MolNFT v1 · #189551 · protein
Crystal structure of human CD38 ecd in complex with UNIDAB(TM) F11A
7VKE · ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1: “Crystal structure of human CD38 ecd in complex with UNIDAB(TM) F11A”. X-ray diffraction, 3 ligands (NA, MG, CL), 6 pockets (best druggability 0.61). MolNFT v1 #189551 on GenesisL1…
- PDB
- 7VKE
- Type
- protein
- Length
- 380 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1; Unidab F11A
- EC
- 3.2.2.6, 2.4.99.20
- UniProt
- P28907
- Ligands
- NA, MG, CL
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% 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 | 255 | 43% helix, 14% strand | P28907 |
| B | Unidab F11A | protein | 125 | 5% helix, 45% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.61 | 0.76 | 40 | EDO, MG |
| 2 | 65 | 0.59 | 0.90 | 17 | empty |
| 3 | 136 | 0.58 | 0.83 | 16 | NA |
| 4 | 79 | 0.36 | 0.76 | 13 | empty |
| 5 | 53 | 0.35 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1106 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7VKE · Crystal structure of human CD38 ECD in complex with UniDab(TM) F11A · 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 0.97
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 7VKE · PDBe 7VKE · UniProt P28907
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