MolNFT v1 · #147466 · protein
Crystal structure of mycobacterium tuberculosis ICL2 in complex with acetyl-CoA, form I
6EDZ · Isocitrate lyase 2: “Crystal structure of mycobacterium tuberculosis ICL2 in complex with acetyl-CoA, form I”. X-ray diffraction, 1 ligand (ACO), 20 pockets (best druggability 0.90). MolNFT v1 #147466 on GenesisL1: 3D structure…
- PDB
- 6EDZ
- Type
- protein
- Length
- 2,919 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
- ACO
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 733 | 51% helix, 15% strand | Q8VJU4 |
| B | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 730 | 52% helix, 15% strand | Q8VJU4 |
| C | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 723 | 52% helix, 14% strand | Q8VJU4 |
| D | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 733 | 51% helix, 15% strand | Q8VJU4 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 4 copies · chains A, C, B, 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 | 982 | 0.90 | 0.93 | 104 | empty |
| 2 | 977 | 0.90 | 0.92 | 102 | empty |
| 3 | 895 | 0.86 | 0.88 | 121 | empty |
| 4 | 649 | 0.86 | 0.90 | 72 | empty |
| 5 | 1020 | 0.86 | 0.86 | 91 | empty |
Interfaces
6 interfaces between chains.
- B–D · 7196 Ų buried · 93 hydrogen bonds · protein-protein
- A–C · 7127 Ų buried · 91 hydrogen bonds · protein-protein
- A–D · 2464 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2422 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2408 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6EDZ · Crystal structure of Mycobacterium tuberculosis ICL2 in complex with acetyl-CoA, form I · the same entry in another collection · chain D against D, TM-score 1.00
- Q8VJU4 · AlphaFold monomer V2.0 prediction for isocitrate lyase 2 (Q8VJU4) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 6EDZ · PDBe 6EDZ · UniProt Q8VJU4
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