- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.15 Å
- Oligo State
- homo-trimer
- Ligands
- 18 x CU: COPPER (II) ION(Non-covalent)
- 3 x NA: SODIUM ION(Non-functional Binders)
NA.7: 2 residues within 4Å:- Chain A: E.78
- Ligands: FMT.16
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.78
- Water bridges: A:K.157
NA.28: 2 residues within 4Å:- Chain B: E.78
- Ligands: FMT.37
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.78
- Water bridges: B:K.157
NA.49: 2 residues within 4Å:- Chain C: E.78
- Ligands: FMT.58
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:E.78
- Water bridges: C:K.157
- 27 x FMT: FORMIC ACID(Non-functional Binders)
FMT.8: 9 residues within 4Å:- Chain A: D.98, H.100, H.134
- Chain B: H.244, V.246, H.294, F.296
- Ligands: CU.2, FMT.9
Ligand excluded by PLIPFMT.9: 4 residues within 4Å:- Chain A: V.140
- Chain B: V.292, V.304
- Ligands: FMT.8
Ligand excluded by PLIPFMT.10: 4 residues within 4Å:- Chain A: H.42, H.83, T.122
- Ligands: CU.3
Ligand excluded by PLIPFMT.11: 2 residues within 4Å:- Chain A: D.167
- Ligands: CU.6
Ligand excluded by PLIPFMT.12: 7 residues within 4Å:- Chain A: N.16, V.17, I.18, H.21, W.63, Y.180, N.181
Ligand excluded by PLIPFMT.13: 7 residues within 4Å:- Chain A: V.190, P.191, N.297, H.298, K.301
- Chain C: Q.187
- Ligands: CU.5
Ligand excluded by PLIPFMT.14: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPFMT.15: 6 residues within 4Å:- Chain A: K.32, M.33, E.34, H.42, I.43, E.44
Ligand excluded by PLIPFMT.16: 5 residues within 4Å:- Chain A: P.128, N.258, N.260
- Chain B: Q.264
- Ligands: NA.7
Ligand excluded by PLIPFMT.29: 9 residues within 4Å:- Chain B: D.98, H.100, H.134
- Chain C: H.244, V.246, H.294, F.296
- Ligands: CU.23, FMT.30
Ligand excluded by PLIPFMT.30: 4 residues within 4Å:- Chain B: V.140
- Chain C: V.292, V.304
- Ligands: FMT.29
Ligand excluded by PLIPFMT.31: 4 residues within 4Å:- Chain B: H.42, H.83, T.122
- Ligands: CU.24
Ligand excluded by PLIPFMT.32: 2 residues within 4Å:- Chain B: D.167
- Ligands: CU.27
Ligand excluded by PLIPFMT.33: 7 residues within 4Å:- Chain B: N.16, V.17, I.18, H.21, W.63, Y.180, N.181
Ligand excluded by PLIPFMT.34: 7 residues within 4Å:- Chain A: Q.187
- Chain B: V.190, P.191, N.297, H.298, K.301
- Ligands: CU.26
Ligand excluded by PLIPFMT.35: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPFMT.36: 6 residues within 4Å:- Chain B: K.32, M.33, E.34, H.42, I.43, E.44
Ligand excluded by PLIPFMT.37: 5 residues within 4Å:- Chain B: P.128, N.258, N.260
- Chain C: Q.264
- Ligands: NA.28
Ligand excluded by PLIPFMT.50: 9 residues within 4Å:- Chain A: H.244, V.246, H.294, F.296
- Chain C: D.98, H.100, H.134
- Ligands: CU.44, FMT.51
Ligand excluded by PLIPFMT.51: 4 residues within 4Å:- Chain A: V.292, V.304
- Chain C: V.140
- Ligands: FMT.50
Ligand excluded by PLIPFMT.52: 4 residues within 4Å:- Chain C: H.42, H.83, T.122
- Ligands: CU.45
Ligand excluded by PLIPFMT.53: 2 residues within 4Å:- Chain C: D.167
- Ligands: CU.48
Ligand excluded by PLIPFMT.54: 7 residues within 4Å:- Chain C: N.16, V.17, I.18, H.21, W.63, Y.180, N.181
Ligand excluded by PLIPFMT.55: 7 residues within 4Å:- Chain B: Q.187
- Chain C: V.190, P.191, N.297, H.298, K.301
- Ligands: CU.47
Ligand excluded by PLIPFMT.56: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPFMT.57: 6 residues within 4Å:- Chain C: K.32, M.33, E.34, H.42, I.43, E.44
Ligand excluded by PLIPFMT.58: 5 residues within 4Å:- Chain A: Q.264
- Chain C: P.128, N.258, N.260
- Ligands: NA.49
Ligand excluded by PLIP- 9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.17: 6 residues within 4Å:- Chain A: D.163, V.166, D.167, R.168, E.169, R.229
