Research workbench
LAT1-CD98HC complex bound to mem-108 Fab
Analyse LAT1-CD98HC complex bound to mem-108 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JMQ
- Type
- protein
- Length
- 1,287 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large neutral amino acids transporter small subunit 1; 4F2 cell-surface antigen heavy…
- UniProt
- Q01650, P08195
- Ligands
- CLR, NAG
- Pockets
- 16 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Large neutral amino acids transporter small subunit 1 | protein | 403 | 72% helix, 0% strand | Q01650 |
| B | 4F2 cell-surface antigen heavy chain | protein | 451 | 29% helix, 16% strand | P08195 |
| C | Antibody | protein | 214 | 4% helix, 38% strand | — |
| D | Antibody | protein | 219 | 5% helix, 44% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.79 | 0.85 | 60 | empty |
| 2 | 401 | 0.76 | 0.86 | 53 | empty |
| 3 | 608 | 0.65 | 0.75 | 53 | empty |
| 4 | 453 | 0.61 | 0.76 | 76 | empty |
| 5 | 167 | 0.59 | 0.83 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1683 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 833 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 289 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 196 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6JMQ · LAT1-CD98hc complex bound to MEM-108 Fab · 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 B against A, TM-score 0.99
- Q01650 · AlphaFold monomer V2.0 prediction for large neutral amino acids transporter small subunit… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q01650
- Every structure of UniProt P08195
- Elsewhere: RCSB PDB 6JMQ · PDBe 6JMQ · UniProt Q01650 · UniProt P08195
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