Research workbench
Binding site elucidation and structure guided design of macrocyclic il-17A antagonists
Analyse Binding site elucidation and structure guided design of macrocyclic il-17A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HI5
- Type
- protein
- Length
- 1,061 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-17A; Cat-2000 Fab heavy chain; Cat-2000 light chain; Synthetic il-17A…
- UniProt
- Q16552
- Ligands
- 63Q
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-17A | protein | 94 | 7% helix, 51% strand | Q16552 |
| B | Interleukin-17A | protein | 87 | 8% helix, 55% strand | Q16552 |
| C, H | Cat-2000 Fab heavy chain | protein | 220 | 8% helix, 53% strand | — |
| D, L | Cat-2000 light chain | protein | 213 | 8% helix, 50% strand | — |
| I | Synthetic il-17A inhibitor | protein | 14 | 50% helix, 36% strand | — |
Ligands and binding sites
- 63Q · (4S,20R)-7-chloro-N-methyl-4-{[(1-methyl-1H-pyrazol-5-yl)carbonyl]amino}-3,18-dioxo-2,19-diazatetracyclo[20.2.2.1~6,10~.1~11,15~]octacosa-1(24),6(28),7,9,11(27),12,14,22,25-nonaene-20-carboxamide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.77 | 0.78 | 93 | 63Q |
| 2 | 458 | 0.58 | 0.74 | 56 | empty |
| 3 | 186 | 0.58 | 0.81 | 31 | empty |
| 4 | 152 | 0.56 | 0.82 | 34 | empty |
| 5 | 143 | 0.55 | 0.82 | 31 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1828 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1743 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1084 Ų buried · 12 hydrogen bonds · protein-protein
- A–I · 646 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 365 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5HI5 · Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists · the same entry in another collection · chain B against B, TM-score 1.00
- Q16552 · AlphaFold monomer V2.0 prediction for interleukin-17A (Q16552) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 Q16552
- Elsewhere: RCSB PDB 5HI5 · PDBe 5HI5 · UniProt Q16552
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