- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CA: CALCIUM ION(Non-covalent)
- 16 x Y1: YTTRIUM ION(Non-covalent)
Y1.2: 1 residues within 4Å:- Chain A: E.30
Ligand excluded by PLIPY1.3: 3 residues within 4Å:- Chain A: P.77
- Ligands: HEC.12, HEC.13
Ligand excluded by PLIPY1.4: 7 residues within 4Å:- Chain A: E.386
- Chain C: E.386
- Ligands: SO4.8, HEC.14, Y1.32, SO4.36, HEC.42
Ligand excluded by PLIPY1.5: 4 residues within 4Å:- Chain A: Q.282
- Chain D: D.301, E.312
- Ligands: SO4.7
Ligand excluded by PLIPY1.16: 1 residues within 4Å:- Chain B: E.30
Ligand excluded by PLIPY1.17: 3 residues within 4Å:- Chain B: P.77
- Ligands: HEC.26, HEC.27
Ligand excluded by PLIPY1.18: 7 residues within 4Å:- Chain B: E.386
- Chain D: E.386
- Ligands: SO4.22, HEC.28, Y1.46, SO4.50, HEC.56
Ligand excluded by PLIPY1.19: 4 residues within 4Å:- Chain B: Q.282
- Chain C: D.301, E.312
- Ligands: SO4.21
Ligand excluded by PLIPY1.30: 1 residues within 4Å:- Chain C: E.30
Ligand excluded by PLIPY1.31: 3 residues within 4Å:- Chain C: P.77
- Ligands: HEC.40, HEC.41
Ligand excluded by PLIPY1.32: 7 residues within 4Å:- Chain A: E.386
- Chain C: E.386
- Ligands: Y1.4, SO4.8, HEC.14, SO4.36, HEC.42
Ligand excluded by PLIPY1.33: 4 residues within 4Å:- Chain B: D.301, E.312
- Chain C: Q.282
- Ligands: SO4.35
Ligand excluded by PLIPY1.44: 1 residues within 4Å:- Chain D: E.30
Ligand excluded by PLIPY1.45: 3 residues within 4Å:- Chain D: P.77
- Ligands: HEC.54, HEC.55
Ligand excluded by PLIPY1.46: 7 residues within 4Å:- Chain B: E.386
- Chain D: E.386
- Ligands: Y1.18, SO4.22, HEC.28, SO4.50, HEC.56
Ligand excluded by PLIPY1.47: 4 residues within 4Å:- Chain A: D.301, E.312
- Chain D: Q.282
- Ligands: SO4.49
Ligand excluded by PLIP- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 6 residues within 4Å:- Chain A: F.70, R.92, Y.196, Q.254, H.255
- Ligands: HEC.10
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:Y.196
- Water bridges: A:R.92, A:R.92, A:R.92
- Salt bridges: A:R.92, A:K.112, A:H.255
SO4.7: 5 residues within 4Å:- Chain A: Q.282, K.287
- Chain D: S.311, E.312
- Ligands: Y1.5
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain D- Salt bridges: A:K.287
- Hydrogen bonds: D:E.312
- Water bridges: D:Q.313
SO4.8: 9 residues within 4Å:- Chain A: I.265, P.385, E.386
- Chain C: K.322, E.386
- Ligands: Y1.4, HEC.14, Y1.32, HEC.42
10 PLIP interactions:6 interactions with chain A, 4 interactions with chain C- Hydrogen bonds: A:I.265, A:E.386, A:E.386, A:E.386, C:E.386
- Water bridges: A:H.266, A:A.384, C:K.322, C:R.325
- Salt bridges: C:K.322
SO4.20: 6 residues within 4Å:- Chain B: F.70, R.92, Y.196, Q.254, H.255
- Ligands: HEC.24
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:Y.196, B:Q.254
- Water bridges: B:R.92, B:R.92, B:R.92
- Salt bridges: B:R.92, B:K.112, B:H.255
SO4.21: 5 residues within 4Å:- Chain B: Q.282, K.287
- Chain C: S.311, E.312
- Ligands: Y1.19
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:E.312
- Water bridges: C:E.312, C:Q.313
- Salt bridges: B:K.287
SO4.22: 9 residues within 4Å:- Chain B: I.265, P.385, E.386
- Chain D: K.322, E.386
- Ligands: Y1.18, HEC.28, Y1.46, HEC.56
9 PLIP interactions:3 interactions with chain D, 6 interactions with chain B- Water bridges: D:K.322, D:R.325, B:H.266, B:H.266, B:A.384
- Salt bridges: D:K.322
- Hydrogen bonds: B:I.265, B:E.386, B:E.386
SO4.34: 6 residues within 4Å:- Chain C: F.70, R.92, Y.196, Q.254, H.255
- Ligands: HEC.38
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:Y.196
- Water bridges: C:R.92, C:R.92, C:R.92
- Salt bridges: C:R.92, C:K.112, C:H.255
SO4.35: 5 residues within 4Å:- Chain B: S.311, E.312
- Chain C: Q.282, K.287
