MolNFT v1 · #167118 · protein
Covalent adduct of cis-2,3-epoxysuccinic acid with isocitrate lyase-1 from mycobacterium tuberculosis
6VB9: “Covalent adduct of cis-2,3-epoxysuccinic acid with isocitrate lyase-1 from mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (OXD, MG), 20 pockets (best druggability 0.87). MolNFT v1 #167118 on GenesisL1: 3D structure…
- PDB
- 6VB9
- Type
- protein
- Length
- 1,708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase
- EC
- 4.1.3.1
- UniProt
- A0A045H6H0
- Ligands
- OXD, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate lyase (EC 4.1.3.1) | protein | 427 | 49% helix, 12% strand | A0A045H6H0 |
Ligands and binding sites
- OXD · Oxalic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 9 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.87 | 0.92 | 92 | empty |
| 2 | 505 | 0.85 | 0.91 | 78 | empty |
| 3 | 357 | 0.85 | 0.94 | 70 | PEG |
| 4 | 436 | 0.83 | 0.91 | 85 | empty |
| 5 | 268 | 0.79 | 0.92 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5131 Ų buried · 95 hydrogen bonds · protein-protein
- C–D · 5070 Ų buried · 95 hydrogen bonds · protein-protein
- B–D · 2247 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 2175 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1051 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6VB9 · Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium… · the same entry in another collection · chain A 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 A0A045H6H0
- Elsewhere: RCSB PDB 6VB9 · PDBe 6VB9 · UniProt A0A045H6H0
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