Research workbench
Isocitrate lyase from bacillus cereus atcc 14579 in complex with magnessium ion, glyoxylate, and succinate
Analyse Isocitrate lyase from bacillus cereus atcc 14579 in complex with magnessium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CMY
- Type
- protein
- Length
- 832 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase
- EC
- 4.1.3.1
- UniProt
- Q81GQ9
- Ligands
- GLV, MG
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Isocitrate lyase (EC 4.1.3.1) | protein | 417 | 50% helix, 12% strand | Q81GQ9 |
| A | Isocitrate lyase (EC 4.1.3.1) | protein | 415 | 50% helix, 12% strand | Q81GQ9 |
Ligands and binding sites
- GLV · Glyoxylic acid · ligand · 2 copies · chains C, A
- MG · Magnesium ion · metal · 2 copies · chains C, A
- SIN · Succinic acid · additive · 2 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.60 | 0.85 | 28 | empty |
| 2 | 194 | 0.54 | 0.78 | 27 | empty |
| 3 | 178 | 0.52 | 0.78 | 22 | empty |
| 4 | 159 | 0.47 | 0.77 | 27 | empty |
| 5 | 60 | 0.41 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- C–A · 4928 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 7CMY · Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion… · the same entry in another collection · chain C against C, 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 Q81GQ9
- Elsewhere: RCSB PDB 7CMY · PDBe 7CMY · UniProt Q81GQ9
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