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Crystal structure of the isocitrate lyase from the A219C mutant of escherichia COLI
Analyse Crystal structure of the isocitrate lyase from the A219C mutant of escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IGW
- Type
- protein
- Length
- 1,628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase
- EC
- 4.1.3.1
- UniProt
- P0A9G6
- Ligands
- PYR, HG, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate lyase (EC 4.1.3.1) | protein | 396 | 51% helix, 13% strand | P0A9G6 |
| B | Isocitrate lyase (EC 4.1.3.1) | protein | 411 | 51% helix, 11% strand | P0A9G6 |
| C | Isocitrate lyase (EC 4.1.3.1) | protein | 416 | 51% helix, 12% strand | P0A9G6 |
| D | Isocitrate lyase (EC 4.1.3.1) | protein | 405 | 51% helix, 13% strand | P0A9G6 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- HG · Mercury (II) ion · metal · 21 copies · chains A, B, D, C
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.85 | 0.93 | 81 | empty |
| 2 | 431 | 0.85 | 0.92 | 80 | empty |
| 3 | 188 | 0.75 | 0.92 | 35 | HG |
| 4 | 90 | 0.71 | 0.95 | 22 | empty |
| 5 | 131 | 0.70 | 0.91 | 26 | HG |
Interfaces
6 interfaces between chains.
- B–C · 4373 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 3922 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 2294 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2267 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 818 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1IGW · Crystal Structure of the Isocitrate Lyase from the A219C mutant of Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9G6 · AlphaFold monomer V2.0 prediction for isocitrate lyase (P0A9G6) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P0A9G6
- Elsewhere: RCSB PDB 1IGW · PDBe 1IGW · UniProt P0A9G6
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