Research workbench
Crystal structure of cystinosin from arabidopsis thaliana in complex with cystine and sybody
Analyse Crystal structure of cystinosin from arabidopsis thaliana in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZKW
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystinosin homolog; Sybody
- UniProt
- P57758
- Ligands
- IYY
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cystinosin homolog | protein | 243 | 80% helix, 0% strand | P57758 |
| C, D | Sybody | protein | 121 | 5% helix, 50% strand | — |
Ligands and binding sites
- IYY · L-cystine · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.81 | 0.91 | 50 | IYY |
| 2 | 396 | 0.79 | 0.88 | 56 | IYY |
| 3 | 228 | 0.48 | 0.74 | 27 | empty |
| 4 | 151 | 0.41 | 0.74 | 25 | empty |
| 5 | 88 | 0.35 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1192 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1140 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7ZKW · Crystal structure of cystinosin from Arabidopsis thaliana in complex with Cystine and… · 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 0.88
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 P57758
- Elsewhere: RCSB PDB 7ZKW · PDBe 7ZKW · UniProt P57758
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