MolNFT v1 · #147468 · protein
Crystal structure of mycobacterium tuberculosis ICL2 in complex with acetyl-CoA
6EE1 · Isocitrate lyase 2: “Crystal structure of mycobacterium tuberculosis ICL2 in complex with acetyl-CoA”. X-ray diffraction, 2 ligands (ACO, MG), 20 pockets (best druggability 0.90). MolNFT v1 #147468 on GenesisL1: 3D structure…
- PDB
- 6EE1
- Type
- protein
- Length
- 2,900 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, MG
- 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 | 719 | 52% helix, 14% strand | Q8VJU4 |
| B | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 729 | 52% helix, 14% strand | Q8VJU4 |
| C | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 722 | 52% helix, 14% strand | Q8VJU4 |
| D | Isocitrate lyase 2 (EC 4.1.3.1) | protein | 730 | 52% helix, 15% strand | Q8VJU4 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 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 | 827 | 0.90 | 0.94 | 98 | empty |
| 2 | 992 | 0.90 | 0.92 | 106 | empty |
| 3 | 1039 | 0.85 | 0.86 | 92 | empty |
| 4 | 1008 | 0.84 | 0.85 | 85 | empty |
| 5 | 715 | 0.84 | 0.88 | 110 | empty |
Interfaces
6 interfaces between chains.
- B–D · 6436 Ų buried · 73 hydrogen bonds · protein-protein
- A–C · 6363 Ų buried · 78 hydrogen bonds · protein-protein
- C–D · 2505 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2411 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 2407 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 6EE1 · Crystal structure of Mycobacterium tuberculosis ICL2 in complex with acetyl-CoA · 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 6EE1 · PDBe 6EE1 · UniProt Q8VJU4
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