Research workbench
Crystal structure of the N-terminal domain of CEP164(1-109) bound to camelid nanobody 10Z
Analyse Crystal structure of the N-terminal domain of CEP164(1-109) bound to camelid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O06
- Type
- protein
- Length
- 433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camelid nanobody 10Z; Centrosomal protein of 164 kda
- UniProt
- Q9UPV0
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Camelid nanobody 10Z | protein | 124 | 5% helix, 53% strand | — |
| C | Centrosomal protein of 164 kda | protein | 93 | 39% helix, 15% strand | Q9UPV0 |
| D | Centrosomal protein of 164 kda | protein | 92 | 41% helix, 15% strand | Q9UPV0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.49 | 0.83 | 17 | empty |
| 2 | 81 | 0.49 | 0.83 | 24 | SO4 |
| 3 | 161 | 0.48 | 0.77 | 30 | empty |
| 4 | 104 | 0.42 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1356 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1355 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 666 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7O06 · Crystal structure of the N-terminal domain of CEP164(1-109) bound to camelid nanobody 10Z · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UPV0 · AlphaFold monomer V2.0 prediction for centrosomal protein of 164 kda (Q9UPV0) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 Q9UPV0
- Elsewhere: RCSB PDB 7O06 · PDBe 7O06 · UniProt Q9UPV0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.