Research workbench
Cryo EM structure of system xc-
Analyse Cryo EM structure of system xc- in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P9V
- Type
- protein
- Length
- 919 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4F2 cell-surface antigen heavy chain; CYSTINE/GLUTAMATE transporter
- UniProt
- P08195, Q9UPY5
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.72
Structure
electron microscopy · 2 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4F2 cell-surface antigen heavy chain | protein | 464 | 34% helix, 15% strand | P08195 |
| B | CYSTINE/GLUTAMATE transporter | protein | 455 | 66% helix, 1% strand | Q9UPY5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.72 | 0.81 | 63 | empty |
| 2 | 938 | 0.71 | 0.76 | 63 | empty |
| 3 | 360 | 0.63 | 0.78 | 24 | empty |
| 4 | 287 | 0.61 | 0.79 | 39 | empty |
| 5 | 182 | 0.58 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1269 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7P9V · Cryo EM structure of System XC- · the same entry in another collection · chain A against A, TM-score 1.00
- P08195 · AlphaFold monomer V2.0 prediction for 4F2 cell-surface antigen heavy chain (P08195) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UPY5 · AlphaFold monomer V2.0 prediction for CYSTINE/GLUTAMATE transporter (Q9UPY5) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P08195
- Every structure of UniProt Q9UPY5
- Elsewhere: RCSB PDB 7P9V · PDBe 7P9V · UniProt P08195 · UniProt Q9UPY5
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