Research workbench
Complex of GABA(A) receptor-associated protein (gabarap) with a synthetic peptide
Analyse Complex of GABA(A) receptor-associated protein (gabarap) with a synthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D32
- Type
- protein
- Length
- 258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor-associated protein; K1 peptide
- UniProt
- O95166
- Ligands
- NA, CL, NH2
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid receptor-associated protein | protein | 118 | 33% helix, 22% strand | O95166 |
| B | Gamma-aminobutyric acid receptor-associated protein | protein | 116 | 33% helix, 22% strand | O95166 |
| C, D | K1 peptide | protein | 12 | 33% helix, 8% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 8 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.53 | 0.79 | 28 | CL |
| 2 | 60 | 0.33 | 0.77 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–C · 740 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 725 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 309 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 248 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3D32 · Complex of GABA(A) receptor-associated protein (GABARAP) with a synthetic peptide · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.95
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 3D32 · PDBe 3D32 · UniProt O95166
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