MolNFT v1 · #184815 · protein
Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 darpin protein
7P3I · Tumor necrosis factor receptor superfamily member 5: “Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 darpin protein”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.55). MolNFT v1 #184815 on…
- PDB
- 7P3I
- Type
- protein
- Length
- 648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 5; Darpin
- UniProt
- P25942
- Ligands
- NA
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 5 | protein | 168 | 4% helix, 36% strand | P25942 |
| B | Darpin | protein | 159 | 56% helix, 0% strand | — |
| C | Tumor necrosis factor receptor superfamily member 5 | protein | 165 | 4% helix, 36% strand | P25942 |
| D | Darpin | protein | 156 | 55% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
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 | 300 | 0.55 | 0.76 | 30 | empty |
| 2 | 97 | 0.33 | 0.73 | 16 | empty |
| 3 | 54 | 0.26 | 0.74 | 15 | empty |
| 4 | 55 | 0.25 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 972 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 182 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 180 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 7P3I · Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein · 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 0.61
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 7P3I · PDBe 7P3I · UniProt P25942
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