Research workbench
Structure of the extracellular domain of the CD40 in complex with CHI220 Fab
Analyse Structure of the extracellular domain of the CD40 in complex with CHI220 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DMI
- Type
- protein
- Length
- 534 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 5; CHI220 Fab heavy chain; CHI220 Fab…
- UniProt
- P25942
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 5 | protein | 98 | 3% helix, 22% strand | P25942 |
| H | CHI220 Fab heavy chain | protein | 223 | 6% helix, 47% strand | — |
| L | CHI220 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.60 | 0.74 | 58 | empty |
| 2 | 155 | 0.46 | 0.76 | 31 | empty |
| 3 | 207 | 0.45 | 0.73 | 42 | empty |
| 4 | 64 | 0.31 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1790 Ų buried · 17 hydrogen bonds · protein-protein
- A–L · 417 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 378 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 5DMI · Structure of the extracellular domain of the CD40 in complex with CHI220 FAB · the same entry in another collection · chain A against A, TM-score 1.00
- P25942 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 5… · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P25942
- Elsewhere: RCSB PDB 5DMI · PDBe 5DMI · UniProt P25942
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