354 HEC.37: 20 residues within 4Å: Chain A: R.325, K.329 Chain D: Y.323, T.324, R.325, K.331, R.347, Q.351 Chain F: C.116, H.120, T.123, N.124, S.129, K.133, C.136, C.139, H.140 Ligands: HEC.17, HEC.18, HEC.36 16 PLIP interactions: 11 interactions with chain D, 3 interactions with chain F, 2 interactions with chain A, Hydrophobic interactions: D:Y.323, D:R.325, D:Q.351, F:T.123, F:K.133 Hydrogen bonds: D:Y.323, D:T.324, D:R.325, D:Q.351 Salt bridges: D:R.325, D:R.325, D:R.347, A:R.325, A:K.329 pi-Stacking: D:Y.323 Metal complexes: F:H.140

8 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: E.235, Y.236, D.283, K.295, A.296, Q.297 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.235, A:E.235, A:Y.236, A:K.295, H2O.1 CA.7: 5 residues within 4Å: Chain A: G.78, E.117, A.118 Ligands: HEC.3, HEC.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.78, A:E.117, A:A.118 CA.13: 4 residues within 4Å: Chain B: E.235, Y.236, K.295, Q.297 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.235, B:E.235, B:Y.236, B:K.295, H2O.2 CA.14: 5 residues within 4Å: Chain B: G.78, E.117, A.118 Ligands: HEC.10, HEC.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.78, B:E.117, B:A.118 CA.25: 5 residues within 4Å: Chain D: E.235, Y.236, D.283, K.295, Q.297 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.235, D:E.235, D:Y.236, D:K.295 CA.26: 5 residues within 4Å: Chain D: G.78, E.117, A.118 Ligands: HEC.22, HEC.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.78, D:E.117, D:A.118 CA.32: 5 residues within 4Å: Chain E: E.235, Y.236, D.283, K.295, Q.297 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.235, E:E.235, E:Y.236, E:K.295 CA.33: 5 residues within 4Å: Chain E: G.78, E.117, A.118 Ligands: HEC.29, HEC.30 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:G.78, E:E.117, E:A.118

2 x HQO: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE(Non-covalent)

HQO.19: 11 residues within 4Å: Chain C: M.34, T.37, F.42, N.67, H.70, F.81, K.82, A.85, G.86, D.89 Ligands: HEC.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.81, C:A.85 Hydrogen bonds: C:N.67, C:D.89 HQO.38: 10 residues within 4Å: Chain F: T.37, F.42, N.67, H.70, F.81, K.82, A.85, G.86, D.89 Ligands: HEC.34 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.81, F:A.85 Hydrogen bonds: F:N.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodrigues, M.L. et al., Quinol Oxidation by C-Type Cytochromes: Structural Characterization of the Menaquinol Binding Site of Nrfha. J.Mol.Biol. (2008)

Release Date

2008-06-03

Peptides

CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA: ABDE
NAPC/NIRT CYTOCHROME C FAMILY PROTEIN: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

E
E

C
C

F
F

Membrane

We predict this structure to be a membrane protein.
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CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA

NAPC/NIRT CYTOCHROME C FAMILY PROTEIN

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