Research workbench
Crystal structure of protein cite from mycobacterium tuberculosis in complex with magnesium, acetoacetate and coenzyme a
Analyse Crystal structure of protein cite from mycobacterium tuberculosis in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AS5
- Type
- protein
- Length
- 801 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
- COA, AAE, MG, SO4
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Citrate lyase subunit beta-like protein (EC 4.1.-.-) | protein | 267 | 46% helix, 18% strand | P9WPE0 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 3 copies · chains A, C, B
- AAE · Acetoacetic acid · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.76 | 0.85 | 35 | empty |
| 2 | 255 | 0.74 | 0.88 | 37 | MG, COA, AAE |
| 3 | 278 | 0.73 | 0.87 | 39 | MG, COA, AAE |
| 4 | 755 | 0.73 | 0.79 | 71 | SO4, GOL |
| 5 | 261 | 0.73 | 0.87 | 35 | MG, COA, AAE |
Interfaces
3 interfaces between chains.
- A–C · 1450 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1441 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1419 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6AS5 · 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 6AS5 · PDBe 6AS5 · UniProt P9WPE0
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