MolNFT v1 · #106279 · protein
Crystal structure of phosphoapantetheine adenylyltransferase PPAT/COAD with CoA and pyrophosphate from pseudomonas aeruginosa
4RUK · Phosphopantetheine adenylyltransferase: “Crystal structure of phosphoapantetheine adenylyltransferase PPAT/COAD with CoA and pyrophosphate from…”. X-ray diffraction, 3 ligands (COA, POP, CA), 12 pockets (best druggability 0.84).…
- PDB
- 4RUK
- Type
- protein
- Length
- 947 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- A3LHH1
- Ligands
- COA, POP, CA
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 47% helix, 18% strand | A3LHH1 |
| B, C, D, E, F | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 158 | 44% helix, 18% strand | A3LHH1 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 6 copies · chains A, F, B, E, C, D
- POP · Pyrophosphate 2- · ligand · 2 copies · chains D, F
- CA · Calcium ion · metal · 2 copies · chains E, F
- FMT · Formic acid · additive · 15 copies · chains A, B, E, C, D
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, F, B, D, E
- ACT · Acetate ion · additive · 4 copies · chains A, C, E, F
- GOL · Glycerol · additive · chains 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 | 1078 | 0.84 | 0.84 | 109 | COA, ACT |
| 2 | 801 | 0.80 | 0.83 | 76 | COA, DMS, ACT |
| 3 | 214 | 0.75 | 0.90 | 28 | empty |
| 4 | 462 | 0.75 | 0.84 | 50 | COA, CA, ACT |
| 5 | 717 | 0.75 | 0.80 | 77 | COA, POP, DMS |
Interfaces
13 interfaces between chains.
- C–D · 1265 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1182 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1165 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 673 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 663 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RUK · crystal structure of Phosphoapantetheine adenylyltransferase PPAT/CoaD with CoA and… · the same entry in another collection · chain A against A, TM-score 1.00
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 A3LHH1
- Elsewhere: RCSB PDB 4RUK · PDBe 4RUK · UniProt A3LHH1
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