Research workbench
S-adenosylmethionine synthetase cocrystallized with CTP
Analyse S-adenosylmethionine synthetase cocrystallized with CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LO2
- Type
- protein
- Length
- 1,503 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
- POP, MG, K, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 381 | 32% helix, 25% strand | V0ZE41 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 372 | 33% helix, 26% strand | V0ZE41 |
| C | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 375 | 33% helix, 26% strand | V0ZE41 |
| D | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 375 | 34% helix, 26% strand | V0ZE41 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- K · Potassium ion · metal · 3 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, D, B, C
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.83 | 0.94 | 33 | empty |
| 2 | 252 | 0.82 | 0.94 | 29 | empty |
| 3 | 754 | 0.73 | 0.79 | 81 | MG, PO4, POP, K, EDO |
| 4 | 762 | 0.73 | 0.79 | 77 | MG, PO4, K, POP |
| 5 | 638 | 0.72 | 0.80 | 73 | MG, K, POP, PO4 |
Interfaces
6 interfaces between chains.
- C–D · 2257 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2210 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 528 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7LO2 · S-adenosylmethionine synthetase cocrystallized with CTP · 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 V0ZE41
- Elsewhere: RCSB PDB 7LO2 · PDBe 7LO2 · UniProt V0ZE41
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