Research workbench
Crystal structure of phosphopantetheine adenylyltransferase from pseudomonas aeruginosa
Analyse Crystal structure of phosphopantetheine adenylyltransferase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X6F
- Type
- protein
- Length
- 948 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- Q9I6D1
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 158 | 42% helix, 18% strand | Q9I6D1 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains B, D, F
- IPA · Isopropyl alcohol · additive · 2 copies · chains F
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 | 584 | 0.75 | 0.82 | 54 | GOL |
| 2 | 488 | 0.74 | 0.83 | 47 | empty |
| 3 | 391 | 0.69 | 0.82 | 46 | empty |
| 4 | 565 | 0.68 | 0.78 | 47 | IPA, GOL |
| 5 | 277 | 0.66 | 0.82 | 36 | empty |
Interfaces
8 interfaces between chains.
- B–D · 1061 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1054 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 761 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 706 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 385 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5X6F · Crystal structure of Phosphopantetheine adenylyltransferase from Pseudomonas aeruginosa · the same entry in another collection · chain F against F, TM-score 1.00
- Q9I6D1 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (Q9I6D1) · a predicted model of the same protein · chain D 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 Q9I6D1
- Elsewhere: RCSB PDB 5X6F · PDBe 5X6F · UniProt Q9I6D1
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