MolNFT v1 · #118743 · protein
Structure of interleukin-16 bound to the 14.1 antibody
5FB8 · Anti-il-16 antibody 14.1 Fab domain kappa chain: “Structure of interleukin-16 bound to the 14.1 antibody”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.63). MolNFT v1 #118743 on GenesisL1: 3D structure, binding…
- PDB
- 5FB8
- Type
- protein
- Length
- 525 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-il-16 antibody 14.1 Fab domain kappa chain; Anti-il-16 antibody 14.1 Fab domain…
- UniProt
- Q14005
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-il-16 antibody 14.1 Fab domain kappa chain | protein | 218 | 6% helix, 52% strand | — |
| B | Anti-il-16 antibody 14.1 Fab domain heavy chain | protein | 223 | 12% helix, 51% strand | — |
| C | Pro-interleukin-16 | protein | 84 | 12% helix, 55% strand | Q14005 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.63 | 0.74 | 61 | EDO |
| 2 | 282 | 0.60 | 0.79 | 39 | EDO |
| 3 | 51 | 0.54 | 0.89 | 21 | empty |
| 4 | 123 | 0.46 | 0.78 | 27 | SO4, TRS |
| 5 | 125 | 0.39 | 0.74 | 26 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1927 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 726 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 348 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 Q14005
- Elsewhere: RCSB PDB 5FB8 · PDBe 5FB8 · UniProt Q14005
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