Research workbench
Gabarap-L1 ATG4B lir complex
Analyse Gabarap-L1 ATG4B lir complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LXI
- Type
- protein
- Length
- 251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor-associated protein-like 1; Cysteine protease ATG4B
- EC
- 3.4.22.-
- UniProt
- Q9H0R8, Q9Y4P1
- Ligands
- MG, PER
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Gamma-aminobutyric acid receptor-associated protein-like 1 | protein | 117 | 33% helix, 22% strand | Q9H0R8 |
| B | Gamma-aminobutyric acid receptor-associated protein-like 1 | protein | 116 | 33% helix, 22% strand | Q9H0R8 |
| C | Cysteine protease ATG4B (EC 3.4.22.-) | protein | 10 | 0% helix, 20% strand | Q9Y4P1 |
| E | Cysteine protease ATG4B (EC 3.4.22.-) | protein | 8 | 0% helix, 25% strand | Q9Y4P1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains D, B
- PER · Peroxide ion · ion · 2 copies · chains D, C
- PGE · Triethylene glycol · additive · 2 copies · chains D
- EDO · 1,2-ethanediol · additive · chains D
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
4 interfaces between chains.
- D–C · 718 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 660 Ų buried · 14 hydrogen bonds · protein-protein
- D–B · 331 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5LXI · GABARAP-L1 ATG4B LIR Complex · the same entry in another collection · chain E against E, TM-score 1.00
- Q9H0R8 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor-associated… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9Y4P1 · AlphaFold monomer V2.0 prediction for cysteine protease ATG4B (Q9Y4P1) · a predicted model of the same protein · chain E against A, TM-score 0.46
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 Q9H0R8
- Every structure of UniProt Q9Y4P1
- Elsewhere: RCSB PDB 5LXI · PDBe 5LXI · UniProt Q9H0R8 · UniProt Q9Y4P1
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