MolNFT v1 · #72589 · protein
Crystal structure of phosphopantetheine adenylyltransferase (ppat) from enterococcus faecalis
3ND5: “Crystal structure of phosphopantetheine adenylyltransferase (ppat) from enterococcus faecalis”. X-ray diffraction, 13 pockets (best druggability 0.81). MolNFT v1 #72589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ND5
- 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
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% 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 | 47% helix, 20% strand | Q831P9 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.81 | 0.82 | 113 | empty |
| 2 | 589 | 0.75 | 0.82 | 71 | empty |
| 3 | 494 | 0.73 | 0.82 | 49 | empty |
| 4 | 429 | 0.72 | 0.82 | 49 | empty |
| 5 | 428 | 0.72 | 0.82 | 49 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1262 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1224 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1129 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 602 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 600 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ND5 · Crystal structure of phosphopantetheine adenylyltransferase (PPAT) from Enterococcus… · 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 3ND5 · PDBe 3ND5 · UniProt Q831P9
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