Research workbench
Crystal structure of human CD38 in complex with the Fab fragment of antibody HB7
Analyse Crystal structure of human CD38 in complex with the Fab fragment of antibody HB7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RAJ
- Type
- protein
- Length
- 653 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cyclase 1; Heavy chain of the Fab fragment of antibody HB7; Light chain of…
- EC
- 3.2.2.5
- UniProt
- P28907
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 230 | 35% helix, 15% strand | P28907 |
| H | Heavy chain of the Fab fragment of antibody HB7 | protein | 215 | 3% helix, 44% strand | — |
| L | Light chain of the Fab fragment of antibody HB7 | protein | 208 | 4% helix, 41% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.62 | 0.80 | 35 | empty |
| 2 | 181 | 0.52 | 0.78 | 25 | empty |
| 3 | 219 | 0.50 | 0.76 | 34 | empty |
| 4 | 55 | 0.48 | 0.86 | 18 | empty |
| 5 | 56 | 0.47 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1627 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 335 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 307 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3RAJ · Crystal structure of human CD38 in complex with the Fab fragment of antibody HB7 · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.94
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 3RAJ · PDBe 3RAJ · UniProt P28907
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