Research workbench
Crystal structure of MAT2A at 1.79 angstron resolution
Analyse Crystal structure of MAT2A at 1.79 angstron resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FWB
- Type
- protein
- Length
- 1,472 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
- NA, SO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 373 | 33% helix, 27% strand | P31153 |
| A | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 368 | 31% helix, 28% strand | P31153 |
| C | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 364 | 32% helix, 27% strand | P31153 |
| D | S-adenosylmethionine synthase isoform type-2 (EC 2.5.1.6) | protein | 367 | 31% helix, 28% strand | P31153 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 19 copies · chains B, D, A, C
- PG4 · Tetraethylene glycol · additive · 7 copies · chains B, C, D, A
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 680 | 0.75 | 0.81 | 77 | SO4 |
| 2 | 595 | 0.75 | 0.81 | 60 | SO4, PG4 |
| 3 | 533 | 0.74 | 0.82 | 48 | PG4 |
| 4 | 618 | 0.72 | 0.80 | 68 | SO4 |
| 5 | 517 | 0.71 | 0.81 | 62 | empty |
Interfaces
6 interfaces between chains.
- B–A · 2439 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2375 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 543 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 543 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6FWB · Crystal structure of Mat2A at 1.79 Angstron resolution · 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 6FWB · PDBe 6FWB · UniProt P31153
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