Research workbench
Crystal structure of phosphopantetheine adenylyltransferase (ppat) in complex with ATP from enterococcus faecalis
Analyse Crystal structure of phosphopantetheine adenylyltransferase (ppat) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ND6
- Type
- protein
- Length
- 912 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- Q831P9
- Ligands
- ATP
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 152 | 46% helix, 20% strand | Q831P9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · 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
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.78 | 0.80 | 113 | ATP |
| 2 | 96 | 0.74 | 0.96 | 25 | empty |
| 3 | 353 | 0.72 | 0.84 | 47 | ATP |
| 4 | 440 | 0.69 | 0.80 | 48 | ATP |
| 5 | 201 | 0.65 | 0.85 | 29 | ATP |
Interfaces
15 interfaces between chains.
- E–F · 1260 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1250 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1162 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 592 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 578 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3ND6 · Crystal structure of phosphopantetheine adenylyltransferase (PPAT) in complex with ATP… · the same entry in another collection · chain F against F, TM-score 1.00
- Q831P9 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (Q831P9) · a predicted model of the same protein · chain C 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 Q831P9
- Elsewhere: RCSB PDB 3ND6 · PDBe 3ND6 · UniProt Q831P9
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