MolNFT v1 · #123326 · protein
Crystal structure of gtma in complex with S-adenosylmethionine
5JGL · UBIE/COQ5 family methyltransferase, putative: “Crystal structure of gtma in complex with S-adenosylmethionine”. X-ray diffraction, 2 ligands (SAM, NA), 6 pockets (best druggability 0.74). MolNFT v1 #123326 on GenesisL1: 3D…
- PDB
- 5JGL
- Type
- protein
- Length
- 541 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UBIE/COQ5 family methyltransferase, putative
- UniProt
- A0A0J5Q3C4
- Ligands
- SAM, NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UBIE/COQ5 family methyltransferase, putative | protein | 273 | 45% helix, 25% strand | A0A0J5Q3C4 |
| B | UBIE/COQ5 family methyltransferase, putative | protein | 268 | 47% helix, 25% strand | A0A0J5Q3C4 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, 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 | 755 | 0.74 | 0.79 | 60 | empty |
| 2 | 619 | 0.67 | 0.77 | 58 | empty |
| 3 | 365 | 0.60 | 0.76 | 53 | SAM, NA |
| 4 | 163 | 0.49 | 0.77 | 31 | SAM |
| 5 | 85 | 0.46 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 885 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5JGL · Crystal structure of GtmA in complex with S-Adenosylmethionine · 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 A0A0J5Q3C4
- Elsewhere: RCSB PDB 5JGL · PDBe 5JGL · UniProt A0A0J5Q3C4
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