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:D.163, A:V.166
- Hydrogen bonds: A:E.169
- Water bridges: A:E.169, A:Y.231, A:Y.231
MPD.18: 7 residues within 4Å:- Chain A: D.55, S.192, Y.193, T.212, Q.300, K.301, G.302
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.193
- Hydrogen bonds: A:S.192, A:K.301
MPD.19: 5 residues within 4Å:- Chain A: V.75, A.200, L.201, K.202, P.203
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:A.200
MPD.38: 6 residues within 4Å:- Chain B: D.163, V.166, D.167, R.168, E.169, R.229
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:D.163, B:V.166
- Hydrogen bonds: B:E.169
- Water bridges: B:E.169, B:Y.231, B:Y.231
MPD.39: 7 residues within 4Å:- Chain B: D.55, S.192, Y.193, T.212, Q.300, K.301, G.302
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.193
- Hydrogen bonds: B:S.192, B:K.301
MPD.40: 5 residues within 4Å:- Chain B: V.75, A.200, L.201, K.202, P.203
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:A.200
MPD.59: 6 residues within 4Å:- Chain C: D.163, V.166, D.167, R.168, E.169, R.229
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:D.163, C:V.166
- Hydrogen bonds: C:E.169
- Water bridges: C:E.169, C:Y.231, C:Y.231
MPD.60: 7 residues within 4Å:- Chain C: D.55, S.192, Y.193, T.212, Q.300, K.301, G.302
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:Y.193
- Hydrogen bonds: C:S.192, C:K.301
MPD.61: 5 residues within 4Å:- Chain C: V.75, A.200, L.201, K.202, P.203
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:A.200
- 3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.20: 2 residues within 4Å:- Chain A: P.124
- Chain B: R.285
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.285
EDO.41: 2 residues within 4Å:- Chain B: P.124
- Chain C: R.285
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.285
EDO.62: 2 residues within 4Å:- Chain A: R.285
- Chain C: P.124
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.285
- 3 x SO4: SULFATE ION(Non-functional Binders)
SO4.21: 7 residues within 4Å:- Chain A: H.262, L.263
- Chain B: H.262, L.263
- Chain C: L.263
- Ligands: SO4.42, SO4.63
10 PLIP interactions:4 interactions with chain A, 2 interactions with chain C, 4 interactions with chain B- Water bridges: A:N.260, A:H.262, A:H.262, A:H.262, C:H.262, C:H.262, B:H.262, B:H.262, B:H.262, B:H.262
SO4.42: 7 residues within 4Å:- Chain A: L.263
- Chain B: H.262, L.263
- Chain C: H.262, L.263
- Ligands: SO4.21, SO4.63
10 PLIP interactions:4 interactions with chain B, 2 interactions with chain A, 4 interactions with chain C- Water bridges: B:N.260, B:H.262, B:H.262, B:H.262, A:H.262, A:H.262, C:H.262, C:H.262, C:H.262, C:H.262
SO4.63: 7 residues within 4Å:- Chain A: H.262, L.263
- Chain B: L.263
- Chain C: H.262, L.263
- Ligands: SO4.21, SO4.42
10 PLIP interactions:4 interactions with chain C, 4 interactions with chain A, 2 interactions with chain B- Water bridges: C:N.260, C:H.262, C:H.262, C:H.262, A:H.262, A:H.262, A:H.262, A:H.262, B:H.262, B:H.262
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fukuda, Y. et al., Copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with formate. to be published
- Release Date
- 2013-12-11
- Peptides
- Nitrite reductase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.15 Å
- Oligo State
- homo-trimer
- Ligands
- 18 x CU: COPPER (II) ION(Non-covalent)
- 3 x NA: SODIUM ION(Non-functional Binders)
- 27 x FMT: FORMIC ACID(Non-functional Binders)
- 9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fukuda, Y. et al., Copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with formate. to be published
- Release Date
- 2013-12-11
- Peptides
- Nitrite reductase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A