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Crystal structure of phosphopantetheine adenylyltransferase from enterococcus faecalis in the ligand-unbound state and in complex with ATP and pantetheine
Analyse Crystal structure of phosphopantetheine adenylyltransferase from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ND7
- 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
- PNY
- Pockets
- 12 · best druggability 0.79
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
- PNY · (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide · ligand · 6 copies · chains A, C, B, F, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.79 | 0.81 | 115 | PNY |
| 2 | 701 | 0.75 | 0.80 | 74 | PNY |
| 3 | 491 | 0.72 | 0.81 | 50 | PNY |
| 4 | 467 | 0.71 | 0.81 | 49 | PNY |
| 5 | 522 | 0.71 | 0.80 | 52 | PNY |
Interfaces
15 interfaces between chains.
- E–F · 1252 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1198 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1186 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 602 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ND7 · Crystal structure of phosphopantetheine adenylyltransferase from Enterococcus faecalis in… · 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 B 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 3ND7 · PDBe 3ND7 · UniProt Q831P9
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