MolNFT v1 · #153701 · protein
CD98HC extracellular domain bound to HBJ127 Fab and mem-108 Fab
6JMR · Antibody: “CD98HC extracellular domain bound to HBJ127 Fab and mem-108 Fab”. Electron microscopy, 1 ligand (NAG), 16 pockets (best druggability 0.78). MolNFT v1 #153701 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JMR
- Type
- protein
- Length
- 1,287 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody; 4F2 cell-surface antigen heavy chain
- UniProt
- P08195
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Antibody | protein | 215 | 3% helix, 48% strand | — |
| F | Antibody | protein | 218 | 4% helix, 43% strand | — |
| B | 4F2 cell-surface antigen heavy chain | protein | 421 | 23% helix, 14% strand | P08195 |
| C | Antibody | protein | 214 | 4% helix, 39% strand | — |
| D | Antibody | protein | 219 | 5% helix, 46% strand | — |
Ligands and binding sites
- 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.78 | 0.86 | 69 | empty |
| 2 | 464 | 0.64 | 0.77 | 76 | empty |
| 3 | 113 | 0.61 | 0.87 | 26 | empty |
| 4 | 348 | 0.61 | 0.78 | 37 | empty |
| 5 | 570 | 0.61 | 0.74 | 60 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1832 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1472 Ų buried · 4 hydrogen bonds · protein-protein
- F–B · 369 Ų buried · 4 hydrogen bonds · protein-protein
- E–B · 341 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6JMR · CD98hc extracellular domain bound to HBJ127 Fab and MEM-108 Fab · the same entry in another collection · chain E against E, 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 0.98
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
- Elsewhere: RCSB PDB 6JMR · PDBe 6JMR · UniProt P08195
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