MolNFT v1 · #119467 · protein
Wnt modulator kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4)
5FWW · Low-density lipoprotein receptor-related protein 6: “Wnt modulator kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4)”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.80). MolNFT v1 #119467 on GenesisL1: 3D…
- PDB
- 5FWW
- Type
- protein
- Length
- 976 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low-density lipoprotein receptor-related protein 6; Kremen protein 1; Dickkopf-related…
- UniProt
- O75581, Q96MU8, O94907
- Ligands
- CA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low-density lipoprotein receptor-related protein 6 | protein | 612 | 3% helix, 47% strand | O75581 |
| B | Kremen protein 1 | protein | 288 | 7% helix, 35% strand | Q96MU8 |
| C | Dickkopf-related protein 1 | protein | 76 | 7% helix, 37% strand | O94907 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.80 | 0.97 | 33 | empty |
| 2 | 743 | 0.79 | 0.83 | 63 | empty |
| 3 | 704 | 0.72 | 0.78 | 65 | empty |
| 4 | 94 | 0.66 | 0.91 | 28 | empty |
| 5 | 471 | 0.62 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1103 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1028 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 144 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 5FWW · Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) · the same entry in another collection · chain A against A, TM-score 1.00
- Q96MU8 · AlphaFold monomer V2.0 prediction for kremen protein 1 (Q96MU8) · a predicted model of the same protein · chain B against A, TM-score 1.00
- O75581 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor-related protein 6… · a predicted model of the same protein · chain A against A, TM-score 0.98
- O94907 · AlphaFold monomer V2.0 prediction for dickkopf-related protein 1 (O94907) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 O75581
- Every structure of UniProt Q96MU8
- Every structure of UniProt O94907
- Elsewhere: RCSB PDB 5FWW · PDBe 5FWW · UniProt O75581 · UniProt Q96MU8 · UniProt O94907
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