MolNFT v1 · #176278 · protein
Crystal structure of CD38 in complex with daratumumab
7DHA · ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1: “Crystal structure of CD38 in complex with daratumumab”. X-ray diffraction, 11 pockets (best druggability 0.60). MolNFT v1 #176278 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DHA
- Type
- protein
- Length
- 682 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1; Light chain; Heavy chain
- EC
- 3.2.2.6, 2.4.99.20
- UniProt
- P28907
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1 (EC 3.2.2.6, 2.4.99.20) | protein | 248 | 43% helix, 14% strand | P28907 |
| B | Light chain | protein | 212 | 6% helix, 52% strand | — |
| C | Heavy chain | protein | 222 | 8% helix, 49% strand | — |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.60 | 0.88 | 17 | empty |
| 2 | 280 | 0.57 | 0.77 | 31 | empty |
| 3 | 398 | 0.56 | 0.74 | 40 | empty |
| 4 | 122 | 0.53 | 0.82 | 27 | empty |
| 5 | 53 | 0.52 | 0.88 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1907 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 941 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 299 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 7DHA · crystal structure of CD38 in complex with daratumumab · 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 0.95
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 7DHA · PDBe 7DHA · UniProt P28907
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