- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 8 x Y1: YTTRIUM ION(Non-covalent)
Y1.2: 1 residues within 4Å:- Chain A: E.30
No protein-ligand interaction detected (PLIP)Y1.3: 3 residues within 4Å:- Chain A: P.77
- Ligands: HEC.12, HEC.13
No protein-ligand interaction detected (PLIP)Y1.4: 7 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: SO4.8, HEC.14, Y1.18, SO4.22, HEC.28
No protein-ligand interaction detected (PLIP)Y1.5: 2 residues within 4Å:- Chain A: Q.282
- Ligands: SO4.7
No protein-ligand interaction detected (PLIP)Y1.16: 1 residues within 4Å:- Chain B: E.30
No protein-ligand interaction detected (PLIP)Y1.17: 3 residues within 4Å:- Chain B: P.77
- Ligands: HEC.26, HEC.27
No protein-ligand interaction detected (PLIP)Y1.18: 7 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: Y1.4, SO4.8, HEC.14, SO4.22, HEC.28
No protein-ligand interaction detected (PLIP)Y1.19: 2 residues within 4Å:- Chain B: Q.282
- Ligands: SO4.21
No protein-ligand interaction detected (PLIP)- 6 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: 3 residues within 4Å:- Chain A: Q.282, K.287
- Ligands: Y1.5
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.287
SO4.8: 9 residues within 4Å:- Chain A: I.265, P.385, E.386
- Chain B: K.322, E.386
- Ligands: Y1.4, HEC.14, Y1.18, HEC.28
7 PLIP interactions:3 interactions with chain B, 4 interactions with chain A- Water bridges: B:K.322, B:R.325, A:H.266, A:A.384
- Salt bridges: B:K.322
- Hydrogen bonds: A:I.265, A:E.386
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: 3 residues within 4Å:- Chain B: Q.282, K.287
- Ligands: Y1.19
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:K.287
SO4.22: 9 residues within 4Å:- Chain A: K.322, E.386
- Chain B: I.265, P.385, E.386
- Ligands: Y1.4, HEC.14, Y1.18, HEC.28
7 PLIP interactions:4 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:I.265, B:E.386
- Water bridges: B:H.266, B:A.384, A:K.322, A:R.325
- Salt bridges: A:K.322
- 2 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
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.23, B:Y.34, B:Y.34
- Water bridges: B:E.23
- 10 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
9 PLIP interactions:9 interactions with chain A,- Hydrophobic interactions: A:P.77, A:K.112, A:H.277, A:V.293
- Hydrogen bonds: A:S.48, 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 B: I.265, H.308, E.310, E.386
- Ligands: Y1.4, SO4.8, HEC.13, Y1.18, SO4.22, HEC.28
15 PLIP interactions:11 interactions with chain A, 4 interactions with chain B,- 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, B:I.265
- Salt bridges: A:K.322, B:H.308
- Metal complexes: A:H.266, A:H.308
- Water bridges: B:H.308, B: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
19 PLIP interactions:19 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:R.92, B:R.92, B:H.255, 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
16 PLIP interactions:16 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:Y.280, 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
9 PLIP interactions:9 interactions with chain B,- Hydrophobic interactions: B:P.77, B:K.112, B:H.277, B:V.293
- Hydrogen bonds: B:S.48, B:Y.82, B:D.86
- 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
14 PLIP interactions:14 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
- Metal complexes: B:H.277, B:H.383
HEC.28: 24 residues within 4Å:- Chain A: I.265, H.308, E.310, E.386
- 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
- Ligands: Y1.4, SO4.8, HEC.14, Y1.18, SO4.22, HEC.27
15 PLIP interactions:4 interactions with chain A, 11 interactions with chain B,- Hydrophobic interactions: A:I.265, B:I.265, B:I.265, B:K.269, B:V.271, B:P.296, B:L.315, B:I.318, B:F.382
- Water bridges: A:H.308, A:H.308
- Salt bridges: A:H.308, B:K.322
- Metal complexes: B:H.266, B:H.308
- 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: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 8 x Y1: YTTRIUM ION(Non-covalent)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 10 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: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A