MolNFT v1 · #167183 · protein
Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 2 (ATMAT2) in complex with S-adenosylmethionine
6VD2: “Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 2 (ATMAT2) in complex with…”. X-ray diffraction, 4 ligands (SAM, MG, K), 7 pockets (best druggability 0.83). MolNFT v1 #167183 on GenesisL1: 3D structure…
- PDB
- 6VD2
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase 2
- EC
- 2.5.1.6
- UniProt
- P17562
- Ligands
- SAM, MG, K, PO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase 2 (EC 2.5.1.6) | protein | 394 | 32% helix, 25% strand | P17562 |
| B | S-adenosylmethionine synthase 2 (EC 2.5.1.6) | protein | 392 | 32% helix, 25% strand | P17562 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.83 | 0.95 | 47 | SAM, MG, K, PO4 |
| 2 | 253 | 0.83 | 0.95 | 42 | MG, SAM, K, PO4 |
| 3 | 616 | 0.72 | 0.79 | 62 | PE8 |
| 4 | 53 | 0.38 | 0.81 | 15 | MPO |
| 5 | 66 | 0.38 | 0.78 | 16 | MPO |
Interfaces
1 interface between chains.
- A–B · 3056 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6VD2 · Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P17562 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase 2 (P17562) · a predicted model of the same protein · chain B 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 P17562
- Elsewhere: RCSB PDB 6VD2 · PDBe 6VD2 · UniProt P17562
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