Research workbench
Paak family AMP-ligase with AMP and substrate
Analyse Paak family AMP-ligase with AMP and substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SIY
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMP-dependent synthetase and ligase
- UniProt
- A0A022MRT4
- Ligands
- 3HA, AMP, MG, ZN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMP-dependent synthetase and ligase | protein | 433 | 31% helix, 23% strand | A0A022MRT4 |
| B | AMP-dependent synthetase and ligase | protein | 436 | 31% helix, 23% strand | A0A022MRT4 |
Ligands and binding sites
- 3HA · 3-hydroxyanthranilic acid · ligand · 4 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.78 | 0.83 | 64 | AMP, 3HA, MG |
| 2 | 593 | 0.77 | 0.83 | 59 | 3HA, AMP |
| 3 | 233 | 0.56 | 0.78 | 24 | empty |
| 4 | 237 | 0.56 | 0.78 | 20 | empty |
| 5 | 169 | 0.55 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 4553 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 6SIY · PaaK family AMP-ligase with AMP and substrate · the same entry in another collection · chain A against A, 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 6SIY · PDBe 6SIY · UniProt A0A022MRT4
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