Research workbench
Crystal structure of the patched ectodomain in complex with nanobody NB64
Analyse Crystal structure of the patched ectodomain in complex with nanobody NB64 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RTY
- Type
- protein
- Length
- 396 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
- NAG
- Pockets
- 5 · best druggability 0.77
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, 18% strand | Q13635 |
| B | Llama-derived nanobody NB64 | protein | 119 | 3% helix, 55% strand | — |
Ligands and binding sites
- 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.77 | 0.84 | 66 | empty |
| 2 | 189 | 0.51 | 0.77 | 21 | empty |
| 3 | 116 | 0.51 | 0.81 | 17 | empty |
| 4 | 68 | 0.44 | 0.82 | 23 | empty |
| 5 | 52 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 917 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6RTY · Crystal structure of the Patched ectodomain in complex with nanobody NB64 · 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 6RTY · PDBe 6RTY · UniProt Q13635
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