MolNFT v1 · #167177 · protein
Crystal structure of medicago truncatula S-adenosylmethionine synthase 3A (MTMAT3A)
6VCW: “Crystal structure of medicago truncatula S-adenosylmethionine synthase 3A (MTMAT3A)”. X-ray diffraction, 2 ligands (MG, CL), 5 pockets (best druggability 0.81). MolNFT v1 #167177 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6VCW
- Type
- protein
- Length
- 755 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
- G7L3W1
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 378 | 32% helix, 26% strand | G7L3W1 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 377 | 31% helix, 27% strand | G7L3W1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
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 | 1028 | 0.81 | 0.83 | 116 | MG, EDO |
| 2 | 639 | 0.78 | 0.83 | 58 | empty |
| 3 | 243 | 0.52 | 0.76 | 38 | empty |
| 4 | 129 | 0.43 | 0.76 | 28 | empty |
| 5 | 66 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1800 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6VCW · Crystal structure of Medicago truncatula S-adenosylmethionine Synthase 3A (MtMAT3A) · 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 G7L3W1
- Elsewhere: RCSB PDB 6VCW · PDBe 6VCW · UniProt G7L3W1
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