Research workbench
Crystal structure of cystinosin from arabidopsis thaliana bound to sybody and nanobody
Analyse Crystal structure of cystinosin from arabidopsis thaliana bound to sybody and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZK1
- Type
- protein
- Length
- 491 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystinosin homolog; Llama derived nanobody; Synthetic nanobody (sybody)
- UniProt
- P57758
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystinosin homolog | protein | 243 | 76% helix, 0% strand | P57758 |
| B | Llama derived nanobody | protein | 127 | 6% helix, 44% strand | — |
| C | Synthetic nanobody (sybody) | protein | 121 | 5% helix, 52% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.81 | 0.91 | 43 | empty |
| 2 | 232 | 0.63 | 0.82 | 28 | empty |
| 3 | 111 | 0.36 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1118 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 686 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7ZK1 · Crystal structure of cystinosin from Arabidopsis thaliana bound to sybody and nanobody · the same entry in another collection · chain A against A, TM-score 1.00
- P57758 · AlphaFold monomer V2.0 prediction for cystinosin homolog (P57758) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P57758
- Elsewhere: RCSB PDB 7ZK1 · PDBe 7ZK1 · UniProt P57758
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