MolNFT v1 · #163958 · protein
Paak family AMP-ligase with AMP
6SIW · Paak-like ligase (AMP-dependent synthetase and ligase): “Paak family AMP-ligase with AMP”. X-ray diffraction, 3 ligands (AMP, MG, ZN), 10 pockets (best druggability 0.79). MolNFT v1 #163958 on GenesisL1: 3D structure, binding sites…
- PDB
- 6SIW
- Type
- protein
- Length
- 865 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paak-like ligase (AMP-dependent synthetase and ligase)
- UniProt
- A0A022MRT4
- Ligands
- AMP, MG, ZN
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paak-like ligase (AMP-dependent synthetase and ligase) | protein | 432 | 30% helix, 23% strand | A0A022MRT4 |
| B | Paak-like ligase (AMP-dependent synthetase and ligase) | protein | 433 | 30% helix, 23% strand | A0A022MRT4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.79 | 0.85 | 60 | AMP, MG |
| 2 | 640 | 0.77 | 0.83 | 71 | AMP, MG |
| 3 | 211 | 0.70 | 0.87 | 35 | 7PE |
| 4 | 162 | 0.55 | 0.81 | 26 | EDO |
| 5 | 180 | 0.54 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4463 Ų buried · 84 hydrogen bonds · protein-protein
Compared structures
- 6SIW · PaaK family AMP-ligase with AMP · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A022MRT4
- Elsewhere: RCSB PDB 6SIW · PDBe 6SIW · UniProt A0A022MRT4
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