Research workbench
S-adenosyl methionine transferase cocrystallized with ATP
Analyse S-adenosyl methionine transferase cocrystallized with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LOO
- Type
- protein
- Length
- 1,512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- V0ZE41
- Ligands
- SAM, POP, MG, K, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 379 | 35% helix, 25% strand | V0ZE41 |
| B, Q | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 378 | 34% helix, 25% strand | V0ZE41 |
| R | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 377 | 33% helix, 25% strand | V0ZE41 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 6 copies · chains A, Q, B, R
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, Q, B, R
- MG · Magnesium ion · metal · 8 copies · chains A, B, R, Q
- K · Potassium ion · metal · 4 copies · chains A, Q
- PO4 · Phosphate ion · ion · 4 copies · chains A, Q, B, R
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, R, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.85 | 0.96 | 52 | POP, PO4, MG, K, SAM |
| 2 | 298 | 0.84 | 0.95 | 49 | POP, MG, SAM |
| 3 | 278 | 0.84 | 0.95 | 51 | MG, POP, SAM |
| 4 | 278 | 0.83 | 0.95 | 50 | MG, POP, PO4, K, SAM |
| 5 | 472 | 0.77 | 0.85 | 36 | EDO, SAM, PO4 |
Interfaces
6 interfaces between chains.
- B–R · 2938 Ų buried · 53 hydrogen bonds · protein-protein
- A–Q · 2934 Ų buried · 56 hydrogen bonds · protein-protein
- A–R · 497 Ų buried · 7 hydrogen bonds · protein-protein
- B–Q · 490 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7LOO · S-adenosyl methionine transferase cocrystallized with ATP · the same entry in another collection · chain B against B, 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 V0ZE41
- Elsewhere: RCSB PDB 7LOO · PDBe 7LOO · UniProt V0ZE41
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.