Research workbench
Structure of the extracellular domain of the CD40 in complex with 3H56-5 dab
Analyse Structure of the extracellular domain of the CD40 in complex with 3H56-5 dab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IHL
- Type
- protein
- Length
- 1,134 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 5; 3H56-5 domain antibody (dab)
- UniProt
- P25942
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 5 | protein | 168 | 2% helix, 27% strand | P25942 |
| B, G, I | 3H56-5 domain antibody (dab) | protein | 117 | 8% helix, 44% strand | — |
| D | Tumor necrosis factor receptor superfamily member 5 | protein | 165 | 2% helix, 21% strand | P25942 |
| E | 3H56-5 domain antibody (dab) | protein | 118 | 8% helix, 48% strand | — |
| F | Tumor necrosis factor receptor superfamily member 5 | protein | 165 | 2% helix, 22% strand | P25942 |
| H | Tumor necrosis factor receptor superfamily member 5 | protein | 167 | 2% helix, 20% strand | P25942 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.77 | 0.85 | 54 | empty |
| 2 | 246 | 0.55 | 0.77 | 29 | empty |
| 3 | 192 | 0.54 | 0.79 | 20 | empty |
| 4 | 73 | 0.37 | 0.78 | 23 | empty |
| 5 | 99 | 0.35 | 0.74 | 16 | empty |
Interfaces
10 interfaces between chains.
- F–G · 842 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 835 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 802 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 787 Ų buried · 6 hydrogen bonds · protein-protein
- F–H · 421 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide (disulfide).
Compared structures
- 5IHL · Structure of the extracellular domain of the CD40 in complex with 3H56-5 dab · the same entry in another collection · chain I against I, 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 D against A, TM-score 0.61
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 5IHL · PDBe 5IHL · UniProt P25942
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