MolNFT v1 · #69954 · protein
Crystal structure of the complex between il-13 and C836 Fab
3L5W · C836 light chain: “Crystal structure of the complex between il-13 and C836 Fab”. X-ray diffraction, 12 pockets (best druggability 0.66). MolNFT v1 #69954 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3L5W
- Type
- protein
- Length
- 1,057 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C836 light chain; C836 heavy chain; Interleukin-13
- UniProt
- P35225
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | C836 light chain | protein | 213 | 6% helix, 50% strand | — |
| H | C836 heavy chain | protein | 223 | 7% helix, 49% strand | — |
| I | Interleukin-13 | protein | 101 | 51% helix, 6% strand | P35225 |
| B | C836 heavy chain | protein | 221 | 8% helix, 50% strand | — |
| J | Interleukin-13 | protein | 86 | 58% helix, 5% strand | P35225 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.66 | 0.74 | 77 | GOL |
| 2 | 602 | 0.64 | 0.75 | 63 | empty |
| 3 | 137 | 0.43 | 0.76 | 28 | empty |
| 4 | 181 | 0.42 | 0.73 | 27 | empty |
| 5 | 95 | 0.40 | 0.77 | 18 | empty |
Interfaces
8 interfaces between chains.
- L–H · 2007 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1900 Ų buried · 12 hydrogen bonds · protein-protein
- B–J · 477 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 477 Ų buried · 9 hydrogen bonds · protein-protein
- A–J · 201 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
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 P35225
- Elsewhere: RCSB PDB 3L5W · PDBe 3L5W · UniProt P35225
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