Research workbench
Porcine CD38 complexed with complexed with a covalent intermediate, ribo-F-ribose-5'-phosphate
Analyse Porcine CD38 complexed with complexed with a covalent intermediate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BNI
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- F1S5D9
- Ligands
- AVW
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 232 | 39% helix, 15% strand | F1S5D9 |
| B | Uncharacterized protein | protein | 231 | 42% helix, 16% strand | F1S5D9 |
Ligands and binding sites
- AVW · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4S)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 643 | 0.72 | 0.79 | 48 | empty |
| 2 | 212 | 0.56 | 0.79 | 33 | AVW |
| 3 | 62 | 0.54 | 0.88 | 16 | empty |
| 4 | 73 | 0.52 | 0.85 | 20 | empty |
| 5 | 78 | 0.44 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 620 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5BNI · Porcine CD38 complexed with complexed with a covalent intermediate… · the same entry in another collection · chain A against A, TM-score 1.00
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 F1S5D9
- Elsewhere: RCSB PDB 5BNI · PDBe 5BNI · UniProt F1S5D9
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