Research workbench
Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from methanocaldococcus jannaschii in complex with dmnb- SAM (4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine)
Analyse Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P8M
- Type
- protein
- Length
- 812 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
- Q58605
- Ligands
- 3PO, 6IH, MG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 404 | 36% helix, 28% strand | Q58605 |
| C | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 408 | 34% helix, 29% strand | Q58605 |
Ligands and binding sites
- 3PO · Triphosphate · ligand · 2 copies · chains A, C
- 6IH · 4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine · ligand · chains A, C
- MG · Magnesium ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.82 | 0.92 | 37 | empty |
| 2 | 721 | 0.82 | 0.86 | 71 | MG, 3PO, 6IH |
| 3 | 879 | 0.75 | 0.79 | 77 | 3PO, MG |
| 4 | 63 | 0.71 | 0.98 | 27 | empty |
| 5 | 352 | 0.61 | 0.77 | 51 | empty |
Interfaces
1 interface between chains.
- A–C · 2659 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 7P8M · Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58605 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q58605) · a predicted model of the same protein · chain C 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 Q58605
- Elsewhere: RCSB PDB 7P8M · PDBe 7P8M · UniProt Q58605
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