Research workbench
Isocitrate lyase-1 from mycobacterium tuberculosis covalently modified by 5-descarboxy-5-nitro-D-isocitric acid
Analyse Isocitrate lyase-1 from mycobacterium tuberculosis covalently modified by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RB1
- Type
- protein
- Length
- 1,708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase
- EC
- 4.1.3.1
- UniProt
- P9WKK7
- Ligands
- 54I, 48J, GLV, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate lyase (EC 4.1.3.1) | protein | 427 | 50% helix, 12% strand | P9WKK7 |
Ligands and binding sites
- 54I · (3E)-3-(hydroxyimino)propanoic acid · ligand · 4 copies · chains A, B, C, D
- 48J · dihydroxyacetic acid · ligand · 3 copies · chains A, B, C
- GLV · Glyoxylic acid · ligand · chains D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.89 | 0.92 | 113 | empty |
| 2 | 520 | 0.87 | 0.94 | 94 | empty |
| 3 | 582 | 0.85 | 0.91 | 100 | empty |
| 4 | 508 | 0.85 | 0.92 | 81 | empty |
| 5 | 314 | 0.80 | 0.91 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5075 Ų buried · 87 hydrogen bonds · protein-protein
- C–D · 5068 Ų buried · 81 hydrogen bonds · protein-protein
- B–C · 2214 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 2213 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1061 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7RB1 · Isocitrate Lyase-1 from Mycobacterium tuberculosis covalently modified by… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WKK7 · AlphaFold monomer V2.0 prediction for isocitrate lyase (P9WKK7) · a predicted model of the same protein · chain B 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 P9WKK7
- Elsewhere: RCSB PDB 7RB1 · PDBe 7RB1 · UniProt P9WKK7
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