MolNFT v1 · #26376 · protein
Crystal structure of blasticidin S deaminase (bsd) complexed with tetrahedral intermediate of blasticidin S
1WN6 · Blasticidin-S deaminase: “Crystal structure of blasticidin S deaminase (bsd) complexed with tetrahedral intermediate of blasticidin S”. X-ray diffraction, 3 ligands (BST, ZN, ARS), 2 pockets (best druggability 0.31). MolNFT v1…
- PDB
- 1WN6
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blasticidin-S deaminase
- EC
- 3.5.4.23
- UniProt
- P78986
- Ligands
- BST, ZN, ARS
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 126 | 31% helix, 25% strand | P78986 |
| B | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 126 | 32% helix, 25% strand | P78986 |
Ligands and binding sites
- BST · 6-(4-amino-4-hydroxy-2-oxo-3,4-dihydro-2H-pyrimidin-1-yl)-3-[3-amino-5-(N-methyl-guanidino)-pent anoylamino]-3,6-dihydro-2H-pyran-2-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ARS · Arsenic · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.31 | 0.75 | 19 | BST |
| 2 | 50 | 0.28 | 0.75 | 17 | BST |
Interfaces
1 interface between chains.
- A–B · 1290 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1WN6 · Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral… · 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 P78986
- Elsewhere: RCSB PDB 1WN6 · PDBe 1WN6 · UniProt P78986
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