Research workbench
Crystal structure of CD40/ABBV-323 Fab complex
Analyse Crystal structure of CD40/ABBV-323 Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PE8
- Type
- protein
- Length
- 1,183 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Tumor necrosis factor receptor superfamily member 5
- UniProt
- P25942
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab heavy chain | protein | 213 | 7% helix, 53% strand | — |
| B | Fab light chain | protein | 220 | 6% helix, 52% strand | — |
| H | Fab heavy chain | protein | 212 | 9% helix, 51% strand | — |
| L | Fab light chain | protein | 219 | 6% helix, 51% strand | — |
| T | Tumor necrosis factor receptor superfamily member 5 | protein | 159 | 2% helix, 33% strand | P25942 |
| U | Tumor necrosis factor receptor superfamily member 5 | protein | 160 | 2% helix, 34% strand | P25942 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains T, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.69 | 0.79 | 52 | empty |
| 2 | 208 | 0.65 | 0.84 | 31 | empty |
| 3 | 178 | 0.63 | 0.84 | 38 | empty |
| 4 | 165 | 0.62 | 0.84 | 35 | empty |
| 5 | 437 | 0.62 | 0.76 | 50 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1695 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1621 Ų buried · 13 hydrogen bonds · protein-protein
- H–T · 547 Ų buried · 9 hydrogen bonds · protein-protein
- A–U · 486 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 465 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide (disulfide).
Compared structures
- 6PE8 · Crystal structure of CD40/ABBV-323 FAB complex · the same entry in another collection · chain U against U, 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 T against A, TM-score 0.62
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 6PE8 · PDBe 6PE8 · UniProt P25942
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