MolNFT v1 · #135206 · protein
Crystal structure of a phosphopantetheine adenylyltransferase (coad, ppat) from pseudomonas aeruginosa bound to dephospho coenzyme a
5TS2: “Crystal structure of a phosphopantetheine adenylyltransferase (coad, ppat) from pseudomonas aeruginosa bound…”. X-ray diffraction, 3 ligands (COD, CA, CL), 12 pockets (best druggability 0.78). MolNFT v1 #135206 on GenesisL1: 3D…
- PDB
- 5TS2
- Type
- protein
- Length
- 971 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- B7V2S6
- Ligands
- COD, CA, CL
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 165 | 44% helix, 18% strand | B7V2S6 |
| B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 158 | 45% helix, 18% strand | B7V2S6 |
| D | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 159 | 45% helix, 18% strand | B7V2S6 |
| F | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 159 | 43% helix, 18% strand | B7V2S6 |
Ligands and binding sites
- COD · Dephospho coenzyme A · ligand · 6 copies · chains A, E, B, D, C, F
- CA · Calcium ion · metal · 2 copies · chains A, E
- CL · Chloride ion · ion · 11 copies · chains A, B, C, F, D, E
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 | 433 | 0.78 | 0.87 | 45 | empty |
| 2 | 743 | 0.77 | 0.81 | 67 | COD, CL |
| 3 | 600 | 0.76 | 0.82 | 54 | COD, CL |
| 4 | 599 | 0.75 | 0.82 | 56 | COD, CL |
| 5 | 564 | 0.75 | 0.82 | 56 | COD, CL |
Interfaces
12 interfaces between chains.
- C–F · 1341 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1284 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1235 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 648 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 642 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5TS2 · Crystal structure of a phosphopantetheine adenylyltransferase (CoaD, PPAT) from… · the same entry in another collection · chain F against F, TM-score 1.00
- B7V2S6 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (B7V2S6) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 B7V2S6
- Elsewhere: RCSB PDB 5TS2 · PDBe 5TS2 · UniProt B7V2S6
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