MolNFT v1 · #165796 · protein
IL36R extracellular domain in complex with BI655130 Fab
6U6U · BI00655130 Fab heavy chain: “IL36R extracellular domain in complex with BI655130 Fab”. X-ray diffraction, 2 ligands (NAG, NA), 6 pockets (best druggability 0.65). MolNFT v1 #165796 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6U6U
- Type
- protein
- Length
- 632 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BI00655130 Fab heavy chain; BI00655130 Fab light chain; Interleukin-1 receptor-like 2
- UniProt
- Q9HB29
- Ligands
- NAG, NA
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | BI00655130 Fab heavy chain | protein | 221 | 8% helix, 53% strand | — |
| L | BI00655130 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| R | Interleukin-1 receptor-like 2 | protein | 197 | 5% helix, 48% strand | Q9HB29 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains R
- NA · Sodium ion · metal · chains H, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.65 | 0.75 | 61 | empty |
| 2 | 152 | 0.62 | 0.84 | 25 | empty |
| 3 | 188 | 0.51 | 0.77 | 26 | empty |
| 4 | 126 | 0.43 | 0.76 | 20 | empty |
| 5 | 53 | 0.29 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1884 Ų buried · 16 hydrogen bonds · protein-protein
- H–R · 815 Ų buried · 18 hydrogen bonds · protein-protein
- L–R · 401 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
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 Q9HB29
- Elsewhere: RCSB PDB 6U6U · PDBe 6U6U · UniProt Q9HB29
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