Research workbench
Electron cryo-microscopy of F420-reducing nife hydrogenase frh
Analyse Electron cryo-microscopy of F420-reducing nife hydrogenase frh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CI0
- Type
- protein
- Length
- 893 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F420-reducing hydrogenase, subunit alpha; F420-reducing hydrogenase, subunit gamma…
- EC
- 1.12.98.1
- UniProt
- D9PYF9, D9PYF7, D9PYF6
- Ligands
- SF4, FAD, FE, NI, FE2, ZN
- Pockets
- 9 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F420-reducing hydrogenase, subunit alpha (EC 1.12.98.1) | protein | 385 | 48% helix, 16% strand | D9PYF9 |
| B | F420-reducing hydrogenase, subunit gamma (EC 1.12.98.1) | protein | 228 | 39% helix, 14% strand | D9PYF7 |
| C | F420-reducing hydrogenase, subunit beta (EC 1.12.98.1) | protein | 280 | 39% helix, 20% strand | D9PYF6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C
- FAD · Flavin-adenine dinucleotide · ligand · chains C
- FE · Fe (III) ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- FE2 · Fe (II) ion · metal · chains A
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.81 | 0.86 | 62 | FAD |
| 2 | 263 | 0.72 | 0.85 | 45 | empty |
| 3 | 148 | 0.56 | 0.82 | 31 | empty |
| 4 | 184 | 0.51 | 0.77 | 36 | empty |
| 5 | 99 | 0.42 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2324 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2048 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4CI0 · Electron cryo-microscopy of F420-reducing NiFe hydrogenase Frh · 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 D9PYF9
- Every structure of UniProt D9PYF7
- Every structure of UniProt D9PYF6
- Elsewhere: RCSB PDB 4CI0 · PDBe 4CI0 · UniProt D9PYF9 · UniProt D9PYF7 · UniProt D9PYF6
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