MolNFT v1 · #147464 · protein
Crystal structure of mycobacterium tuberculosis ICL2 in the apo form
6EDW · Isocitrate lyase 2: “Crystal structure of mycobacterium tuberculosis ICL2 in the apo form”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.90). MolNFT v1 #147464 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6EDW
- Type
- protein
- Length
- 2,953 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase 2
- EC
- 4.1.3.1
- UniProt
- Q8VJU4
- Ligands
- MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 742 | 50% helix, 14% strand | Q8VJU4 |
| B | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 746 | 51% helix, 14% strand | Q8VJU4 |
| C | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 724 | 51% helix, 14% strand | Q8VJU4 |
| D | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 741 | 50% helix, 14% strand | Q8VJU4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.90 | 0.93 | 97 | empty |
| 2 | 917 | 0.90 | 0.93 | 103 | empty |
| 3 | 410 | 0.88 | 0.96 | 82 | empty |
| 4 | 383 | 0.86 | 0.95 | 72 | empty |
| 5 | 646 | 0.86 | 0.90 | 70 | empty |
Interfaces
6 interfaces between chains.
- B–D · 6406 Ų buried · 74 hydrogen bonds · protein-protein
- A–C · 6279 Ų buried · 81 hydrogen bonds · protein-protein
- B–C · 3432 Ų buried · 59 hydrogen bonds · protein-protein
- A–D · 3415 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 2499 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
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 Q8VJU4
- Elsewhere: RCSB PDB 6EDW · PDBe 6EDW · UniProt Q8VJU4
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