- Ligands: Y1.33
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:E.312
- Water bridges: B:Q.313
- Salt bridges: C:K.287
SO4.36: 9 residues within 4Å:- Chain A: K.322, E.386
- Chain C: I.265, P.385, E.386
- Ligands: Y1.4, HEC.14, Y1.32, HEC.42
10 PLIP interactions:4 interactions with chain A, 6 interactions with chain C- Hydrogen bonds: A:E.386, C:I.265, C:E.386, C:E.386, C:E.386
- Water bridges: A:K.322, A:R.325, C:H.266, C:A.384
- Salt bridges: A:K.322
SO4.48: 6 residues within 4Å:- Chain D: F.70, R.92, Y.196, Q.254, H.255
- Ligands: HEC.52
9 PLIP interactions:9 interactions with chain D- Hydrogen bonds: D:Y.196, D:Y.196, D:Q.254
- Water bridges: D:R.92, D:R.92, D:R.92
- Salt bridges: D:R.92, D:K.112, D:H.255
SO4.49: 5 residues within 4Å:- Chain A: S.311, E.312
- Chain D: Q.282, K.287
- Ligands: Y1.47
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:E.312
- Water bridges: A:E.312, A:Q.313
- Salt bridges: D:K.287
SO4.50: 9 residues within 4Å:- Chain B: K.322, E.386
- Chain D: I.265, P.385, E.386
- Ligands: Y1.18, HEC.28, Y1.46, HEC.56
8 PLIP interactions:3 interactions with chain B, 5 interactions with chain D- Water bridges: B:K.322, B:R.325, D:H.266, D:A.384
- Salt bridges: B:K.322
- Hydrogen bonds: D:I.265, D:E.386, D:E.386
- 4 x ACT: ACETATE ION(Non-functional Binders)
ACT.9: 4 residues within 4Å:- Chain A: G.21, I.22, E.23, Y.34
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.23, A:Y.34, A:Y.34
- Water bridges: A:E.23
ACT.23: 4 residues within 4Å:- Chain B: G.21, I.22, E.23, Y.34
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.23, B:Y.34
ACT.37: 4 residues within 4Å:- Chain C: G.21, I.22, E.23, Y.34
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:E.23, C:Y.34, C:Y.34
- Water bridges: C:E.23
ACT.51: 4 residues within 4Å:- Chain D: G.21, I.22, E.23, Y.34
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.23, D:Y.34
- 20 x HEC: HEME C(Covalent)
HEC.10: 25 residues within 4Å:- Chain A: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378
- Ligands: SO4.6, HEC.12
19 PLIP interactions:19 interactions with chain A,- Hydrophobic interactions: A:P.77, A:T.90, A:T.93, A:L.104, A:Y.196, A:F.198, A:V.216, A:H.255
- Hydrogen bonds: A:N.75, A:N.75, A:A.376
- Water bridges: A:R.92, A:R.92, A:H.255, A:H.255
- Salt bridges: A:R.92, A:H.255, A:H.378
- pi-Stacking: A:H.255
HEC.11: 18 residues within 4Å:- Chain A: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEC.12
16 PLIP interactions:16 interactions with chain A,- Hydrophobic interactions: A:W.31, A:Y.35, A:Y.35, A:Q.38, A:F.39, A:W.42, A:L.157, A:L.157
- Hydrogen bonds: A:Q.38, A:Y.280, A:S.289
- Salt bridges: A:H.181, A:R.185, A:H.291
- Metal complexes: A:H.150, A:H.291
HEC.12: 26 residues within 4Å:- Chain A: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, N.148, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: Y1.3, HEC.10, HEC.11, HEC.13
11 PLIP interactions:11 interactions with chain A,- Hydrophobic interactions: A:P.77, A:K.112, A:H.277, A:V.293
- Hydrogen bonds: A:S.48, A:S.48, A:R.78, A:Y.82, A:D.86
- Metal complexes: A:H.80, A:H.193
HEC.13: 21 residues within 4Å:- Chain A: P.77, C.189, H.193, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, H.378, G.379, F.381, F.382, H.383
- Ligands: Y1.3, HEC.12, HEC.14
14 PLIP interactions:14 interactions with chain A,- Hydrophobic interactions: A:H.193, A:Y.261, A:Y.261, A:Y.261, A:Y.261, A:V.271, A:P.296, A:H.378, A:F.381, A:F.382, A:F.382
- Hydrogen bonds: A:N.295
- Metal complexes: A:H.277, A:H.383
HEC.14: 24 residues within 4Å:- Chain A: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, K.322, F.382
- Chain C: I.265, H.308, E.310, E.386
