Research workbench
Crystal structure of the kelch domain of human KLHL12 in complex with DVL1 peptide
Analyse Crystal structure of the kelch domain of human KLHL12 in complex with DVL1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TTK
- Type
- protein
- Length
- 1,171 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch-like protein 12; DVL1
- UniProt
- Q53G59
- Ligands
- NA, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kelch-like protein 12 | protein | 285 | 0% helix, 50% strand | Q53G59 |
| C | Kelch-like protein 12 | protein | 284 | 0% helix, 49% strand | Q53G59 |
| D | Kelch-like protein 12 | protein | 286 | 0% helix, 51% strand | Q53G59 |
| F | DVL1 | protein | 7 | 0% helix, 0% strand | — |
| G, H, E | DVL1 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.76 | 0.85 | 38 | empty |
| 2 | 434 | 0.75 | 0.84 | 38 | empty |
| 3 | 439 | 0.74 | 0.84 | 39 | empty |
| 4 | 410 | 0.73 | 0.84 | 39 | empty |
| 5 | 446 | 0.67 | 0.79 | 38 | NA |
Interfaces
7 interfaces between chains.
- B–C · 505 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 435 Ų buried · 2 hydrogen bonds · protein-protein
- C–G · 424 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 415 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 358 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6TTK · Crystal structure of the kelch domain of human KLHL12 in complex with DVL1 peptide · the same entry in another collection · chain E against E, TM-score 1.00
- Q53G59 · AlphaFold monomer V2.0 prediction for kelch-like protein 12 (Q53G59) · a predicted model of the same protein · chain C 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 6TTK · PDBe 6TTK · UniProt Q53G59
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