Research workbench
Crystal structure of daratumumab Fab and CD38 complex
Analyse Crystal structure of daratumumab Fab and CD38 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DUO
- Type
- protein
- Length
- 652 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1; Fab light chain
- EC
- 3.2.2.6, 2.4.99.20
- UniProt
- P28907
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 210 | 8% helix, 49% strand | — |
| B | ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1 (EC 3.2.2.6, 2.4.99.20) | protein | 229 | 44% helix, 13% strand | P28907 |
| L | Fab light chain | protein | 213 | 6% helix, 51% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.62 | 0.74 | 60 | empty |
| 2 | 181 | 0.59 | 0.81 | 31 | empty |
| 3 | 311 | 0.57 | 0.76 | 37 | empty |
| 4 | 166 | 0.57 | 0.81 | 29 | empty |
| 5 | 62 | 0.46 | 0.84 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1719 Ų buried · 17 hydrogen bonds · protein-protein
- H–B · 675 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 175 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7DUO · Crystal structure of daratumumab fab and CD38 complex · the same entry in another collection · chain H against H, TM-score 1.00
- P28907 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase 1… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P28907
- Elsewhere: RCSB PDB 7DUO · PDBe 7DUO · UniProt P28907
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