- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.38 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x HEC: HEME C(Covalent)(Non-covalent)
- 2 x DHE: HEME D(Non-covalent)
DHE.2: 30 residues within 4Å:- Chain A: R.156, H.182, I.183, R.185, R.198, R.225, S.226, V.227, Y.245, A.283, A.284, I.285, H.327, D.328, G.371, R.372, L.424, F.425, K.427, T.440, F.441, V.482, Q.483, W.498, T.530, G.531, F.533
- Chain B: Y.10, Q.11, A.13
33 PLIP interactions:29 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions,- Hydrophobic interactions: A:I.183, A:R.225, A:R.225, A:A.283, A:F.425, A:F.425, A:W.498, A:W.498, A:F.533, B:Y.10, B:Y.10, B:Q.11
- Hydrogen bonds: A:R.185, A:R.225, A:S.226, A:S.226, A:Y.245, A:I.285, A:Q.483
- Water bridges: A:R.198, A:R.198, A:R.198, A:R.372
- Salt bridges: A:R.156, A:H.182, A:H.182, A:R.185, A:R.198, A:R.225, A:R.372, A:K.427
- Metal complexes: A:H.182, H2O.2
DHE.9: 30 residues within 4Å:- Chain A: Y.10, Q.11, A.13
- Chain B: R.156, V.181, H.182, I.183, R.185, R.198, R.225, S.226, V.227, Y.245, A.283, A.284, I.285, H.327, D.328, G.371, R.372, L.424, F.425, K.427, F.441, V.482, Q.483, W.498, T.530, G.531, F.533
34 PLIP interactions:30 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions,- Hydrophobic interactions: B:I.183, B:R.225, B:R.225, B:A.283, B:F.425, B:F.425, B:W.498, B:W.498, B:F.533, B:F.533, A:Y.10, A:Y.10
- Hydrogen bonds: B:R.185, B:R.225, B:S.226, B:S.226, B:Y.245, B:I.285, B:Q.483
- Water bridges: B:R.156, B:R.156, B:H.182, B:R.198, A:A.13
- Salt bridges: B:R.156, B:H.182, B:H.182, B:R.185, B:R.198, B:R.225, B:R.372, B:K.427
- Metal complexes: B:H.182, H2O.1
- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.3: 4 residues within 4Å:- Chain A: H.289, H.335, Q.539, H.540
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.335, A:H.540
- Salt bridges: A:H.289, A:H.540
PO4.4: 4 residues within 4Å:- Chain A: G.420, G.421, N.442, P.443
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.421, A:N.442, A:N.442
PO4.5: 5 residues within 4Å:- Chain A: Q.45, R.156, Y.179, R.198
- Chain B: A.14
6 PLIP interactions:2 interactions with chain B, 4 interactions with chain A- Water bridges: B:A.14, B:A.14, A:R.156
- Hydrogen bonds: A:Y.179, A:R.198
- Salt bridges: A:R.156
PO4.10: 5 residues within 4Å:- Chain B: G.420, G.421, N.442, P.443, I.447
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:G.421, B:N.442, B:N.442
PO4.11: 4 residues within 4Å:- Chain A: A.14
- Chain B: R.156, Y.179, R.198
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:Y.179, B:Y.179
- Water bridges: B:R.198, A:A.14
- Salt bridges: B:R.156
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.6: 4 residues within 4Å:- Chain A: G.268, M.269
- Chain B: V.264, S.265
Ligand excluded by PLIPCL.7: 4 residues within 4Å:- Chain A: H.291, P.292, N.308, R.356
Ligand excluded by PLIPCL.12: 4 residues within 4Å:- Chain A: V.264, S.265
- Chain B: G.268, M.269
Ligand excluded by PLIPCL.13: 3 residues within 4Å:- Chain B: D.176, R.201, K.214
Ligand excluded by PLIPCL.14: 4 residues within 4Å:- Chain B: H.291, P.292, N.308, R.356
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Klunemann, T. et al., Structure of heme d 1 -free cd 1 nitrite reductase NirS. Acta Crystallogr.,Sect.F (2020)
- Release Date
- 2020-11-18
- Peptides
- Nitrite reductase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.38 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x HEC: HEME C(Covalent)(Non-covalent)
- 2 x DHE: HEME D(Non-covalent)
- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Klunemann, T. et al., Structure of heme d 1 -free cd 1 nitrite reductase NirS. Acta Crystallogr.,Sect.F (2020)
- Release Date
- 2020-11-18
- Peptides
- Nitrite reductase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B