- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.06 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FE9: iron-guanylyl pyridinol cofactor(Non-covalent)
- 10 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 4 residues within 4Å:- Chain A: G.217, Y.218, A.219, S.220
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.218
- Water bridges: A:S.220
GOL.3: 1 residues within 4Å:- Chain A: F.239
1 PLIP interactions:1 interactions with chain A- Water bridges: A:Y.213
GOL.4: 4 residues within 4Å:- Chain A: E.216, G.217, Y.218, N.244
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Y.218
- Water bridges: A:Y.218, A:N.244, A:N.244
GOL.5: 7 residues within 4Å:- Chain A: A.29, N.30, G.33, I.34, P.35, K.82, M.85
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:A.29, A:N.30
- Water bridges: A:N.30, A:K.82
GOL.6: 8 residues within 4Å:- Chain A: L.294, E.295, R.298
- Chain B: T.291, L.294, E.295, R.298
- Ligands: GOL.18
7 PLIP interactions:4 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:E.295, A:E.295, A:R.298, B:E.295, B:R.298
- Water bridges: A:R.298, B:R.298
GOL.14: 4 residues within 4Å:- Chain B: G.217, Y.218, A.219, S.220
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Y.218
- Water bridges: B:S.220
GOL.15: 1 residues within 4Å:- Chain B: F.239
No protein-ligand interaction detected (PLIP)GOL.16: 4 residues within 4Å:- Chain B: E.216, G.217, Y.218, N.244
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.218
- Water bridges: B:N.244, B:N.244
GOL.17: 7 residues within 4Å:- Chain B: A.29, N.30, G.33, I.34, P.35, K.82, M.85
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:A.29, B:N.30
- Water bridges: B:N.30, B:K.82
GOL.18: 8 residues within 4Å:- Chain A: T.291, L.294, E.295, R.298
- Chain B: L.294, E.295, R.298
- Ligands: GOL.6
7 PLIP interactions:4 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:E.295, A:E.295, A:R.298, B:E.295, B:R.298
- Water bridges: A:R.298, B:R.298
- 4 x NA: SODIUM ION(Non-functional Binders)
NA.7: 5 residues within 4Å:- Chain A: L.50, L.51, V.54, D.55, I.57
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:V.54, A:I.57, A:I.57
NA.8: 5 residues within 4Å:- Chain A: I.34, H.52, K.126, V.127, G.128
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.126
NA.19: 5 residues within 4Å:- Chain B: L.50, L.51, V.54, D.55, I.57
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:V.54, B:I.57, B:I.57
NA.20: 5 residues within 4Å:- Chain B: I.34, H.52, K.126, V.127, G.128
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:V.127
- 6 x SCN: THIOCYANATE ION(Non-functional Binders)
SCN.9: 5 residues within 4Å:- Chain A: M.284
- Chain B: G.152, G.153, I.178, K.182
No protein-ligand interaction detected (PLIP)SCN.10: 5 residues within 4Å:- Chain A: D.280, F.281
- Chain B: K.151, G.152, G.153
1 PLIP interactions:1 interactions with chain A- Water bridges: A:M.284
SCN.11: 3 residues within 4Å:- Chain A: I.274, G.324, P.325
No protein-ligand interaction detected (PLIP)SCN.21: 5 residues within 4Å:- Chain A: G.152, G.153, I.178, K.182
- Chain B: M.284
No protein-ligand interaction detected (PLIP)SCN.22: 5 residues within 4Å:- Chain A: K.151, G.152, G.153
- Chain B: D.280, F.281
1 PLIP interactions:1 interactions with chain B- Water bridges: B:M.284
SCN.23: 3 residues within 4Å:- Chain B: I.274, G.324, P.325
No protein-ligand interaction detected (PLIP)- 2 x E4M: 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol(Non-covalent)
E4M.12: 20 residues within 4Å:- Chain A: S.13, H.14, C.17, K.113, P.114, P.150, K.151, C.176, G.203, C.250, D.251, M.252, S.254
- Chain B: A.277, P.278, F.281, T.317, S.320, M.321
- Ligands: FE9.1
15 PLIP interactions:9 interactions with chain A, 6 interactions with chain B- Hydrogen bonds: A:P.114, A:K.151, A:C.250, A:M.252, A:S.254, B:T.317, B:S.320
- Water bridges: A:K.151, A:K.151, A:K.151, B:G.276, B:G.276
- Salt bridges: A:K.151
- Hydrophobic interactions: B:A.277, B:F.281
E4M.24: 20 residues within 4Å:- Chain A: A.277, P.278, F.281, T.317, S.320, M.321
- Chain B: S.13, H.14, C.17, K.113, P.114, P.150, K.151, C.176, G.203, C.250, D.251, M.252, S.254
- Ligands: FE9.13
15 PLIP interactions:6 interactions with chain A, 9 interactions with chain B- Hydrophobic interactions: A:A.277, A:F.281
- Hydrogen bonds: A:T.317, A:S.320, B:P.114, B:K.151, B:C.250, B:M.252, B:S.254
- Water bridges: A:G.276, A:G.276, B:K.151, B:K.151, B:K.151
- Salt bridges: B:K.151
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, G. et al., The atomic-resolution crystal structure of activated [Fe]-hydrogenase. Nat Catal (2019)
- Release Date
- 2019-08-28
- Peptides
- 5,10-methenyltetrahydromethanopterin hydrogenase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.06 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FE9: iron-guanylyl pyridinol cofactor(Non-covalent)
- 10 x GOL: GLYCEROL(Non-functional Binders)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 6 x SCN: THIOCYANATE ION(Non-functional Binders)
- 2 x E4M: 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, G. et al., The atomic-resolution crystal structure of activated [Fe]-hydrogenase. Nat Catal (2019)
- Release Date
- 2019-08-28
- Peptides
- 5,10-methenyltetrahydromethanopterin hydrogenase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A