MolNFT v1 · #175320 · protein
Isocitrate lyase from bacillus cereus atcc 14579 in complex with magnessium ion, glyoxylate, and succinate
7CMY: “Isocitrate lyase from bacillus cereus atcc 14579 in complex with magnessium ion, glyoxylate, and succinate”. X-ray diffraction, 2 ligands (GLV, MG), 12 pockets (best druggability 0.60). MolNFT v1 #175320 on GenesisL1: 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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