MolNFT v1 · #163191 · protein
Crystal structure of patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75
6RVC · Protein patched homolog 1: “Crystal structure of patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75”. X-ray diffraction, 2 ligands (NAG, SO4), 9 pockets (best druggability 0.51). MolNFT v1 #163191 on GenesisL1: 3D…
- PDB
- 6RVC
- Type
- protein
- Length
- 650 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1; Nanobody NB75
- UniProt
- Q13635
- Ligands
- NAG, SO4
- Pockets
- 9 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein patched homolog 1 | protein | 94 | 54% helix, 6% strand | Q13635 |
| D | Nanobody NB75 | protein | 124 | 10% helix, 49% strand | — |
| E, F | Nanobody NB75 | protein | 122 | 10% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, F, C
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.51 | 0.74 | 39 | empty |
| 2 | 130 | 0.48 | 0.79 | 20 | empty |
| 3 | 112 | 0.47 | 0.80 | 17 | empty |
| 4 | 111 | 0.46 | 0.79 | 19 | empty |
| 5 | 153 | 0.42 | 0.74 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–F · 684 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 657 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 629 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 341 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 293 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6RVC · Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75 · the same entry in another collection · chain C against C, 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 0.97
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 6RVC · PDBe 6RVC · UniProt Q13635
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