Research workbench
Crystal structure of phosphopantetheine adenylyltransferase from mycobacterium abcessus in complex with 5-methyl-1-phenyl-pyrazole-4- carboxylic acid (fragment 1)
Analyse Crystal structure of phosphopantetheine adenylyltransferase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O0A
- Type
- protein
- Length
- 465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- B1MDL6
- Ligands
- 9FH
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 46% helix, 20% strand | B1MDL6 |
| B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 155 | 46% helix, 20% strand | B1MDL6 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 153 | 48% helix, 20% strand | B1MDL6 |
Ligands and binding sites
- 9FH · 5-methyl-1-phenyl-pyrazole-4-carboxylic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.69 | 0.80 | 49 | 9FH |
| 2 | 452 | 0.68 | 0.80 | 49 | 9FH |
| 3 | 394 | 0.67 | 0.80 | 49 | 9FH |
| 4 | 67 | 0.32 | 0.76 | 13 | empty |
| 5 | 54 | 0.31 | 0.76 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–C · 618 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 583 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 572 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O0A · Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus… · the same entry in another collection · chain A against A, TM-score 1.00
- B1MDL6 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (B1MDL6) · a predicted model of the same protein · chain C 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 B1MDL6
- Elsewhere: RCSB PDB 5O0A · PDBe 5O0A · UniProt B1MDL6
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