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Cryo-EM structure of the F420-reducing nife-hydrogenase from a methanogenic archaeon with bound substrate
Analyse Cryo-EM structure of the F420-reducing nife-hydrogenase from a methanogenic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZFS
- Type
- protein
- Length
- 878 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, F42, FAD, FCO, NI, FE2
- Pockets
- 4 · best druggability 0.41
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F420-reducing hydrogenase, subunit alpha (EC 1.12.98.1) | protein | 385 | 0% helix, 0% strand | D9PYF9 |
| B | F420-reducing hydrogenase, subunit gamma (EC 1.12.98.1) | protein | 215 | 0% helix, 0% strand | D9PYF7 |
| C | F420-reducing hydrogenase, subunit beta (EC 1.12.98.1) | protein | 278 | 0% helix, 0% strand | D9PYF6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains B, C
- F42 · Coenzyme F420 · ligand · chains C
- FAD · Flavin-adenine dinucleotide · ligand · chains C
- FCO · Carbonmonoxide-(dicyano) iron · metal
- NI · Nickel (II) ion · metal · chains A
- FE2 · Fe (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.41 | 0.73 | 35 | empty |
| 2 | 123 | 0.39 | 0.72 | 29 | empty |
| 3 | 109 | 0.38 | 0.73 | 28 | FCO, NI |
| 4 | 57 | 0.30 | 0.73 | 23 | SF4 |
Interfaces
3 interfaces between chains.
- B–C · 237 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 191 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 covalent (flavinylation, covalent ligand).
Compared structures
- 3ZFS · Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with… · 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 3ZFS · PDBe 3ZFS · UniProt D9PYF9 · UniProt D9PYF7 · UniProt D9PYF6
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