MolNFT v1 · #167180 · protein
Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 2 (ATMAT2)
6VCZ: “Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 2 (ATMAT2)”. X-ray diffraction, 2 ligands (MG, PO4), 5 pockets (best druggability 0.73). MolNFT v1 #167180 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6VCZ
- Type
- protein
- Length
- 758 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
- MG, PO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase 2 (EC 2.5.1.6) | protein | 378 | 30% helix, 27% strand | P17562 |
| B | S-adenosylmethionine synthase 2 (EC 2.5.1.6) | protein | 380 | 29% helix, 27% strand | P17562 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B
- PO4 · Phosphate ion · ion · 8 copies · chains A, B
- PGR · R-1,2-propanediol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains B
- MXE · 2-methoxyethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.73 | 0.80 | 63 | PGE |
| 2 | 548 | 0.72 | 0.80 | 66 | MG, PO4 |
| 3 | 563 | 0.71 | 0.80 | 66 | PO4, MG |
| 4 | 139 | 0.42 | 0.75 | 25 | empty |
| 5 | 120 | 0.42 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2548 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6VCZ · Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) · 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 A 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 6VCZ · PDBe 6VCZ · UniProt P17562
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