MolNFT v1 · #116729 · protein
Structure of the extracellular domain of the CD40 in complex with CHI220 Fab
5DMI · Tumor necrosis factor receptor superfamily member 5: “Structure of the extracellular domain of the CD40 in complex with CHI220 Fab”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.60). MolNFT v1 #116729 on…
- 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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