Research workbench
Crystal structure of a S-adenosylmethionine synthase from neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, pyrophosphate, phosphate, and magnesium
Analyse Crystal structure of a S-adenosylmethionine synthase from neisseria gonorrhoeae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T8S
- Type
- protein
- Length
- 764 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
- Q5FAC0
- Ligands
- AMP, POP, SAM, 3PO, MG, PO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 388 | 35% helix, 23% strand | Q5FAC0 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 376 | 34% helix, 24% strand | Q5FAC0 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, B
- POP · Pyrophosphate 2- · ligand · chains A, B
- SAM · S-adenosylmethionine · ligand · chains A, B
- 3PO · Triphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 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 | 268 | 0.83 | 0.95 | 53 | MG, SAM, 3PO |
| 2 | 748 | 0.74 | 0.79 | 75 | empty |
| 3 | 375 | 0.69 | 0.82 | 46 | AMP, MG, POP, PO4 |
| 4 | 71 | 0.39 | 0.79 | 15 | empty |
| 5 | 112 | 0.36 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2675 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 5T8S · Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5FAC0 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q5FAC0) · a predicted model of the same protein · 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 Q5FAC0
- Elsewhere: RCSB PDB 5T8S · PDBe 5T8S · UniProt Q5FAC0
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