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Crystal structure of isocitrate lyase from brucella melitensis, bound to the product mimic malonate
Analyse Crystal structure of isocitrate lyase from brucella melitensis, bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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