- Ligands: Y1.4, SO4.8, HEC.13, Y1.32, SO4.36, HEC.42
15 PLIP interactions:11 interactions with chain A, 4 interactions with chain C,- Hydrophobic interactions: A:I.265, A:I.265, A:K.269, A:V.271, A:P.296, A:L.315, A:I.318, A:F.382, C:I.265
- Salt bridges: A:K.322, C:H.308
- Metal complexes: A:H.266, A:H.308
- Water bridges: C:H.308, C:H.308
HEC.24: 25 residues within 4Å:- Chain B: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378
- Ligands: SO4.20, HEC.26
21 PLIP interactions:21 interactions with chain B,- Hydrophobic interactions: B:P.77, B:T.90, B:T.93, B:L.104, B:Y.196, B:F.198, B:V.216, B:H.255
- Hydrogen bonds: B:N.75, B:N.75, B:A.376
- Water bridges: B:Y.74, B:Y.74, B:Y.74, B:R.92, B:R.92, B:H.255
- Salt bridges: B:R.92, B:H.255, B:H.378
- pi-Stacking: B:H.255
HEC.25: 18 residues within 4Å:- Chain B: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEC.26
15 PLIP interactions:15 interactions with chain B,- Hydrophobic interactions: B:W.31, B:Y.35, B:Y.35, B:Q.38, B:F.39, B:W.42, B:L.157, B:L.157
- Hydrogen bonds: B:Q.38, B:S.289
- Salt bridges: B:H.181, B:R.185, B:H.291
- Metal complexes: B:H.150, B:H.291
HEC.26: 26 residues within 4Å:- Chain B: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, N.148, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: Y1.17, HEC.24, HEC.25, HEC.27
10 PLIP interactions:10 interactions with chain B,- Hydrophobic interactions: B:P.77, B:K.112, B:H.277, B:V.293
- Hydrogen bonds: B:S.48, B:S.48, B:R.78, B:Y.82
- Metal complexes: B:H.80, B:H.193
HEC.27: 21 residues within 4Å:- Chain B: P.77, C.189, H.193, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, H.378, G.379, F.381, F.382, H.383
- Ligands: Y1.17, HEC.26, HEC.28
15 PLIP interactions:15 interactions with chain B,- Hydrophobic interactions: B:H.193, B:Y.261, B:Y.261, B:Y.261, B:Y.261, B:V.271, B:P.296, B:H.378, B:F.381, B:F.382, B:F.382
- Hydrogen bonds: B:N.295
- Water bridges: B:H.378
- Metal complexes: B:H.277, B:H.383
HEC.28: 24 residues within 4Å:- Chain B: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, K.322, F.382
- Chain D: I.265, H.308, E.310, E.386
- Ligands: Y1.18, SO4.22, HEC.27, Y1.46, SO4.50, HEC.56
14 PLIP interactions:11 interactions with chain B, 3 interactions with chain D,- Hydrophobic interactions: B:I.265, B:I.265, B:K.269, B:V.271, B:P.296, B:L.315, B:I.318, B:F.382, D:I.265
- Salt bridges: B:K.322, D:H.308
- Metal complexes: B:H.266, B:H.308
- Water bridges: D:E.310
HEC.38: 25 residues within 4Å:- Chain C: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378
- Ligands: SO4.34, HEC.40
19 PLIP interactions:19 interactions with chain C,- Hydrophobic interactions: C:P.77, C:T.90, C:T.93, C:L.104, C:Y.196, C:F.198, C:V.216, C:H.255
- Hydrogen bonds: C:N.75, C:N.75, C:A.376
- Water bridges: C:R.92, C:R.92, C:H.255, C:H.255
- Salt bridges: C:R.92, C:H.255, C:H.378
- pi-Stacking: C:H.255
HEC.39: 18 residues within 4Å:- Chain C: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEC.40
16 PLIP interactions:16 interactions with chain C,- Hydrophobic interactions: C:W.31, C:Y.35, C:Y.35, C:Q.38, C:F.39, C:W.42, C:L.157, C:L.157
- Hydrogen bonds: C:Q.38, C:Y.280, C:S.289
- Salt bridges: C:H.181, C:R.185, C:H.291
- Metal complexes: C:H.150, C:H.291
HEC.40: 26 residues within 4Å:- Chain C: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, N.148, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: Y1.31, HEC.38, HEC.39, HEC.41
11 PLIP interactions:11 interactions with chain C,- Hydrophobic interactions: C:P.77, C:K.112, C:H.277, C:V.293
- Hydrogen bonds: C:S.48, C:S.48, C:R.78, C:Y.82, C:D.86
- Metal complexes: C:H.80, C:H.193
