Research workbench
Crystal structure analysis of bst-1/CD157 complexed with nicotinamide
Analyse Crystal structure analysis of bst-1/CD157 complexed with nicotinamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ISM
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone marrow stromal cell antigen 1
- EC
- 3.2.2.5
- UniProt
- Q10588
- Ligands
- NCA, NAG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bone marrow stromal cell antigen 1 (EC 3.2.2.5) | protein | 250 | 42% helix, 12% strand | Q10588 |
Ligands and binding sites
- NCA · Nicotinamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.75 | 0.78 | 80 | empty |
| 2 | 224 | 0.58 | 0.80 | 30 | NCA |
| 3 | 217 | 0.57 | 0.79 | 32 | NCA |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1ISM · Crystal Structure Analysis of BST-1/CD157 complexed with nicotinamide · the same entry in another collection · chain A against A, TM-score 1.00
- Q10588 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase 2… · a predicted model of the same protein · 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 Q10588
- Elsewhere: RCSB PDB 1ISM · PDBe 1ISM · UniProt Q10588
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