MolNFT v1 · #74578 · protein
Crystal structure of isocitrate lyase from brucella melitensis, bound to magnesium isocitrate
3P0X: “Crystal structure of isocitrate lyase from brucella melitensis, bound to magnesium isocitrate”. X-ray diffraction, 2 ligands (ICT, MG), 18 pockets (best druggability 0.87). MolNFT v1 #74578 on GenesisL1: 3D structure, binding sites…
- PDB
- 3P0X
- Type
- protein
- Length
- 1,691 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase
- EC
- 4.1.3.1
- UniProt
- Q57BR0
- Ligands
- ICT, MG
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate lyase (EC 4.1.3.1) | protein | 422 | 48% helix, 11% strand | Q57BR0 |
| C | Isocitrate lyase (EC 4.1.3.1) | protein | 423 | 48% helix, 11% strand | Q57BR0 |
| D | Isocitrate lyase (EC 4.1.3.1) | protein | 424 | 48% helix, 11% strand | Q57BR0 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.87 | 0.96 | 95 | empty |
| 2 | 372 | 0.86 | 0.95 | 88 | empty |
| 3 | 363 | 0.84 | 0.94 | 65 | EDO |
| 4 | 283 | 0.84 | 0.95 | 51 | empty |
| 5 | 213 | 0.82 | 0.95 | 34 | empty |
Interfaces
6 interfaces between chains.
- C–D · 5219 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 5198 Ų buried · 83 hydrogen bonds · protein-protein
- A–C · 1875 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1865 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1048 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3P0X · Crystal structure of isocitrate lyase from Brucella melitensis, bound to magnesium… · the same entry in another collection · chain B against B, 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 Q57BR0
- Elsewhere: RCSB PDB 3P0X · PDBe 3P0X · UniProt Q57BR0
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