- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.71 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 8 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x DTZ: zinc(II)hydrogensulfide(Non-covalent)
DTZ.4: 4 residues within 4Å:- Chain A: C.206, C.208
- Chain D: K.251
- Ligands: DTZ.19
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:C.206, A:C.208, H2O.7
DTZ.19: 4 residues within 4Å:- Chain A: K.251
- Chain D: C.206, C.208
- Ligands: DTZ.4
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:C.206, D:C.208, H2O.36
- 2 x UNL: UNKNOWN LIGAND
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.6: 3 residues within 4Å:- Chain A: A.148
- Chain B: E.233
- Chain F: Y.187
5 PLIP interactions:1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: B:E.233, A:A.148, H2O.3, H2O.11, H2O.12
MG.8: 3 residues within 4Å:- Chain B: E.44, A.347, H.386
6 PLIP interactions:3 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:E.44, B:A.347, B:H.386, H2O.22, H2O.22, H2O.22
MG.9: 1 residues within 4Å:- Chain B: E.296
No protein-ligand interaction detected (PLIP)MG.12: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.21: 3 residues within 4Å:- Chain C: Y.187
- Chain D: A.148
- Chain E: E.233
5 PLIP interactions:1 interactions with chain E, 1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: E:E.233, D:A.148, H2O.33, H2O.40, H2O.41
MG.23: 3 residues within 4Å:- Chain E: E.44, A.347, H.386
6 PLIP interactions:3 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:E.44, E:A.347, E:H.386, H2O.51, H2O.51, H2O.51
MG.24: 1 residues within 4Å:- Chain E: E.296
No protein-ligand interaction detected (PLIP)MG.27: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)
NFU.7: 12 residues within 4Å:- Chain B: C.63, C.66, H.70, A.326, P.327, R.328, D.331, V.349, P.350, T.351, C.380, C.383
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:R.328, B:R.328, B:T.351
- Metal complexes: B:C.63, B:C.66, B:C.66, B:C.380, B:C.383, B:C.383
NFU.22: 12 residues within 4Å:- Chain E: C.63, C.66, H.70, A.326, P.327, R.328, D.331, V.349, P.350, T.351, C.380, C.383
10 PLIP interactions:10 interactions with chain E- Hydrogen bonds: E:R.328, E:R.328, E:T.351, E:T.351
- Metal complexes: E:C.63, E:C.66, E:C.66, E:C.380, E:C.383, E:C.383
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x KEN: N,N-dimethylmethanamine(Non-covalent)
KEN.13: 4 residues within 4Å:- Chain C: R.110, Q.113, I.126, D.204
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.110
- Salt bridges: C:D.204
KEN.28: 4 residues within 4Å:- Chain F: R.110, Q.113, I.126, D.204
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:R.110
- Salt bridges: F:D.204
- 2 x UNK: UNKNOWN(Non-functional Binders)
UNK.14: 6 residues within 4Å:- Chain C: Y.76, C.134, M.135, E.136, I.163
- Ligands: FAD.15
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.163
- Hydrogen bonds: C:M.135, C:E.136
UNK.29: 6 residues within 4Å:- Chain F: Y.76, C.134, M.135, E.136, I.163
- Ligands: FAD.30
4 PLIP interactions:4 interactions with chain F- Hydrophobic interactions: F:I.163
- Hydrogen bonds: F:M.135, F:E.136, F:E.136
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
FAD.15: 31 residues within 4Å:- Chain C: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.132, Y.133, C.134, M.135, E.136, N.137, Y.198, G.208, S.209, V.210
- Ligands: UNK.14
32 PLIP interactions:32 interactions with chain C- Hydrophobic interactions: C:T.74, C:I.132, C:N.137
- Hydrogen bonds: C:Q.24, C:D.25, C:G.27, C:I.28, C:V.29, C:T.30, C:T.30, C:T.30, C:A.48, C:A.71, C:G.73, C:T.74, C:K.75, C:K.75, C:Y.76, C:Y.76, C:N.81, C:M.135, C:Y.198, C:S.209, C:V.210, C:S.217
- Water bridges: C:Q.24, C:T.30, C:S.79, C:N.137, C:S.209, C:S.209
- pi-Stacking: C:Y.76
FAD.30: 31 residues within 4Å:- Chain F: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.132, Y.133, C.134, M.135, E.136, N.137, Y.198, G.208, S.209, V.210
- Ligands: UNK.29
33 PLIP interactions:33 interactions with chain F- Hydrophobic interactions: F:T.74, F:I.132, F:N.137
- Hydrogen bonds: F:Q.24, F:D.25, F:D.25, F:G.27, F:I.28, F:V.29, F:T.30, F:T.30, F:A.48, F:A.71, F:G.73, F:T.74, F:T.74, F:K.75, F:K.75, F:Y.76, F:N.81, F:M.135, F:Y.198, F:Y.198, F:S.209, F:V.210, F:S.217
- Water bridges: F:Q.24, F:T.30, F:S.79, F:N.137, F:S.209, F:S.209
- pi-Stacking: F:Y.76
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vitt, S. et al., The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member. J.Mol.Biol. (2014)
- Release Date
- 2014-06-11
- Peptides
- F420-reducing hydrogenase, subunit gamma: AD
F420-reducing hydrogenase, subunit alpha: BE
F420-reducing hydrogenase, subunit beta: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GD
GB
AE
AC
BF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.71 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 8 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x DTZ: zinc(II)hydrogensulfide(Non-covalent)
- 2 x UNL: UNKNOWN LIGAND
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x KEN: N,N-dimethylmethanamine(Non-covalent)
- 2 x UNK: UNKNOWN(Non-functional Binders)
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vitt, S. et al., The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member. J.Mol.Biol. (2014)
- Release Date
- 2014-06-11
- Peptides
- F420-reducing hydrogenase, subunit gamma: AD
F420-reducing hydrogenase, subunit alpha: BE
F420-reducing hydrogenase, subunit beta: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GD
GB
AE
AC
BF
B