Research workbench
Human wntless in complex with WNT3A
Analyse Human wntless in complex with WNT3A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DRT
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein wnt-3A; Protein wntless homolog
- UniProt
- P56704, Q5T9L3
- Ligands
- PCW, PAM, CLR, LPE, NAG
- Pockets
- 17 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein wnt-3A | protein | 334 | 33% helix, 15% strand | P56704 |
| B | Protein wntless homolog | protein | 496 | 48% helix, 20% strand | Q5T9L3 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
- PAM · Palmitoleic acid · ligand · chains A, B
- CLR · Cholesterol · ligand · chains B
- LPE · 1-O-octadecyl-sn-glycero-3-phosphocholine · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.85 | 0.85 | 93 | PAM, PCW |
| 2 | 1124 | 0.82 | 0.83 | 112 | empty |
| 3 | 52 | 0.59 | 0.92 | 20 | empty |
| 4 | 204 | 0.56 | 0.78 | 23 | empty |
| 5 | 161 | 0.56 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2871 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7DRT · Human Wntless in complex with Wnt3a · the same entry in another collection · chain A against A, TM-score 1.00
- Q5T9L3 · AlphaFold monomer V2.0 prediction for protein wntless homolog (Q5T9L3) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P56704 · AlphaFold monomer V2.0 prediction for protein wnt-3A (P56704) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P56704
- Every structure of UniProt Q5T9L3
- Elsewhere: RCSB PDB 7DRT · PDBe 7DRT · UniProt P56704 · UniProt Q5T9L3
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