Research workbench
A high magnesium structure of the isochorismate synthase, entc
Analyse A high magnesium structure of the isochorismate synthase, entc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JY4
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isochorismate synthase entc
- EC
- 5.4.4.2
- UniProt
- P0AEJ3
- Ligands
- ISC, MG
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isochorismate synthase entc (EC 5.4.4.2) | protein | 375 | 31% helix, 32% strand | P0AEJ3 |
| B | Isochorismate synthase entc (EC 5.4.4.2) | protein | 374 | 31% helix, 32% strand | P0AEJ3 |
Ligands and binding sites
- ISC · (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.79 | 0.80 | 87 | empty |
| 2 | 62 | 0.73 | 0.98 | 21 | ISC |
| 3 | 60 | 0.73 | 0.98 | 22 | ISC |
| 4 | 245 | 0.54 | 0.77 | 38 | empty |
| 5 | 263 | 0.54 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5JY4 · A high magnesium structure of the isochorismate synthase, EntC · the same entry in another collection · chain A against A, TM-score 1.00
- P0AEJ3 · AlphaFold monomer V2.0 prediction for isochorismate synthase entc (P0AEJ3) · 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 P0AEJ3
- Elsewhere: RCSB PDB 5JY4 · PDBe 5JY4 · UniProt P0AEJ3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.