Research workbench
Human S-adenosylmethionine synthetase co-crystallized with uppnhp and met
Analyse Human S-adenosylmethionine synthetase co-crystallized with uppnhp and met in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WKB
- Type
- protein
- Length
- 761 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase isoform type-2
- EC
- 2.5.1.6
- UniProt
- P31153
- Ligands
- U4P, MED, MET
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 381 | 31% helix, 26% strand | P31153 |
| B | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 380 | 33% helix, 25% strand | P31153 |
Ligands and binding sites
- U4P · 5'-deoxyuridine · ligand · 2 copies · chains A, B
- MED · D-methionine · ligand · chains A, B
- MET · Methionine · ligand · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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 | 735 | 0.84 | 0.87 | 75 | U4P, MET |
| 2 | 268 | 0.84 | 0.95 | 45 | MED, U4P |
| 3 | 403 | 0.73 | 0.83 | 37 | empty |
| 4 | 56 | 0.37 | 0.79 | 12 | empty |
| 5 | 105 | 0.37 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2810 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6WKB · Human S-adenosylmethionine synthetase co-crystallized with UppNHp and Met · the same entry in another collection · chain A against A, TM-score 1.00
- P31153 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase isoform type-2… · 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 P31153
- Elsewhere: RCSB PDB 6WKB · PDBe 6WKB · UniProt P31153
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