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Structural basis for acyl-CoA carboxylase-mediated assembly of unusual polyketide synthase extender units incorporated into the stambomycin antibiotics
Analyse Structural basis for acyl-CoA carboxylase-mediated assembly of unusual… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5INF
- Type
- protein
- Length
- 2,898 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.751
- Source
- Streptomyces ambofaciens ATCC 23877
- Molecule
- Carboxyl transferase
- UniProt
- A0ACI9
- Ligands
- HXC
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.751 · 6 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxyl transferase | protein | 478 | 41% helix, 19% strand | A0ACI9 |
| B | Carboxyl transferase | protein | 480 | 42% helix, 19% strand | A0ACI9 |
| C | Carboxyl transferase | protein | 486 | 41% helix, 17% strand | A0ACI9 |
| D | Carboxyl transferase | protein | 479 | 42% helix, 20% strand | A0ACI9 |
| E | Carboxyl transferase | protein | 481 | 40% helix, 19% strand | A0ACI9 |
| F | Carboxyl transferase | protein | 494 | 42% helix, 19% strand | A0ACI9 |
Ligands and binding sites
- HXC · Hexanoyl-coenzyme A · ligand · chains B, F
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 | 1074 | 0.80 | 0.82 | 115 | empty |
| 2 | 1066 | 0.80 | 0.82 | 95 | empty |
| 3 | 1002 | 0.80 | 0.82 | 89 | empty |
| 4 | 670 | 0.77 | 0.82 | 81 | HXC |
| 5 | 79 | 0.74 | 0.97 | 27 | empty |
Interfaces
12 interfaces between chains.
- B–F · 4554 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 4338 Ų buried · 46 hydrogen bonds · protein-protein
- C–E · 4296 Ų buried · 53 hydrogen bonds · protein-protein
- D–E · 1287 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1257 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5INF · Structural basis for acyl-CoA carboxylase-mediated assembly of unusual polyketide… · the same entry in another collection · chain A 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 A0ACI9
- Elsewhere: RCSB PDB 5INF · PDBe 5INF · UniProt A0ACI9
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