MolNFT v1 · #164390 · protein
Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form)
6SW5 · S-adenosylmethionine synthase isoform type-1: “Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form)”. X-ray diffraction, 14 pockets (best druggability 0.81). MolNFT v1 #164390 on GenesisL1: 3D…
- PDB
- 6SW5
- Type
- protein
- Length
- 1,442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase isoform type-1
- EC
- 2.5.1.6
- UniProt
- Q00266
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase isoform type-1 (EC 2.5.1.6) | protein | 360 | 31% helix, 26% strand | Q00266 |
| B | S-adenosylmethionine synthase isoform type-1 (EC 2.5.1.6) | protein | 365 | 31% helix, 27% strand | Q00266 |
| C | S-adenosylmethionine synthase isoform type-1 (EC 2.5.1.6) | protein | 362 | 32% helix, 27% strand | Q00266 |
| D | S-adenosylmethionine synthase isoform type-1 (EC 2.5.1.6) | protein | 355 | 31% helix, 26% strand | Q00266 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.81 | 0.91 | 73 | empty |
| 2 | 618 | 0.80 | 0.86 | 78 | empty |
| 3 | 472 | 0.78 | 0.85 | 56 | PEG, EDO |
| 4 | 444 | 0.77 | 0.85 | 55 | EDO |
| 5 | 249 | 0.73 | 0.88 | 38 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1662 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1648 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 374 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6SW5 · Crystal structure of the human S-adenosylmethionine synthetase 1 (ligand-free form) · the same entry in another collection · chain D against D, TM-score 1.00
- Q00266 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase isoform type-1… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q00266
- Elsewhere: RCSB PDB 6SW5 · PDBe 6SW5 · UniProt Q00266
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