Research workbench
Crystal structure of a complex of human il-7RALPHA with an anti-il- 7RALPHA 2B8 Fab
Analyse Crystal structure of a complex of human il-7RALPHA with an anti-il- 7RALPHA 2B8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P67
- Type
- protein
- Length
- 2,512 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-il-7R 2B8 Fab heavy chain; Anti-il-7R 2B8 Fab light chain; Interleukin-7 receptor…
- UniProt
- P16871
- Ligands
- NAG, BMA, FUC
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H | Anti-il-7R 2B8 Fab heavy chain | protein | 223 | 4% helix, 49% strand | — |
| B, D, F, L | Anti-il-7R 2B8 Fab light chain | protein | 213 | 7% helix, 52% strand | — |
| E | Anti-il-7R 2B8 Fab heavy chain | protein | 220 | 5% helix, 50% strand | — |
| G, J | Interleukin-7 receptor subunit alpha | protein | 195 | 2% helix, 49% strand | P16871 |
| I | Interleukin-7 receptor subunit alpha | protein | 193 | 3% helix, 52% strand | P16871 |
| K | Interleukin-7 receptor subunit alpha | protein | 188 | 4% helix, 46% strand | P16871 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, I, D, J, B, K
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.76 | 0.79 | 88 | empty |
| 2 | 199 | 0.74 | 0.89 | 37 | empty |
| 3 | 228 | 0.73 | 0.88 | 42 | empty |
| 4 | 626 | 0.72 | 0.80 | 58 | empty |
| 5 | 1061 | 0.71 | 0.75 | 95 | empty |
Interfaces
24 interfaces between chains.
- A–B · 1963 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1919 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1915 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1759 Ų buried · 19 hydrogen bonds · protein-protein
- B–L · 1319 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6P67 · Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab · the same entry in another collection · chain L against L, TM-score 1.00
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 P16871
- Elsewhere: RCSB PDB 6P67 · PDBe 6P67 · UniProt P16871
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