Research workbench
Crystal structure of phosphopantetheine adenylyltransferase from mycobacterium abcessus in complex with 3-phenoxymandelic acid (fragment 4)
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
- 5O0D
- Type
- protein
- Length
- 470 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
- 9F5
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 46% helix, 20% strand | B1MDL6 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 156 | 46% helix, 20% strand | B1MDL6 |
Ligands and binding sites
- 9F5 · (2~{S})-2-oxidanyl-2-(3-phenoxyphenyl)ethanoic acid · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.71 | 0.80 | 52 | 9F5 |
| 2 | 475 | 0.68 | 0.79 | 48 | empty |
| 3 | 480 | 0.68 | 0.79 | 57 | 9F5 |
Interfaces
3 interfaces between chains.
- B–C · 600 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 596 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 577 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O0D · 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 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 B1MDL6
- Elsewhere: RCSB PDB 5O0D · PDBe 5O0D · UniProt B1MDL6
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