Research workbench
Human gabarap in complex with stapled peptide PEN8-ortho
Analyse Human gabarap in complex with stapled peptide PEN8-ortho in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZL7
- Type
- protein
- Length
- 262 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor-associated protein; PEN8-ortho
- UniProt
- O95166
- Ligands
- ACE, OXE, NA, CL, NH2
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gamma-aminobutyric acid receptor-associated protein | protein | 119 | 33% helix, 22% strand | O95166 |
| D, B | PEN8-ortho | protein | 12 | 0% helix, 17% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains D, C, A, B
- OXE · Ortho-xylene · ligand · 2 copies · chains D, C, A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 8 copies · chains A, C
- NH2 · Amino group · ion · 2 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.76 | 0.90 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 717 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 699 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 7ZL7 · Human GABARAP in complex with stapled peptide Pen8-ortho · the same entry in another collection · chain B against B, TM-score 1.00
- O95166 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor-associated protein… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 O95166
- Elsewhere: RCSB PDB 7ZL7 · PDBe 7ZL7 · UniProt O95166
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.