MolNFT v1 · #10473 · protein
Crystal structure analysis of bst-1/CD157 complexed with nmn
1ISJ · Bone marrow stromal cell antigen 1: “Crystal structure analysis of bst-1/CD157 complexed with nmn”. X-ray diffraction, 2 ligands (NMN, NAG), 5 pockets (best druggability 0.78). MolNFT v1 #10473 on GenesisL1: 3D structure, binding…
- PDB
- 1ISJ
- 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
- NMN, NAG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% 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 | 40% helix, 12% strand | Q10588 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.78 | 0.81 | 76 | empty |
| 2 | 192 | 0.57 | 0.80 | 20 | NMN |
| 3 | 218 | 0.57 | 0.79 | 34 | NMN |
| 4 | 84 | 0.37 | 0.77 | 18 | empty |
| 5 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1405 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1ISJ · Crystal Structure Analysis of BST-1/CD157 complexed with NMN · 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 1ISJ · PDBe 1ISJ · UniProt Q10588
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