Research workbench
Crystal structure of 2-vinyl glyoxylate modified isocitrate lyase from mycobacterium tuberculosis
Analyse Crystal structure of 2-vinyl glyoxylate modified isocitrate lyase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DQL
- Type
- protein
- Length
- 1,708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase 1
- EC
- 4.1.3.1, 4.1.3.30
- UniProt
- H8EVV4
- Ligands
- VGX, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate lyase 1 (EC 4.1.3.1, 4.1.3.30) | protein | 427 | 50% helix, 12% strand | H8EVV4 |
Ligands and binding sites
- VGX · 4-hydroxy-2-oxobutanoic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.89 | 0.92 | 115 | empty |
| 2 | 482 | 0.87 | 0.94 | 99 | empty |
| 3 | 406 | 0.86 | 0.94 | 92 | empty |
| 4 | 481 | 0.85 | 0.92 | 75 | empty |
| 5 | 276 | 0.80 | 0.92 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5044 Ų buried · 93 hydrogen bonds · protein-protein
- C–D · 5034 Ų buried · 83 hydrogen bonds · protein-protein
- A–D · 2299 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2236 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1085 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5DQL · Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium… · the same entry in another collection · chain D against D, TM-score 1.00
- H8EVV4 · AlphaFold monomer V2.0 prediction for isocitrate lyase 1 (H8EVV4) · a predicted model of the same protein · chain C 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 H8EVV4
- Elsewhere: RCSB PDB 5DQL · PDBe 5DQL · UniProt H8EVV4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.