MolNFT v1 · #118645 · protein
RV2258C-unbound
5F8C · Methyltransferase: “RV2258C-unbound”. X-ray diffraction, 7 pockets (best druggability 0.81). MolNFT v1 #118645 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F8C
- Type
- protein
- Length
- 1,071 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase
- UniProt
- O53532
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methyltransferase | protein | 354 | 52% helix, 15% strand | O53532 |
| B | Methyltransferase | protein | 363 | 50% helix, 15% strand | O53532 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains C
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 | 925 | 0.81 | 0.83 | 77 | empty |
| 2 | 1057 | 0.81 | 0.82 | 90 | GOL |
| 3 | 852 | 0.80 | 0.83 | 90 | empty |
| 4 | 233 | 0.52 | 0.76 | 41 | empty |
| 5 | 132 | 0.46 | 0.77 | 23 | empty |
Interfaces
2 interfaces between chains.
- B–C · 3849 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 105 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 5F8C · PDBe 5F8C · UniProt O53532
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