Research workbench
Chronobacterium ammoniagenes acps-CoA complex
Analyse Chronobacterium ammoniagenes acps-CoA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NFD
- Type
- protein
- Length
- 819 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine protein transferase, PPT1P
- UniProt
- O31302
- Ligands
- COA
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Phosphopantetheine protein transferase, PPT1P | protein | 136 | 43% helix, 29% strand | O31302 |
| B | Phosphopantetheine protein transferase, PPT1P | protein | 137 | 45% helix, 31% strand | O31302 |
| C | Phosphopantetheine protein transferase, PPT1P | protein | 137 | 44% helix, 29% strand | O31302 |
| D | Phosphopantetheine protein transferase, PPT1P | protein | 134 | 44% helix, 29% strand | O31302 |
| E | Phosphopantetheine protein transferase, PPT1P | protein | 139 | 43% helix, 30% strand | O31302 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.61 | 0.77 | 31 | COA |
| 2 | 376 | 0.60 | 0.76 | 41 | COA |
| 3 | 337 | 0.59 | 0.77 | 32 | COA |
| 4 | 299 | 0.59 | 0.77 | 37 | COA |
| 5 | 287 | 0.58 | 0.77 | 35 | COA |
Interfaces
6 interfaces between chains.
- A–B · 1018 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1000 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 982 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 980 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3NFD · Chronobacterium ammoniagenes ACPS-CoA complex · 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 O31302
- Elsewhere: RCSB PDB 3NFD · PDBe 3NFD · UniProt O31302
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