MolNFT v1 · #181974 · protein
Crystal structure of S-adenosylmethionine-dependent methyltransferase umaa from mycobacterium tuberculosis in complex with compound 8918
7MCJ: “Crystal structure of S-adenosylmethionine-dependent methyltransferase umaa from mycobacterium tuberculosis in…”. X-ray diffraction, 4 ligands (FD7, MG, NO3), 4 pockets (best druggability 0.73). MolNFT v1 #181974 on GenesisL1: 3D…
- PDB
- 7MCJ
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine-dependent methyltransferase umaa
- EC
- 2.1.1.-
- UniProt
- Q6MX39
- Ligands
- FD7, MG, NO3, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine-dependent methyltransferase umaa (EC 2.1.1.-) | protein | 276 | 49% helix, 17% strand | Q6MX39 |
| B | S-adenosylmethionine-dependent methyltransferase umaa (EC 2.1.1.-) | protein | 274 | 50% helix, 17% strand | Q6MX39 |
Ligands and binding sites
- FD7 · N-(2,6-diethylphenyl)-N'-(N-ethylcarbamimidoyl)urea · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.73 | 0.79 | 59 | FD7, EDO |
| 2 | 672 | 0.72 | 0.78 | 61 | FD7, NO3 |
| 3 | 246 | 0.69 | 0.85 | 30 | empty |
| 4 | 589 | 0.67 | 0.77 | 75 | EDO |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7MCJ · Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6MX39 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine-dependent methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q6MX39
- Elsewhere: RCSB PDB 7MCJ · PDBe 7MCJ · UniProt Q6MX39
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