Research workbench
Complex structure of bat CD26 and MERS-rbd
Analyse Complex structure of bat CD26 and MERS-rbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L8Q
- Type
- protein
- Length
- 3,728 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4; Spike glycoprotein
- UniProt
- L5LQ33, A0A0A0Q7F3
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Dipeptidyl peptidase 4 | protein | 724 | 18% helix, 37% strand | L5LQ33 |
| B, D, F, H | Spike glycoprotein | protein | 208 | 16% helix, 35% strand | A0A0A0Q7F3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, B, C, D, E, F, G, H
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.85 | 0.88 | 104 | empty |
| 2 | 549 | 0.83 | 0.89 | 69 | empty |
| 3 | 428 | 0.82 | 0.90 | 48 | empty |
| 4 | 210 | 0.78 | 0.92 | 28 | empty |
| 5 | 954 | 0.73 | 0.77 | 106 | empty |
Interfaces
15 interfaces between chains.
- A–B · 935 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 929 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 911 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 872 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 781 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 6L8Q · Complex structure of bat CD26 and MERS-RBD · the same entry in another collection · chain D against D, TM-score 1.00
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 L5LQ33
- Every structure of UniProt A0A0A0Q7F3
- Elsewhere: RCSB PDB 6L8Q · PDBe 6L8Q · UniProt L5LQ33 · UniProt A0A0A0Q7F3
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