MolNFT v1 · #143158 · protein
Crystal structure of protein cite from mycobacterium tuberculosis in complex with magnesium, pyruvate and coenzyme a
6ARB · Citrate lyase subunit beta-like protein: “Crystal structure of protein cite from mycobacterium tuberculosis in complex with magnesium, pyruvate and…”. X-ray diffraction, 4 ligands (PYR, COA, MG), 14 pockets (best druggability 0.76).…
- PDB
- 6ARB
- Type
- protein
- Length
- 804 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate lyase subunit beta-like protein
- EC
- 4.1.-.-
- UniProt
- P9WPE0
- Ligands
- PYR, COA, MG, PO4
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Citrate lyase subunit beta-like protein (EC 4.1.-.-) | protein | 268 | 49% helix, 18% strand | P9WPE0 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, C, B
- COA · Coenzyme A · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.76 | 0.85 | 35 | empty |
| 2 | 836 | 0.76 | 0.80 | 85 | GOL |
| 3 | 89 | 0.75 | 0.97 | 12 | empty |
| 4 | 239 | 0.74 | 0.88 | 38 | MG, PYR, COA |
| 5 | 263 | 0.74 | 0.87 | 39 | MG, PYR, COA |
Interfaces
3 interfaces between chains.
- A–C · 1465 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1446 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1416 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6ARB · CRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPE0 · AlphaFold monomer V2.0 prediction for citrate lyase subunit beta-like protein (P9WPE0) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P9WPE0
- Elsewhere: RCSB PDB 6ARB · PDBe 6ARB · UniProt P9WPE0
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