MolNFT v1 · #165383 · protein
Crystal structure of the kelch domain of human KLHL12 in complex with DVL1 peptide
6TTK · Kelch-like protein 12: “Crystal structure of the kelch domain of human KLHL12 in complex with DVL1 peptide”. X-ray diffraction, 2 ligands (NA, CL), 11 pockets (best druggability 0.76). MolNFT v1 #165383 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.