MolNFT v1 · #26375 · protein
Crystal structure of blasticidin S deaminase (bsd) complexed with cacodylic acid
1WN5 · Blasticidin-S deaminase: “Crystal structure of blasticidin S deaminase (bsd) complexed with cacodylic acid”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.58). MolNFT v1 #26375 on GenesisL1: 3D structure, binding…
- PDB
- 1WN5
- Type
- protein
- Length
- 500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blasticidin-S deaminase
- EC
- 3.5.4.23
- UniProt
- P78986
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 125 | 32% helix, 26% strand | P78986 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.58 | 0.87 | 21 | ZN, CAC |
| 2 | 95 | 0.57 | 0.86 | 21 | CAC |
| 3 | 93 | 0.57 | 0.86 | 21 | ZN, CAC |
| 4 | 87 | 0.57 | 0.86 | 20 | CAC |
Interfaces
6 interfaces between chains.
- B–C · 1150 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1134 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 658 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 656 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1WN5 · Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Cacodylic Acid · 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 1WN5 · PDBe 1WN5 · UniProt P78986
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