HEC.41: 21 residues within 4Å:- Chain C: P.77, C.189, H.193, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, H.378, G.379, F.381, F.382, H.383
- Ligands: Y1.31, HEC.40, HEC.42
14 PLIP interactions:14 interactions with chain C,- Hydrophobic interactions: C:H.193, C:Y.261, C:Y.261, C:Y.261, C:Y.261, C:V.271, C:P.296, C:H.378, C:F.381, C:F.382, C:F.382
- Hydrogen bonds: C:N.295
- Metal complexes: C:H.277, C:H.383
HEC.42: 24 residues within 4Å:- Chain A: I.265, H.308, E.310, E.386
- Chain C: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, K.322, F.382
- Ligands: Y1.4, SO4.8, HEC.14, Y1.32, SO4.36, HEC.41
15 PLIP interactions:11 interactions with chain C, 4 interactions with chain A,- Hydrophobic interactions: C:I.265, C:I.265, C:K.269, C:V.271, C:P.296, C:L.315, C:I.318, C:F.382, A:I.265
- Salt bridges: C:K.322, A:H.308
- Metal complexes: C:H.266, C:H.308
- Water bridges: A:H.308, A:H.308
HEC.52: 25 residues within 4Å:- Chain D: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378
- Ligands: SO4.48, HEC.54
21 PLIP interactions:21 interactions with chain D,- Hydrophobic interactions: D:P.77, D:T.90, D:T.93, D:L.104, D:Y.196, D:F.198, D:V.216, D:H.255
- Hydrogen bonds: D:N.75, D:N.75, D:A.376
- Water bridges: D:Y.74, D:Y.74, D:Y.74, D:R.92, D:R.92, D:H.255
- Salt bridges: D:R.92, D:H.255, D:H.378
- pi-Stacking: D:H.255
HEC.53: 18 residues within 4Å:- Chain D: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEC.54
15 PLIP interactions:15 interactions with chain D,- Hydrophobic interactions: D:W.31, D:Y.35, D:Y.35, D:Q.38, D:F.39, D:W.42, D:L.157, D:L.157
- Hydrogen bonds: D:Q.38, D:S.289
- Salt bridges: D:H.181, D:R.185, D:H.291
- Metal complexes: D:H.150, D:H.291
HEC.54: 26 residues within 4Å:- Chain D: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, N.148, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: Y1.45, HEC.52, HEC.53, HEC.55
10 PLIP interactions:10 interactions with chain D,- Hydrophobic interactions: D:P.77, D:K.112, D:H.277, D:V.293
- Hydrogen bonds: D:S.48, D:S.48, D:R.78, D:Y.82
- Metal complexes: D:H.80, D:H.193
HEC.55: 21 residues within 4Å:- Chain D: P.77, C.189, H.193, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, H.378, G.379, F.381, F.382, H.383
- Ligands: Y1.45, HEC.54, HEC.56
15 PLIP interactions:15 interactions with chain D,- Hydrophobic interactions: D:H.193, D:Y.261, D:Y.261, D:Y.261, D:Y.261, D:V.271, D:P.296, D:H.378, D:F.381, D:F.382, D:F.382
- Hydrogen bonds: D:N.295
- Water bridges: D:H.378
- Metal complexes: D:H.277, D:H.383
HEC.56: 24 residues within 4Å:- Chain B: I.265, H.308, E.310, E.386
- Chain D: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, K.322, F.382
- Ligands: Y1.18, SO4.22, HEC.28, Y1.46, SO4.50, HEC.55
14 PLIP interactions:11 interactions with chain D, 3 interactions with chain B,- Hydrophobic interactions: D:I.265, D:I.265, D:K.269, D:V.271, D:P.296, D:L.315, D:I.318, D:F.382, B:I.265
- Salt bridges: D:K.322, B:H.308
- Metal complexes: D:H.266, D:H.308
- Water bridges: B:E.310
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Einsle, O. et al., Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs. J.Biol.Chem. (2000)
- Release Date
- 2001-01-17
- Peptides
- CYTOCHROME C NITRITE REDUCTASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CA: CALCIUM ION(Non-covalent)
- 16 x Y1: YTTRIUM ION(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 20 x HEC: HEME C(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Einsle, O. et al., Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs. J.Biol.Chem. (2000)
- Release Date
- 2001-01-17
- Peptides
- CYTOCHROME C NITRITE REDUCTASE: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A