MolNFT v2 · #129162 · protein
Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with Dephospho-coenzyme A
5O08: “Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with…”. X-ray diffraction at 1.552, 1 ligand (COD), 2 pockets (best druggability 0.84). MolNFT v2 #129162 on GenesisL1: 3D structure…
- PDB
- 5O08
- Type
- protein
- Length
- 475 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.552
- Source
- Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569…
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- B1MDL6
- Ligands
- COD
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.552 · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 160 | 44% helix, 18% strand | B1MDL6 |
| B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 46% helix, 18% strand | B1MDL6 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 158 | 46% helix, 20% strand | B1MDL6 |
Ligands and binding sites
- COD · Dephospho coenzyme A · ligand · 3 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.84 | 0.85 | 129 | COD, EDO |
| 2 | 586 | 0.80 | 0.85 | 72 | COD, EDO |
Interfaces
3 interfaces between chains.
- B–C · 645 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 643 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5O08 · 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 0.96
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 5O08 · PDBe 5O08 · UniProt B1MDL6
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