Research workbench
Crystal structure of MAT2A bound to the allosteric inhibitor pf- 02929366
Analyse Crystal structure of MAT2A bound to the allosteric inhibitor pf- 02929366 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UGH
- Type
- protein
- Length
- 1,468 residues
- Chains
- 4
- 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
- 8AJ
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 369 | 31% helix, 27% strand | P31153 |
| B | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 365 | 32% helix, 27% strand | P31153 |
| C | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 368 | 31% helix, 28% strand | P31153 |
| D | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 366 | 31% helix, 27% strand | P31153 |
Ligands and binding sites
- 8AJ · 2-(7-chloro-5-phenyl[1,2,4]triazolo[4,3-a]quinolin-1-yl)-N,N-dimethylethan-1-amine · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.78 | 0.86 | 53 | 8AJ |
| 2 | 585 | 0.76 | 0.83 | 62 | 8AJ |
| 3 | 635 | 0.75 | 0.81 | 71 | empty |
| 4 | 632 | 0.72 | 0.80 | 81 | empty |
| 5 | 463 | 0.68 | 0.79 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2313 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2299 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 436 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 256 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5UGH · Crystal structure of Mat2a bound to the allosteric inhibitor PF-02929366 · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.99
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 5UGH · PDBe 5UGH · UniProt P31153
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.