Research workbench
Crystal structure of phosphopantetheine adenylyltransferase from mycobacterium abcessus in complex with 2-(4-chloro-3-nitrobenzoyl) benzoic acid (fragment 6)
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
- 5O0H
- 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
- 9FN
- Pockets
- 4 · best druggability 0.69
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 | 44% helix, 20% strand | B1MDL6 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 156 | 48% helix, 20% strand | B1MDL6 |
Ligands and binding sites
- 9FN · 2-(4-chloranyl-3-nitro-phenyl)carbonylbenzoic acid · ligand · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.69 | 0.79 | 48 | 9FN |
| 2 | 545 | 0.69 | 0.78 | 48 | empty |
| 3 | 235 | 0.58 | 0.79 | 29 | 9FN |
| 4 | 204 | 0.58 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 604 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 567 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 519 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5O0H · 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 5O0H · PDBe 5O0H · UniProt B1MDL6
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