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Structure of phosphopantetheine adenylyltransferase (CBU_0288) from coxiella burnetii
Analyse Structure of phosphopantetheine adenylyltransferase (CBU_0288) from coxiella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F3R
- Type
- protein
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- Q83EM7
- Ligands
- CA
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 146 | 45% helix, 20% strand | Q83EM7 |
| B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 149 | 44% helix, 19% strand | Q83EM7 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 147 | 44% helix, 20% strand | Q83EM7 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.67 | 0.77 | 54 | CA |
| 2 | 245 | 0.61 | 0.81 | 37 | empty |
| 3 | 274 | 0.61 | 0.79 | 39 | empty |
| 4 | 224 | 0.61 | 0.81 | 33 | empty |
| 5 | 288 | 0.60 | 0.79 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 522 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 460 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4F3R · Structure of phosphopantetheine adenylyltransferase (CBU_0288) from Coxiella burnetii · the same entry in another collection · chain A against A, TM-score 1.00
- Q83EM7 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (Q83EM7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q83EM7
- Elsewhere: RCSB PDB 4F3R · PDBe 4F3R · UniProt Q83EM7
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