MolNFT v1 · #191049 · protein
Crystal structure of cystinosin from arabidopsis thaliana bound to sybody and nanobody
7ZK1 · Cystinosin homolog: “Crystal structure of cystinosin from arabidopsis thaliana bound to sybody and nanobody”. X-ray diffraction, 3 pockets (best druggability 0.81). MolNFT v1 #191049 on GenesisL1: 3D structure, binding sites and…
- 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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