MolNFT v1 · #56061 · protein
Crystal structure of blasticidin S deaminase (bsd) mutant E56Q complexed with substrate
2Z3I · Blasticidin-S deaminase: “Crystal structure of blasticidin S deaminase (bsd) mutant E56Q complexed with substrate”. X-ray diffraction, 2 ligands (BLS, ZN), 4 pockets (best druggability 0.60). MolNFT v1 #56061 on GenesisL1: 3D…
- PDB
- 2Z3I
- Type
- protein
- Length
- 516 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
- P0C2P0
- Ligands
- BLS, ZN
- Pockets
- 4 · best druggability 0.60
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 | 129 | 32% helix, 26% strand | P0C2P0 |
Ligands and binding sites
- BLS · Blasticidin S · ligand · 4 copies · chains A, B, C, D
- 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 | 203 | 0.60 | 0.81 | 36 | BLS |
| 2 | 159 | 0.60 | 0.83 | 30 | BLS |
| 3 | 141 | 0.59 | 0.84 | 28 | BLS |
| 4 | 210 | 0.58 | 0.80 | 38 | BLS |
Interfaces
6 interfaces between chains.
- B–C · 1287 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1274 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 739 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 731 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2Z3I · Crystal structure of blasticidin S deaminase (BSD) mutant E56Q complexed with substrate · the same entry in another collection · chain B against B, TM-score 1.00
- P0C2P0 · AlphaFold monomer V2.0 prediction for blasticidin-S deaminase (P0C2P0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0C2P0
- Elsewhere: RCSB PDB 2Z3I · PDBe 2Z3I · UniProt P0C2P0
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