MolNFT v1 · #163141 · protein
Crystal structure of the patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and cholesterol-hemisuccinate
6RTW · Protein patched homolog 1: “Crystal structure of the patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and…”. X-ray diffraction, 2 ligands (Y01, NAG), 4 pockets (best druggability 0.76). MolNFT v1 #163141 on GenesisL1: 3D…
- PDB
- 6RTW
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1; Llama-derived nanobody NB64
- UniProt
- Q13635
- Ligands
- Y01, NAG
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1 | protein | 277 | 36% helix, 19% strand | Q13635 |
| B | Llama-derived nanobody NB64 | protein | 124 | 5% helix, 51% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 553 | 0.76 | 0.82 | 63 | Y01 |
| 2 | 94 | 0.51 | 0.83 | 16 | empty |
| 3 | 149 | 0.44 | 0.75 | 19 | empty |
| 4 | 57 | 0.32 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6RTW · Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13635 · AlphaFold monomer V2.0 prediction for protein patched homolog 1 (Q13635) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q13635
- Elsewhere: RCSB PDB 6RTW · PDBe 6RTW · UniProt Q13635
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