Research workbench
Chronobacterium ammoiniagenes apo-acps structure
Analyse Chronobacterium ammoiniagenes apo-acps structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NE9
- Type
- protein
- Length
- 409 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine protein transferase, PPT1P
- UniProt
- O31302
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantetheine protein transferase, PPT1P | protein | 138 | 42% helix, 30% strand | O31302 |
| B | Phosphopantetheine protein transferase, PPT1P | protein | 138 | 38% helix, 30% strand | O31302 |
| C | Phosphopantetheine protein transferase, PPT1P | protein | 133 | 41% helix, 32% strand | O31302 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.61 | 0.78 | 44 | SO4 |
| 2 | 372 | 0.61 | 0.77 | 42 | SO4 |
| 3 | 327 | 0.59 | 0.77 | 39 | SO4 |
| 4 | 133 | 0.45 | 0.77 | 25 | empty |
| 5 | 66 | 0.37 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1035 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1016 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1007 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3NE9 · Chronobacterium ammoiniagenes apo-ACPS structure · 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 3NE9 · PDBe 3NE9 · UniProt O31302
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