MolNFT v1 · #74220 · protein
Crystal structure of isocitrate lyase from brucella melitensis, bound to the product mimic malonate
3OQ8: “Crystal structure of isocitrate lyase from brucella melitensis, bound to the product mimic malonate”. X-ray diffraction, 1 ligand (NA), 16 pockets (best druggability 0.91). MolNFT v1 #74220 on GenesisL1: 3D structure, binding sites…
- PDB
- 3OQ8
- Type
- protein
- Length
- 1,692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase
- EC
- 4.1.3.1
- UniProt
- Q2YQA0
- Ligands
- NA
- Pockets
- 16 · best druggability 0.91
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate lyase (EC 4.1.3.1) | protein | 424 | 49% helix, 11% strand | Q2YQA0 |
| B | Isocitrate lyase (EC 4.1.3.1) | protein | 422 | 49% helix, 11% strand | Q2YQA0 |
| C, D | Isocitrate lyase (EC 4.1.3.1) | protein | 423 | 49% helix, 11% strand | Q2YQA0 |
Ligands and binding sites
- NA · Sodium ion · metal · 9 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- MLA · Malonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.91 | 0.93 | 153 | EDO, NA |
| 2 | 598 | 0.88 | 0.93 | 98 | empty |
| 3 | 418 | 0.86 | 0.94 | 70 | empty |
| 4 | 685 | 0.86 | 0.90 | 101 | NA |
| 5 | 218 | 0.49 | 0.75 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 5284 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 5197 Ų buried · 83 hydrogen bonds · protein-protein
- B–D · 1956 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1910 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1022 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3OQ8 · Crystal structure of isocitrate lyase from Brucella melitensis, bound to the product… · 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 Q2YQA0
- Elsewhere: RCSB PDB 3OQ8 · PDBe 3OQ8 · UniProt Q2YQA0
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