Research workbench
Crystal structure of 3-bromopyruvate modified isocitrate lyase (icl) from mycobacterium tuberculosis
Analyse Crystal structure of 3-bromopyruvate modified isocitrate lyase (icl) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F8M
- 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
- P0A5H3
- Ligands
- PYR, MG
- Pockets
- 20 · best druggability 0.90
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 (EC 4.1.3.1) | protein | 427 | 50% helix, 12% strand | P0A5H3 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.90 | 0.95 | 138 | empty |
| 2 | 570 | 0.88 | 0.94 | 113 | empty |
| 3 | 300 | 0.83 | 0.94 | 66 | empty |
| 4 | 302 | 0.80 | 0.92 | 32 | empty |
| 5 | 212 | 0.78 | 0.92 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5060 Ų buried · 93 hydrogen bonds · protein-protein
- C–D · 5045 Ų buried · 91 hydrogen bonds · protein-protein
- B–C · 2321 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2308 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1054 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1F8M · Crystal structure of 3-bromopyruvate modified isocitrate lyase (icl) 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 P0A5H3
- Elsewhere: RCSB PDB 1F8M · PDBe 1F8M · UniProt P0A5H3
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