MolNFT v1 · #77983 · protein
Crystal structure of S-adenosylmethionine synthetase from mycobacterium marinum
3RV2 · S-adenosylmethionine synthase: “Crystal structure of S-adenosylmethionine synthetase from mycobacterium marinum”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.76). MolNFT v1 #77983 on GenesisL1: 3D structure…
- PDB
- 3RV2
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- B2HP50
- Ligands
- CA
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 373 | 34% helix, 27% strand | B2HP50 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.76 | 0.81 | 70 | CA |
| 2 | 508 | 0.74 | 0.82 | 35 | empty |
| 3 | 653 | 0.72 | 0.79 | 71 | CA, GOL |
| 4 | 69 | 0.38 | 0.78 | 16 | empty |
| 5 | 69 | 0.37 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2191 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3RV2 · Crystal structure of S-adenosylmethionine synthetase from Mycobacterium marinum · the same entry in another collection · chain A against A, TM-score 1.00
- B2HP50 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (B2HP50) · a predicted model of the same protein · chain A 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 B2HP50
- Elsewhere: RCSB PDB 3RV2 · PDBe 3RV2 · UniProt B2HP50
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