Research workbench
Crystal structure of CD38 with a novel CD38-targeting antibody SAR650984
Analyse Crystal structure of CD38 with a novel CD38-targeting antibody SAR650984 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CMH
- Type
- protein
- Length
- 669 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cyclase 1; Heavy chain of SAR650984-Fab fragment; Light chain of…
- EC
- 3.2.2.5
- UniProt
- P28907
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 240 | 44% helix, 15% strand | P28907 |
| B | Heavy chain of SAR650984-Fab fragment | protein | 216 | 8% helix, 52% strand | — |
| C | Light chain of SAR650984-Fab fragment | protein | 213 | 6% helix, 48% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.65 | 0.79 | 38 | empty |
| 2 | 485 | 0.61 | 0.75 | 63 | empty |
| 3 | 225 | 0.56 | 0.78 | 41 | empty |
| 4 | 163 | 0.50 | 0.78 | 22 | empty |
| 5 | 191 | 0.49 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1735 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 932 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4CMH · Crystal structure of CD38 with a novel CD38-targeting antibody SAR650984 · 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 0.99
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 4CMH · PDBe 4CMH · UniProt P28907
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