MolNFT v1 · #190793 · protein
Mycobacterium abscessus phosphopantetheine adenylyltransferase ternary complex with 4'-phosphopantetheine & non-hydrolyzable ATP analogue (ampcpp)
7YY1: “Mycobacterium abscessus phosphopantetheine adenylyltransferase ternary complex with 4'-phosphopantetheine &…”. X-ray diffraction, 2 ligands (PNS, APC), 3 pockets (best druggability 0.69). MolNFT v1 #190793 on GenesisL1: 3D…
- PDB
- 7YY1
- Type
- protein
- Length
- 468 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
- PNS, APC
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 157 | 48% helix, 20% strand | B1MDL6 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 154 | 47% helix, 20% strand | B1MDL6 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 3 copies · chains A, C, B
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 3 copies · chains A, 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 | 534 | 0.69 | 0.79 | 55 | PNS, APC |
| 2 | 554 | 0.69 | 0.78 | 69 | PNS, APC |
| 3 | 476 | 0.67 | 0.79 | 46 | PNS, APC |
Interfaces
3 interfaces between chains.
- A–C · 629 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 617 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 608 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7YY1 · Mycobacterium abscessus Phosphopantetheine adenylyltransferase ternary complex with… · 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 7YY1 · PDBe 7YY1 · UniProt B1MDL6
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