MolNFT v1 · #177220 · protein
Crystal structure of isocitrate lyase-1 from candida albicans
7EBE: “Crystal structure of isocitrate lyase-1 from candida albicans”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.90). MolNFT v1 #177220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EBE
- Type
- protein
- Length
- 4,313 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase
- EC
- 4.1.3.1
- UniProt
- Q59RB8
- Ligands
- MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 8 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate lyase (EC 4.1.3.1) | protein | 544 | 51% helix, 10% strand | Q59RB8 |
| B | Isocitrate lyase (EC 4.1.3.1) | protein | 540 | 51% helix, 10% strand | Q59RB8 |
| C | Isocitrate lyase (EC 4.1.3.1) | protein | 535 | 51% helix, 10% strand | Q59RB8 |
| D | Isocitrate lyase (EC 4.1.3.1) | protein | 541 | 52% helix, 10% strand | Q59RB8 |
| E | Isocitrate lyase (EC 4.1.3.1) | protein | 542 | 51% helix, 10% strand | Q59RB8 |
| F | Isocitrate lyase (EC 4.1.3.1) | protein | 543 | 52% helix, 10% strand | Q59RB8 |
| G | Isocitrate lyase (EC 4.1.3.1) | protein | 535 | 51% helix, 10% strand | Q59RB8 |
| H | Isocitrate lyase (EC 4.1.3.1) | protein | 533 | 52% helix, 10% strand | Q59RB8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 12 copies · chains A, C, B, D, G, E, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.90 | 0.93 | 136 | empty |
| 2 | 1087 | 0.88 | 0.89 | 159 | empty |
| 3 | 618 | 0.87 | 0.93 | 93 | empty |
| 4 | 1140 | 0.87 | 0.88 | 144 | empty |
| 5 | 1192 | 0.86 | 0.87 | 150 | empty |
Interfaces
14 interfaces between chains.
- B–D · 5117 Ų buried · 61 hydrogen bonds · protein-protein
- E–G · 5066 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 5057 Ų buried · 58 hydrogen bonds · protein-protein
- F–H · 4910 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 3193 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7EBE · Crystal structure of Isocitrate lyase-1 from Candida albicans · 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 Q59RB8
- Elsewhere: RCSB PDB 7EBE · PDBe 7EBE · UniProt Q59RB8
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