Research workbench
S-adenosylmethionine synthetase from lactobacillus plantarum complexed with amppnp, methionine and SAM
Analyse S-adenosylmethionine synthetase from lactobacillus plantarum complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R3B
- Type
- protein
- Length
- 2,936 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- A0A0G9F5E5
- Ligands
- PPK, ANP, PHE, SAM, MG, K
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 364 | 32% helix, 23% strand | A0A0G9F5E5 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 362 | 33% helix, 23% strand | A0A0G9F5E5 |
| C | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 371 | 31% helix, 23% strand | A0A0G9F5E5 |
| D | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 369 | 32% helix, 24% strand | A0A0G9F5E5 |
| E | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 371 | 32% helix, 23% strand | A0A0G9F5E5 |
| F | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 369 | 32% helix, 23% strand | A0A0G9F5E5 |
| G | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 366 | 33% helix, 23% strand | A0A0G9F5E5 |
| H | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 364 | 32% helix, 23% strand | A0A0G9F5E5 |
Ligands and binding sites
- PPK · (diphosphono)aminophosphonic acid · ligand · 4 copies · chains A, B, G, H
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains C, D, E, F
- PHE · Phenylalanine · ligand · 2 copies · chains A, H
- SAM · S-adenosylmethionine · ligand · 2 copies · chains G, H
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 5 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.78 | 0.94 | 26 | empty |
| 2 | 334 | 0.77 | 0.87 | 28 | empty |
| 3 | 826 | 0.76 | 0.80 | 65 | empty |
| 4 | 837 | 0.75 | 0.79 | 67 | empty |
| 5 | 688 | 0.75 | 0.81 | 74 | MG, SAM, PPK, K |
Interfaces
17 interfaces between chains.
- A–B · 2245 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2133 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2111 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2044 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 532 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7R3B · S-adenosylmethionine synthetase from Lactobacillus plantarum complexed with AMPPNP… · the same entry in another collection · 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 A0A0G9F5E5
- Elsewhere: RCSB PDB 7R3B · PDBe 7R3B · UniProt A0A0G9F5E5
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