MolNFT v1 · #114016 · protein
Crystal structure of lgg-1 complexed with a unc-51 peptide
5AZG · Protein lgg-1: “Crystal structure of lgg-1 complexed with a unc-51 peptide”. X-ray diffraction, 1 ligand (CD), 3 pockets (best druggability 0.47). MolNFT v1 #114016 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AZG
- Type
- protein
- Length
- 249 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein lgg-1; SERINE/THREONINE-protein kinase unc-51
- UniProt
- Q09490, Q23023
- Ligands
- CD
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein lgg-1 | protein | 119 | 32% helix, 22% strand | Q09490 |
| C | SERINE/THREONINE-protein kinase unc-51 | protein | 5 | 0% helix, 40% strand | Q23023 |
| D | SERINE/THREONINE-protein kinase unc-51 | protein | 6 | 0% helix, 33% strand | Q23023 |
Ligands and binding sites
- CD · Cadmium ion · metal · 14 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.47 | 0.85 | 13 | empty |
| 2 | 152 | 0.46 | 0.76 | 21 | empty |
| 3 | 55 | 0.28 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 489 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 293 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 186 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5AZG · Crystal structure of LGG-1 complexed with a UNC-51 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q09490 · AlphaFold monomer V2.0 prediction for protein lgg-1 (Q09490) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q23023 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase unc-51 (Q23023) · a predicted model of the same protein · chain C against A, TM-score 0.81
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 Q09490
- Every structure of UniProt Q23023
- Elsewhere: RCSB PDB 5AZG · PDBe 5AZG · UniProt Q09490 · UniProt Q23023
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