Research workbench
Crystal structure of GH3.12 from arabidopsis thaliana in complex with ampcpp and salicylate
Analyse Crystal structure of GH3.12 from arabidopsis thaliana in complex with ampcpp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L39
- Type
- protein
- Length
- 1,083 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-substituted benzoates-glutamate ligase GH3.12
- EC
- 6.3.2.-
- UniProt
- Q9LYU4
- Ligands
- SAL, APC, MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-substituted benzoates-glutamate ligase GH3.12 (EC 6.3.2.-) | protein | 541 | 40% helix, 17% strand | Q9LYU4 |
| B | 4-substituted benzoates-glutamate ligase GH3.12 (EC 6.3.2.-) | protein | 542 | 39% helix, 17% strand | Q9LYU4 |
Ligands and binding sites
- SAL · 2-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.84 | 0.85 | 103 | SAL, APC |
| 2 | 1074 | 0.84 | 0.85 | 91 | MG, SAL, APC |
| 3 | 382 | 0.76 | 0.86 | 61 | empty |
| 4 | 676 | 0.73 | 0.80 | 59 | empty |
| 5 | 62 | 0.61 | 0.91 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1113 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4L39 · Crystal structure of GH3.12 from Arabidopsis thaliana in complex with AMPCPP and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LYU4 · AlphaFold monomer V2.0 prediction for 4-substituted benzoates- glutamate ligase GH3.12… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9LYU4
- Elsewhere: RCSB PDB 4L39 · PDBe 4L39 · UniProt Q9LYU4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.