MolNFT v1 · #20486 · protein
S-adenosylmethionine synthetase complexed with SAM and ppnp
1RG9: “S-adenosylmethionine synthetase complexed with SAM and ppnp”. X-ray diffraction, 4 ligands (SAM, PPK, MG), 20 pockets (best druggability 0.84). MolNFT v1 #20486 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RG9
- Type
- protein
- Length
- 1,532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthetase
- EC
- 2.5.1.6
- UniProt
- P0A817
- Ligands
- SAM, PPK, MG, K
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | S-adenosylmethionine synthetase (EC 2.5.1.6) | protein | 383 | 33% helix, 25% strand | P0A817 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- PPK · (diphosphono)aminophosphonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.84 | 0.96 | 48 | K, MG, SAM, PPK |
| 2 | 312 | 0.84 | 0.94 | 50 | K, MG, SAM, PPK |
| 3 | 275 | 0.84 | 0.95 | 49 | MG, SAM, K, PPK |
| 4 | 267 | 0.83 | 0.95 | 48 | K, MG, SAM, PPK |
| 5 | 519 | 0.80 | 0.87 | 48 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2936 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 2856 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 488 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 486 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1RG9 · S-Adenosylmethionine synthetase complexed with SAM and PPNP · the same entry in another collection · chain D against D, TM-score 1.00
- P0A817 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (P0A817) · a predicted model of the same protein · chain C 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 P0A817
- Elsewhere: RCSB PDB 1RG9 · PDBe 1RG9 · UniProt P0A817
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