MolNFT v1 · #121977 · protein
Human antibody 6639 in complex with influenza hemagglutinin H1 X-181
5IBL: “Human antibody 6639 in complex with influenza hemagglutinin H1 X-181”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.67). MolNFT v1 #121977 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IBL
- Type
- protein
- Length
- 1,687 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; 6639 heavy chain; 6639 light chain
- UniProt
- C9EL84
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 7 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 106 | 80% helix, 0% strand | C9EL84 |
| B | Hemagglutinin | protein | 298 | 7% helix, 36% strand | C9EL84 |
| C | 6639 heavy chain | protein | 216 | 3% helix, 47% strand | — |
| D, L | 6639 light chain | protein | 215 | 7% helix, 49% strand | — |
| E | Hemagglutinin | protein | 115 | 74% helix, 0% strand | C9EL84 |
| F | Hemagglutinin | protein | 306 | 7% helix, 38% strand | C9EL84 |
| H | 6639 heavy chain | protein | 216 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.67 | 0.82 | 25 | empty |
| 2 | 277 | 0.65 | 0.81 | 28 | empty |
| 3 | 180 | 0.56 | 0.80 | 29 | NAG |
| 4 | 215 | 0.54 | 0.79 | 26 | empty |
| 5 | 322 | 0.52 | 0.73 | 40 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1904 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1832 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1295 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 896 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 551 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5IBL · Human antibody 6639 in complex with influenza hemagglutinin H1 X-181 · the same entry in another collection · chain B against B, 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 C9EL84
- Elsewhere: RCSB PDB 5IBL · PDBe 5IBL · UniProt C9EL84
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