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The F420-reducing [nife]-hydrogenase complex from methanothermobacter marburgensis, the first X-ray structure of a group 3 family member
Analyse The F420-reducing [nife]-hydrogenase complex from methanothermobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OMF
- Type
- protein
- Length
- 896 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F420-reducing hydrogenase, subunit gamma; F420-reducing hydrogenase, subunit alpha…
- EC
- 1.12.98.1
- UniProt
- D9PYF7, D9PYF9, D9PYF6
- Ligands
- SF4, DTZ, UNL, NFU, KEN, UNK, FAD, MG, CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | F420-reducing hydrogenase, subunit gamma (EC 1.12.98.1) | protein | 231 | 40% helix, 18% strand | D9PYF7 |
| A | F420-reducing hydrogenase, subunit alpha (EC 1.12.98.1) | protein | 385 | 49% helix, 17% strand | D9PYF9 |
| B | F420-reducing hydrogenase, subunit beta (EC 1.12.98.1) | protein | 280 | 40% helix, 24% strand | D9PYF6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains G, A, B
- DTZ · zinc(II)hydrogensulfide · ligand · chains G
- UNL · Unknown ligand · ligand · chains G
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · chains A
- KEN · N,N-dimethylmethanamine · ligand · chains B
- UNK · Unknown · ligand · chains B
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains G, A, B
- CL · Chloride ion · ion · chains G, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.81 | 0.88 | 58 | UNK, FAD |
| 2 | 78 | 0.56 | 0.86 | 19 | empty |
| 3 | 264 | 0.54 | 0.76 | 36 | KEN |
| 4 | 86 | 0.52 | 0.84 | 25 | empty |
| 5 | 171 | 0.51 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- G–A · 2417 Ų buried · 40 hydrogen bonds · protein-protein
- G–B · 2137 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4OMF · The F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt D9PYF7
- Every structure of UniProt D9PYF9
- Every structure of UniProt D9PYF6
- Elsewhere: RCSB PDB 4OMF · PDBe 4OMF · UniProt D9PYF7 · UniProt D9PYF9 · UniProt D9PYF6
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