MolNFT v1 · #171936 · protein
Aerobic crystal structure of F420H2-oxidase from methanothermococcus thermolithotrophicus at 1.8A resolution under 125 bars of krypton
6ZLF · Coenzyme F420H2 oxidase (fpra): “Aerobic crystal structure of F420H2-oxidase from methanothermococcus thermolithotrophicus at 1.8A resolution…”. X-ray diffraction, 4 ligands (FEO, FMN, KR), 20 pockets (best druggability 0.81).…
- PDB
- 6ZLF
- Type
- protein
- Length
- 3,267 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420H2 oxidase (fpra)
- UniProt
- A0A452CSW8
- Ligands
- FEO, FMN, KR, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme F420H2 oxidase (fpra) | protein | 409 | 39% helix, 25% strand | A0A452CSW8 |
| F, G, H, I, J, K | Coenzyme F420H2 oxidase (fpra) | protein | 408 | 38% helix, 25% strand | A0A452CSW8 |
| L | Coenzyme F420H2 oxidase (fpra) | protein | 410 | 39% helix, 25% strand | A0A452CSW8 |
Ligands and binding sites
- FEO · Mu-oxo-diiron · ligand · 8 copies · chains A, F, G, H, I, J, K, L
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, I, F, H, G, J, K, L
- KR · Krypton · ion · 48 copies · chains A, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 8 copies · chains A, F, G, H, I, J, K, L
- HEZ · Hexane-1,6-diol · additive · 22 copies · chains A, F, G, L, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.81 | 0.90 | 52 | FMN |
| 2 | 1003 | 0.81 | 0.82 | 79 | empty |
| 3 | 1007 | 0.80 | 0.81 | 80 | empty |
| 4 | 933 | 0.79 | 0.81 | 72 | empty |
| 5 | 912 | 0.79 | 0.81 | 74 | empty |
Interfaces
12 interfaces between chains.
- A–I · 2112 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 2101 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 2085 Ų buried · 18 hydrogen bonds · protein-protein
- G–J · 2078 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 1639 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6ZLF · Aerobic crystal structure of F420H2-Oxidase from Methanothermococcus thermolithotrophicus… · 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 6ZLF · PDBe 6ZLF · UniProt A0A452CSW8
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