Research workbench
Crystal structure of the CD40 and CD154 (CD40L) complex
Analyse Crystal structure of the CD40 and CD154 (CD40L) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QD6
- Type
- protein
- Length
- 1,276 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD40 ligand; Tumor necrosis factor receptor superfamily member 5
- UniProt
- P29965, P25942
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | CD40 ligand | protein | 135 | 0% helix, 46% strand | P29965 |
| R, T | Tumor necrosis factor receptor superfamily member 5 | protein | 114 | 3% helix, 25% strand | P25942 |
| S, U | Tumor necrosis factor receptor superfamily member 5 | protein | 119 | 3% helix, 27% strand | P25942 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.81 | 0.82 | 101 | empty |
| 2 | 145 | 0.69 | 0.90 | 36 | empty |
| 3 | 126 | 0.69 | 0.90 | 34 | empty |
| 4 | 351 | 0.64 | 0.79 | 52 | empty |
| 5 | 333 | 0.64 | 0.80 | 45 | empty |
Interfaces
17 interfaces between chains.
- D–E · 1030 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1015 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1011 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1007 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 995 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 7 glycan (disulfide, N-glycosylation, 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 P29965
- Every structure of UniProt P25942
- Elsewhere: RCSB PDB 3QD6 · PDBe 3QD6 · UniProt P29965 · UniProt P25942
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