Research workbench
Crystal structure of E.COLI phosphopantetheine adenylyltransferase (PPAT/COAD) in complex with (R)-2,4-dihydroxy-N-(2-(4-hydroxy-1H- BENZO[D]IMIDAZOL-2-YL)ETHYL)-3,3-dimethylbutanamide
Analyse Crystal structure of E.COLI phosphopantetheine adenylyltransferase (PPAT/COAD)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CCN
- Type
- protein
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- P0A6I6
- Ligands
- EXS, SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 50% helix, 18% strand | P0A6I6 |
| B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 160 | 50% helix, 18% strand | P0A6I6 |
Ligands and binding sites
- EXS · (2R)-2,4-dihydroxy-N-[2-(7-hydroxy-1H-benzimidazol-2-yl)ethyl]-3,3-dimethylbutanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.66 | 0.80 | 47 | EXS, SO4 |
| 2 | 314 | 0.62 | 0.79 | 44 | EXS, SO4 |
Interfaces
1 interface between chains.
- A–B · 1136 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6CCN · Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6I6 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (P0A6I6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A6I6
- Elsewhere: RCSB PDB 6CCN · PDBe 6CCN · UniProt P0A6I6
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