MolNFT v1 · #143125 · protein
Crystal structure of protein cite from mycobacterium tuberculosis in complex with magnesium, pyruvate and citramalyl-CoA
6AQ4: “Crystal structure of protein cite from mycobacterium tuberculosis in complex with magnesium, pyruvate and…”. X-ray diffraction, 5 ligands (CQM, PYR, MG), 15 pockets (best druggability 0.77). MolNFT v1 #143125 on GenesisL1: 3D…
- PDB
- 6AQ4
- Type
- protein
- Length
- 802 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein cite
- UniProt
- P9WPE0
- Ligands
- CQM, PYR, MG, CL, PO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein cite | protein | 267 | 48% helix, 18% strand | P9WPE0 |
| B | Protein cite | protein | 268 | 47% helix, 18% strand | P9WPE0 |
| C | Protein cite | protein | 267 | 48% helix, 18% strand | P9WPE0 |
Ligands and binding sites
- CQM · Citramalyl-CoA · ligand · 2 copies · chains A, C, B
- PYR · Pyruvic acid · ligand · chains B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.77 | 0.85 | 34 | empty |
| 2 | 253 | 0.74 | 0.88 | 38 | MG, CQM |
| 3 | 87 | 0.74 | 0.97 | 12 | PO4 |
| 4 | 271 | 0.73 | 0.87 | 41 | MG, CQM |
| 5 | 217 | 0.72 | 0.88 | 38 | MG, PYR |
Interfaces
3 interfaces between chains.
- A–B · 1467 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1441 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1440 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 6AQ4 · 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 6AQ4 · PDBe 6AQ4 · UniProt P9WPE0
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