- Coordinates
- PDB Format
- Method
- NEUTRON DIFFRACTION 1.30 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
MRD.2: 8 residues within 4Å:- Chain A: D.148, V.151, D.152, R.153, E.154, R.214, Y.216
- Ligands: MPD.1
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:V.151, A:V.151
- Hydrogen bonds: A:E.154, A:E.154
MRD.8: 8 residues within 4Å:- Chain B: D.148, V.151, D.152, R.153, E.154, R.214, Y.216
- Ligands: MPD.7
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:V.151, B:V.151
- Hydrogen bonds: B:E.154, B:E.154
MRD.14: 8 residues within 4Å:- Chain C: D.148, V.151, D.152, R.153, E.154, R.214, Y.216
- Ligands: MPD.13
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:V.151, C:V.151
- Hydrogen bonds: C:E.154, C:E.154
- 3 x NO2: NITRITE ION(Non-covalent)
NO2.3: 10 residues within 4Å:- Chain A: D.83, H.85, H.119, V.125
- Chain B: H.229, V.231, V.277, H.279, F.281
- Ligands: CU.5
No protein-ligand interaction detected (PLIP)NO2.9: 10 residues within 4Å:- Chain B: D.83, H.85, H.119, V.125
- Chain C: H.229, V.231, V.277, H.279, F.281
- Ligands: CU.11
No protein-ligand interaction detected (PLIP)NO2.15: 10 residues within 4Å:- Chain A: H.229, V.231, V.277, H.279, F.281
- Chain C: D.83, H.85, H.119, V.125
- Ligands: CU.17
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:H.119
- 9 x CU: COPPER (II) ION(Non-covalent)
CU.4: 5 residues within 4Å:- Chain A: W.48, H.80, A.120, H.128, M.133
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:H.80, A:H.128
CU.5: 7 residues within 4Å:- Chain A: D.83, H.85, H.119
- Chain B: H.229, H.279, F.281
- Ligands: NO2.3
7 PLIP interactions:2 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: A:H.85, A:H.119, B:H.279, H2O.1, H2O.1, H2O.10, H2O.10
CU.6: 3 residues within 4Å:- Chain A: V.21, H.27, H.68
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.27, A:H.68, H2O.10, H2O.10
CU.10: 5 residues within 4Å:- Chain B: W.48, H.80, A.120, H.128, M.133
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.80, B:H.128
CU.11: 7 residues within 4Å:- Chain B: D.83, H.85, H.119
- Chain C: H.229, H.279, F.281
- Ligands: NO2.9
7 PLIP interactions:2 interactions with chain B, 1 interactions with chain C, 4 Ligand-Water interactions- Metal complexes: B:H.85, B:H.119, C:H.279, H2O.13, H2O.13, H2O.23, H2O.23
CU.12: 3 residues within 4Å:- Chain B: V.21, H.27, H.68
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:H.27, B:H.68, H2O.22, H2O.22
CU.16: 5 residues within 4Å:- Chain C: W.48, H.80, A.120, H.128, M.133
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:H.80, C:H.128
CU.17: 7 residues within 4Å:- Chain A: H.229, H.279, F.281
- Chain C: D.83, H.85, H.119
- Ligands: NO2.15
7 PLIP interactions:2 interactions with chain C, 1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: C:H.85, C:H.119, A:H.279, H2O.26, H2O.26, H2O.36, H2O.36
CU.18: 3 residues within 4Å:- Chain C: V.21, H.27, H.68
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:H.27, C:H.68, H2O.35, H2O.35
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fukuda, Y. et al., Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. (2025)
- Release Date
- 2025-06-11
- Peptides
- Copper-containing nitrite reductase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A
- Coordinates
- PDB Format
- Method
- NEUTRON DIFFRACTION 1.30 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- 3 x NO2: NITRITE ION(Non-covalent)
- 9 x CU: COPPER (II) ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fukuda, Y. et al., Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. (2025)
- Release Date
- 2025-06-11
- Peptides
- Copper-containing nitrite reductase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A