MolNFT v1 · #163961 · protein
Paak family AMP-ligase with anp and substrate
6SIZ · AMP-dependent synthetase and ligase: “Paak family AMP-ligase with anp and substrate”. X-ray diffraction, 4 ligands (3HA, ANP, MG), 12 pockets (best druggability 0.79). MolNFT v1 #163961 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SIZ
- Type
- protein
- Length
- 870 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, ANP, MG, ZN
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMP-dependent synthetase and ligase | protein | 433 | 30% helix, 23% strand | A0A022MRT4 |
| B | AMP-dependent synthetase and ligase | protein | 437 | 30% helix, 23% strand | A0A022MRT4 |
Ligands and binding sites
- 3HA · 3-hydroxyanthranilic acid · ligand · 2 copies · chains A, B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.79 | 0.84 | 65 | 3HA, ANP, MG |
| 2 | 706 | 0.78 | 0.83 | 69 | 3HA, ANP, PEG |
| 3 | 274 | 0.60 | 0.79 | 23 | empty |
| 4 | 235 | 0.56 | 0.78 | 22 | empty |
| 5 | 172 | 0.54 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 4471 Ų buried · 79 hydrogen bonds · protein-protein
Compared structures
- 6SIZ · PaaK family AMP-ligase with ANP 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 6SIZ · PDBe 6SIZ · UniProt A0A022MRT4
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