Research workbench
Native crystal structure of anaerobic F420H2-oxidase from methanothermococcus thermolithotrophicus at 1.8A resolution
Analyse Native crystal structure of anaerobic F420H2-oxidase from methanothermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZK8
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420H2 oxidase (fpra)
- UniProt
- A0A452CSW8
- Ligands
- FMN, FE, SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Coenzyme F420H2 oxidase (fpra) | protein | 410 | 39% helix, 25% strand | A0A452CSW8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, O
- FE · Fe (III) ion · metal · 4 copies · chains A, O
- SO4 · Sulfate ion · ion · 11 copies · chains A, O
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, O
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.80 | 0.82 | 79 | empty |
| 2 | 81 | 0.71 | 0.94 | 26 | empty |
| 3 | 70 | 0.68 | 0.93 | 22 | empty |
| 4 | 141 | 0.46 | 0.77 | 23 | empty |
| 5 | 129 | 0.44 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–O · 1598 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6ZK8 · Native crystal structure of anaerobic F420H2-Oxidase from Methanothermococcus… · 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 A0A452CSW8
- Elsewhere: RCSB PDB 6ZK8 · PDBe 6ZK8 · UniProt A0A452CSW8
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