MolNFT v1 · #158047 · protein
Crystal structure of the human TLR2-diprovocim complex
6NIG · Toll-like receptor 2,VARIABLE lymphocyte receptor B: “Crystal structure of the human TLR2-diprovocim complex”. X-ray diffraction, 2 ligands (KQD, NAG), 17 pockets (best druggability 0.86). MolNFT v1 #158047 on GenesisL1: 3D…
- PDB
- 6NIG
- Type
- protein
- Length
- 2,186 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 2,VARIABLE lymphocyte receptor B
- UniProt
- O60603, Q2YE02
- Ligands
- KQD, NAG
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 2,VARIABLE lymphocyte receptor B | protein | 546 | 14% helix, 21% strand | O60603, Q2YE02 |
| B | Toll-like receptor 2,VARIABLE lymphocyte receptor B | protein | 545 | 13% helix, 20% strand | O60603, Q2YE02 |
| C | Toll-like receptor 2,VARIABLE lymphocyte receptor B | protein | 549 | 13% helix, 20% strand | O60603, Q2YE02 |
| D | Toll-like receptor 2,VARIABLE lymphocyte receptor B | protein | 546 | 12% helix, 21% strand | O60603, Q2YE02 |
Ligands and binding sites
- KQD · (3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{n~3~, N~4~-bis[(1s,2r)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de} · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.86 | 0.89 | 59 | KQD |
| 2 | 705 | 0.85 | 0.88 | 55 | KQD |
| 3 | 709 | 0.85 | 0.88 | 56 | KQD |
| 4 | 663 | 0.85 | 0.89 | 62 | KQD |
| 5 | 567 | 0.66 | 0.77 | 74 | empty |
Interfaces
6 interfaces between chains.
- A–B · 910 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 894 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 535 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 490 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 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 O60603
- Every structure of UniProt Q2YE02
- Elsewhere: RCSB PDB 6NIG · PDBe 6NIG · UniProt O60603 · UniProt Q2YE02
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