MolNFT v1 · #157400 · protein
The crystal structure of a rhodanese-like family protein from francisella tularensis subsp. tularensis schu S4
6MXV: “The crystal structure of a rhodanese-like family protein from francisella tularensis subsp. tularensis schu S4”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.64). MolNFT v1 #157400 on GenesisL1: 3D structure…
- PDB
- 6MXV
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodanese-like family protein
- UniProt
- Q5NFU2
- Ligands
- MG
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodanese-like family protein | protein | 250 | 44% helix, 16% strand | Q5NFU2 |
| B | Rhodanese-like family protein | protein | 251 | 43% helix, 16% strand | Q5NFU2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
- 12P · Dodecaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.64 | 0.87 | 21 | MG |
| 2 | 139 | 0.64 | 0.86 | 23 | MG |
| 3 | 331 | 0.56 | 0.75 | 44 | EDO, PG4, PEG |
| 4 | 183 | 0.48 | 0.76 | 27 | PEG |
| 5 | 69 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2865 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 6MXV · The crystal structure of a rhodanese-like family protein from Francisella tularensis… · 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 Q5NFU2
- Elsewhere: RCSB PDB 6MXV · PDBe 6MXV · UniProt Q5NFU2
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