Research workbench
Structure of il-13 antibody H2L6, a humanized variant of C836
Analyse Structure of il-13 antibody H2L6, a humanized variant of C836 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L7F
- Type
- protein
- Length
- 1,303 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H2L6 light chain; H2L6 heavy chain
- Ligands
- CA, SO4
- Pockets
- 19 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, D | H2L6 light chain | protein | 213 | 6% helix, 51% strand | — |
| H | H2L6 heavy chain | protein | 222 | 8% helix, 51% strand | — |
| B, E | H2L6 heavy chain | protein | 221 | 7% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.63 | 0.74 | 62 | empty |
| 2 | 624 | 0.63 | 0.74 | 54 | empty |
| 3 | 581 | 0.62 | 0.74 | 65 | empty |
| 4 | 250 | 0.57 | 0.78 | 31 | SO4 |
| 5 | 52 | 0.55 | 0.90 | 17 | empty |
Interfaces
9 interfaces between chains.
- D–E · 2001 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1949 Ų buried · 14 hydrogen bonds · protein-protein
- L–H · 1878 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 383 Ų buried · 6 hydrogen bonds · protein-protein
- L–D · 359 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 modified (disulfide, cyclization).
Compared structures
- 3L7F · Structure of IL-13 antibody H2L6, A humanized variant OF C836 · 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
- Elsewhere: RCSB PDB 3L7F · PDBe 3L7F
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