- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.05 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x D6N: FeV(Non-covalent)
- 2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)
HCA.2: 11 residues within 4Å:- Chain A: C.52, L.56, K.83, Q.176, K.361, G.405, P.406, H.423
- Chain B: F.59
- Ligands: D6N.1, CMO.5
15 PLIP interactions:15 interactions with chain A- Hydrophobic interactions: A:L.56, A:H.423
- Hydrogen bonds: A:T.82, A:Q.176
- Water bridges: A:K.83, A:K.83, A:K.361, A:G.405, A:G.405, A:R.407
- Salt bridges: A:K.83, A:K.361, A:K.361, A:H.423, A:H.423
HCA.19: 11 residues within 4Å:- Chain D: C.52, L.56, K.83, Q.176, K.361, G.405, P.406, H.423
- Chain E: F.59
- Ligands: D6N.18, CMO.22
16 PLIP interactions:16 interactions with chain D- Hydrophobic interactions: D:L.56, D:H.423
- Hydrogen bonds: D:Q.176
- Water bridges: D:E.46, D:K.83, D:K.83, D:K.361, D:G.405, D:G.405, D:R.407, D:H.423
- Salt bridges: D:K.83, D:K.361, D:K.361, D:H.423, D:H.423
- 2 x BCT: BICARBONATE ION(Non-functional Binders)
BCT.3: 6 residues within 4Å:- Chain A: T.335, G.336, G.337, P.338, R.339
- Ligands: D6N.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.335, A:G.337, A:R.339
BCT.20: 6 residues within 4Å:- Chain D: T.335, G.336, G.337, P.338, R.339
- Ligands: D6N.18
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:G.336, D:G.337, D:G.337
- 4 x CMO: CARBON MONOXIDE(Non-functional Binders)
CMO.4: 5 residues within 4Å:- Chain A: V.57, H.180, F.362
- Ligands: D6N.1, CMO.5
No protein-ligand interaction detected (PLIP)CMO.5: 6 residues within 4Å:- Chain A: V.57, Q.176, F.362
- Ligands: D6N.1, HCA.2, CMO.4
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.176
CMO.21: 5 residues within 4Å:- Chain D: V.57, H.180, F.362
- Ligands: D6N.18, CMO.22
No protein-ligand interaction detected (PLIP)CMO.22: 6 residues within 4Å:- Chain D: V.57, Q.176, F.362
- Ligands: D6N.18, HCA.19, CMO.21
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Q.176
- 11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 6 residues within 4Å:- Chain A: V.107, V.108, F.109, G.110, I.143
- Ligands: TRS.8
No protein-ligand interaction detected (PLIP)EDO.7: 5 residues within 4Å:- Chain A: D.64, D.128, I.129, K.130, R.131
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.64, A:K.130, A:R.131
EDO.13: 6 residues within 4Å:- Chain B: R.256, L.276, V.277, N.278, P.369, R.370
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.256, B:R.370
- Water bridges: B:R.256
EDO.14: 6 residues within 4Å:- Chain B: N.132, L.135, E.136, R.142, K.143, I.144
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.136, B:K.143, B:I.144
- Water bridges: B:R.142
EDO.15: 5 residues within 4Å:- Chain B: A.89, E.93, D.123, G.126, S.127
1 PLIP interactions:1 interactions with chain B- Water bridges: B:E.93
EDO.17: 7 residues within 4Å:- Chain A: R.276
- Chain C: F.22, N.31, V.35, L.57, F.58, D.61
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.276
- Water bridges: A:D.278
EDO.25: 7 residues within 4Å:- Chain E: H.177, G.178, K.179, G.180, A.243, D.244, N.247
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:D.244, E:N.247
EDO.26: 6 residues within 4Å:- Chain E: R.256, L.276, V.277, N.278, P.369, R.370
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:R.256, E:R.370
- Water bridges: E:R.256
EDO.27: 6 residues within 4Å:- Chain E: N.132, L.135, E.136, R.142, K.143, I.144
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.143, E:I.144
- Water bridges: E:R.142
EDO.28: 5 residues within 4Å:- Chain E: E.164, K.167, S.168, K.171, L.265
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:E.164
- Water bridges: E:K.167
EDO.30: 8 residues within 4Å:- Chain D: R.276
- Chain F: W.19, F.22, N.31, V.35, L.57, F.58, D.61
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain F- Hydrogen bonds: D:R.276, F:D.61
- Water bridges: D:D.278
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.8: 3 residues within 4Å:- Chain A: V.107, V.108
- Ligands: EDO.6
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:V.107
TRS.9: 5 residues within 4Å:- Chain A: F.92, Y.96, M.126, D.128
- Chain B: W.391
5 PLIP interactions:1 interactions with chain B, 4 interactions with chain A- Water bridges: B:E.394, A:Y.96, A:Y.96, A:Y.96, A:D.128
TRS.23: 4 residues within 4Å:- Chain D: F.92, Y.96, M.126
- Chain E: W.391
2 PLIP interactions:2 interactions with chain D- Water bridges: D:Y.96, D:Y.96
- 2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)
CLF.10: 19 residues within 4Å:- Chain A: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170
- Chain B: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153
9 PLIP interactions:4 interactions with chain B, 5 interactions with chain A,- Metal complexes: B:C.31, B:C.56, B:C.56, B:C.115, A:C.49, A:C.75, A:C.75, A:C.138
- Salt bridges: A:D.78
CLF.24: 19 residues within 4Å:- Chain D: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170
- Chain E: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153
9 PLIP interactions:5 interactions with chain D, 4 interactions with chain E,- Salt bridges: D:D.78
- Metal complexes: D:C.49, D:C.75, D:C.75, D:C.138, E:C.31, E:C.56, E:C.56, E:C.115
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.11: 2 residues within 4Å:- Chain B: E.70
- Chain E: D.314
6 PLIP interactions:1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: E:D.314, B:E.70, H2O.23, H2O.30, H2O.72, H2O.83
MG.12: 2 residues within 4Å:- Chain B: D.314
- Chain E: E.70
6 PLIP interactions:1 interactions with chain B, 1 interactions with chain E, 4 Ligand-Water interactions- Metal complexes: B:D.314, E:E.70, H2O.24, H2O.34, H2O.71, H2O.79
MG.16: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.29: 1 residues within 4Å:- Chain F: E.14
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rohde, M. et al., Two ligand-binding sites in CO-reducing V nitrogenase reveal a general mechanistic principle. Sci Adv (2021)
- Release Date
- 2021-06-09
- Peptides
- Nitrogenase vanadium-iron protein alpha chain: AD
Nitrogenase vanadium-iron protein beta chain: BE
Nitrogenase vanadium-iron protein delta chain: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.05 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x D6N: FeV(Non-covalent)
- 2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)
- 2 x BCT: BICARBONATE ION(Non-functional Binders)
- 4 x CMO: CARBON MONOXIDE(Non-functional Binders)
- 11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rohde, M. et al., Two ligand-binding sites in CO-reducing V nitrogenase reveal a general mechanistic principle. Sci Adv (2021)
- Release Date
- 2021-06-09
- Peptides
- Nitrogenase vanadium-iron protein alpha chain: AD
Nitrogenase vanadium-iron protein beta chain: BE
Nitrogenase vanadium-iron protein delta chain: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F