MolNFT v1 · #165578 · protein
Crystal structure of the carboxyltransferase subunit of acc (ACCD6) in complex with inhibitor phenyl-cyclodiaone from mycobacterium tuberculosis
6TZV · Probable propionyl-CoA carboxylase beta chain 6: “Crystal structure of the carboxyltransferase subunit of acc (ACCD6) in complex with inhibitor…”. X-ray diffraction, 1 ligand (PKP), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6TZV
- Type
- protein
- Length
- 3,375 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable propionyl-CoA carboxylase beta chain 6
- EC
- 6.4.1.3
- UniProt
- P9WQH5
- Ligands
- PKP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Probable propionyl-CoA carboxylase beta chain 6 (EC 6.4.1.3) | protein | 426 | 42% helix, 22% strand | P9WQH5 |
| B, F | Probable propionyl-CoA carboxylase beta chain 6 (EC 6.4.1.3) | protein | 424 | 43% helix, 21% strand | P9WQH5 |
| C | Probable propionyl-CoA carboxylase beta chain 6 (EC 6.4.1.3) | protein | 410 | 42% helix, 22% strand | P9WQH5 |
| D, H | Probable propionyl-CoA carboxylase beta chain 6 (EC 6.4.1.3) | protein | 428 | 44% helix, 21% strand | P9WQH5 |
| G | Probable propionyl-CoA carboxylase beta chain 6 (EC 6.4.1.3) | protein | 409 | 41% helix, 22% strand | P9WQH5 |
Ligands and binding sites
- PKP · 4'-[(6-chloro-1,3-benzothiazol-2-yl)oxy]-6-hydroxy-4,4-dimethyl-4,5-dihydro[1,1'-biphenyl]-2(3H)-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.84 | 0.86 | 67 | empty |
| 2 | 801 | 0.83 | 0.86 | 67 | empty |
| 3 | 853 | 0.83 | 0.85 | 62 | empty |
| 4 | 932 | 0.82 | 0.84 | 67 | empty |
| 5 | 855 | 0.77 | 0.80 | 104 | PKP |
Interfaces
15 interfaces between chains.
- A–B · 2523 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2520 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2408 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2349 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 577 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6TZV · Crystal Structure of the carboxyltransferase subunit of ACC (AccD6) in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
- P9WQH5 · AlphaFold monomer V2.0 prediction for biotin-dependent acetyl-/propionyl-coenzyme a… · a predicted model of the same protein · chain E 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 P9WQH5
- Elsewhere: RCSB PDB 6TZV · PDBe 6TZV · UniProt P9WQH5
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