MolNFT v1 · #153379 · protein
Crystal structure of cofactor-bound RV0187 from mtb
6JCL · Probable O-methyltransferase: “Crystal structure of cofactor-bound RV0187 from mtb”. X-ray diffraction, 3 ligands (SAH, SR, NA), 20 pockets (best druggability 0.84). MolNFT v1 #153379 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6JCL
- Type
- protein
- Length
- 1,734 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable O-methyltransferase
- UniProt
- O07431
- Ligands
- SAH, SR, NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable O-methyltransferase | protein | 218 | 49% helix, 22% strand | O07431 |
| B, E | Probable O-methyltransferase | protein | 217 | 47% helix, 22% strand | O07431 |
| C, F | Probable O-methyltransferase | protein | 216 | 49% helix, 22% strand | O07431 |
| D | Probable O-methyltransferase | protein | 215 | 48% helix, 23% strand | O07431 |
| G | Probable O-methyltransferase | protein | 219 | 48% helix, 22% strand | O07431 |
| H | Probable O-methyltransferase | protein | 216 | 50% helix, 22% strand | O07431 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 8 copies · chains A, B, C, D, G, H, E, F
- SR · Strontium ion · metal · 10 copies · chains A, C, B, E, D, H, G, F
- NA · Sodium ion · metal · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A, B, C, D, G, H, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.84 | 0.85 | 121 | SAH |
| 2 | 1065 | 0.84 | 0.85 | 125 | SAH |
| 3 | 1023 | 0.80 | 0.81 | 94 | SAH |
| 4 | 901 | 0.77 | 0.80 | 79 | SAH |
| 5 | 73 | 0.74 | 0.98 | 25 | MPD |
Interfaces
8 interfaces between chains.
- G–H · 1944 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1943 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1933 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1916 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1120 Ų buried · 26 hydrogen bonds · protein-protein
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 O07431
- Elsewhere: RCSB PDB 6JCL · PDBe 6JCL · UniProt O07431
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.