Research workbench
Structural elucidation of peptide binding to klhl-12, a substrate specific adapter protein in a CUL3-ring E3 ligase complex
Analyse Structural elucidation of peptide binding to klhl-12, a substrate specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V7O
- Type
- protein
- Length
- 580 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch-like protein 12; DVL3-peptide
- UniProt
- Q53G59
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kelch-like protein 12 | protein | 284 | 0% helix, 50% strand | Q53G59 |
| B | Kelch-like protein 12 | protein | 283 | 0% helix, 51% strand | Q53G59 |
| C | DVL3-peptide | protein | 7 | 0% helix, 0% strand | — |
| D | DVL3-peptide | protein | 6 | 0% helix, 0% strand | — |
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 | 1140 | 0.84 | 0.85 | 74 | empty |
| 2 | 402 | 0.74 | 0.84 | 42 | empty |
| 3 | 107 | 0.35 | 0.73 | 18 | empty |
| 4 | 97 | 0.35 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 588 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 365 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6V7O · Structural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter… · the same entry in another collection · chain A against A, TM-score 1.00
- Q53G59 · AlphaFold monomer V2.0 prediction for kelch-like protein 12 (Q53G59) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q53G59
- Elsewhere: RCSB PDB 6V7O · PDBe 6V7O · UniProt Q53G59
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