Research workbench
Overall structure of erastin-bound xct-4F2HC complex
Analyse Overall structure of erastin-bound xct-4F2HC complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EPZ
- Type
- protein
- Length
- 921 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
- J3KPF3, Q9UPY5
- Ligands
- PX8, J9O, NAG
- Pockets
- 12 · best druggability 0.74
Structure
electron microscopy · 2 distinct chains · 46% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4F2 cell-surface antigen heavy chain | protein | 468 | 29% helix, 15% strand | J3KPF3 |
| B | CYSTINE/GLUTAMATE transporter | protein | 453 | 63% helix, 1% strand | Q9UPY5 |
Ligands and binding sites
- PX8 · 1,2-distearoyl-sn-glycero-3-phosphate · ligand · 2 copies · chains A, B
- J9O · 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one · ligand · chains B
- 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.74 | 0.82 | 60 | J9O |
| 2 | 722 | 0.68 | 0.76 | 63 | empty |
| 3 | 87 | 0.64 | 0.90 | 22 | empty |
| 4 | 374 | 0.63 | 0.78 | 24 | PX8 |
| 5 | 231 | 0.61 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1209 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
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 J3KPF3
- Every structure of UniProt Q9UPY5
- Elsewhere: RCSB PDB 7EPZ · PDBe 7EPZ · UniProt J3KPF3 · UniProt Q9UPY5
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