MolNFT v1 · #146163 · protein
Protein 60 with aldehyde deformylating oxidase activity from kitasatospora setae
6D9F · Putative vlmb homolog: “Protein 60 with aldehyde deformylating oxidase activity from kitasatospora setae”. X-ray diffraction, 2 ligands (FE, SO4), 9 pockets (best druggability 0.82). MolNFT v1 #146163 on GenesisL1: 3D structure…
- PDB
- 6D9F
- Type
- protein
- Length
- 643 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative vlmb homolog
- UniProt
- E4N6B3
- Ligands
- FE, SO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative vlmb homolog | protein | 321 | 74% helix, 2% strand | E4N6B3 |
| B | Putative vlmb homolog | protein | 322 | 73% helix, 2% strand | E4N6B3 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.82 | 0.89 | 72 | empty |
| 2 | 442 | 0.81 | 0.89 | 67 | empty |
| 3 | 123 | 0.43 | 0.77 | 18 | EDO |
| 4 | 91 | 0.38 | 0.76 | 14 | empty |
| 5 | 85 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1458 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6D9F · Protein 60 with aldehyde deformylating oxidase activity from Kitasatospora setae · 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 E4N6B3
- Elsewhere: RCSB PDB 6D9F · PDBe 6D9F · UniProt E4N6B3
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