Research workbench
Flavo di-iron protein H90D mutant from thermotoga maritima
Analyse Flavo di-iron protein H90D mutant from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V8S
- Type
- protein
- Length
- 795 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavoprotein
- UniProt
- Q9WZL4
- Ligands
- FEO, CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavoprotein | protein | 399 | 35% helix, 27% strand | Q9WZL4 |
| B | Flavoprotein | protein | 396 | 35% helix, 28% strand | Q9WZL4 |
Ligands and binding sites
- FEO · Mu-oxo-diiron · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.75 | 0.87 | 34 | CL |
| 2 | 169 | 0.63 | 0.84 | 24 | MRD |
| 3 | 356 | 0.63 | 0.78 | 42 | empty |
| 4 | 141 | 0.51 | 0.79 | 19 | MRD |
| 5 | 131 | 0.46 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2083 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5V8S · Flavo di-iron protein H90D mutant from Thermotoga maritima · 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 Q9WZL4
- Elsewhere: RCSB PDB 5V8S · PDBe 5V8S · UniProt Q9WZL4
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