MolNFT v1 · #126285 · protein
P. calidifontis crenactin in complex with arcadin-2 C-terminal peptide
5LY3 · ACTIN/ACTIN family protein: “P. calidifontis crenactin in complex with arcadin-2 C-terminal peptide”. X-ray diffraction, 1 ligand (ADP), 4 pockets (best druggability 0.71). MolNFT v1 #126285 on GenesisL1: 3D structure, binding sites…
- PDB
- 5LY3
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACTIN/ACTIN family protein; Actin-like protein
- UniProt
- A3MWN5, A3MWN6
- Ligands
- ADP
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ACTIN/ACTIN family protein | protein | 427 | 43% helix, 20% strand | A3MWN5 |
| B | Actin-like protein | protein | 16 | 44% helix, 0% strand | A3MWN6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.71 | 0.79 | 74 | ADP |
| 2 | 207 | 0.57 | 0.79 | 30 | empty |
| 3 | 57 | 0.35 | 0.78 | 18 | empty |
| 4 | 70 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 732 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5LY3 · P. calidifontis crenactin in complex with arcadin-2 C-terminal peptide · the same entry in another collection · chain A against A, TM-score 1.00
- A3MWN5 · AlphaFold monomer V2.0 prediction for crenactin (A3MWN5) · a predicted model of the same protein · chain A against A, TM-score 0.98
- A3MWN6 · AlphaFold monomer V2.0 prediction for arcadin-2 (A3MWN6) · a predicted model of the same protein · chain B against A, TM-score 0.41
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 A3MWN5
- Every structure of UniProt A3MWN6
- Elsewhere: RCSB PDB 5LY3 · PDBe 5LY3 · UniProt A3MWN5 · UniProt A3MWN6
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