MolNFT v1 · #118647 · protein
RV2258C-SFG
5F8F · Methyltransferase: “RV2258C-SFG”. X-ray diffraction, 1 ligand (SFG), 7 pockets (best druggability 0.81). MolNFT v1 #118647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F8F
- Type
- protein
- Length
- 1,068 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase
- UniProt
- O53532
- Ligands
- SFG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase | protein | 353 | 54% helix, 17% strand | O53532 |
| B | Methyltransferase | protein | 361 | 51% helix, 16% strand | O53532 |
| C | Methyltransferase | protein | 354 | 52% helix, 15% strand | O53532 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A
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 | 770 | 0.81 | 0.84 | 89 | SFG |
| 2 | 836 | 0.81 | 0.84 | 70 | SFG |
| 3 | 1041 | 0.81 | 0.82 | 101 | SFG, GOL |
| 4 | 232 | 0.53 | 0.76 | 41 | empty |
| 5 | 135 | 0.45 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3860 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
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 O53532
- Elsewhere: RCSB PDB 5F8F · PDBe 5F8F · UniProt O53532
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