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
- 5DMJ
- Type
- protein
- Length
- 844 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.79
- Source
- Homo sapiens
- Molecule
- Tumor necrosis factor receptor superfamily member 5; 3H65-5 domain antibody (dAb)
- UniProt
- P25942
- Ligands
- K
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.79 · 6 distinct chains · 4% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 5 | protein | 165 | 2% helix, 27% strand | P25942 |
| B | 3H65-5 domain antibody (dAb) | protein | 117 | 5% helix, 49% strand | — |
| D | Tumor necrosis factor receptor superfamily member 5 | protein | 167 | 2% helix, 30% strand | P25942 |
| E | 3H65-5 domain antibody (dAb) | protein | 116 | 5% helix, 48% strand | — |
| F | Tumor necrosis factor receptor superfamily member 5 | protein | 163 | 4% helix, 21% strand | P25942 |
| G | 3H65-5 domain antibody (dAb) | protein | 116 | 5% helix, 48% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, D, F
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 | 592 | 0.66 | 0.76 | 55 | empty |
| 2 | 112 | 0.35 | 0.73 | 23 | empty |
| 3 | 55 | 0.29 | 0.75 | 15 | empty |
| 4 | 60 | 0.27 | 0.72 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 867 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 837 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 764 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 190 Ų buried · 0 hydrogen bonds · protein-protein
- B–G · 170 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide (disulfide).
Compared structures
- 5DMJ · Structure of the extracellular domain of the CD40 in complex with 3H56-5 dab · the same entry in another collection · chain G against G, 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 0.64
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 5DMJ · PDBe 5DMJ · UniProt P25942
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