Research workbench
Crystal structure of blasticidin S deaminase (bsd)
Analyse Crystal structure of blasticidin S deaminase (bsd) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z3G
- Type
- protein
- Length
- 495 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
- GLC, ZN
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 123 | 33% helix, 27% strand | P0C2P0 |
| B | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 127 | 31% helix, 25% strand | P0C2P0 |
| D | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 122 | 33% helix, 26% strand | P0C2P0 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B
- ZN · Zinc ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.55 | 0.82 | 24 | empty |
| 2 | 149 | 0.46 | 0.77 | 22 | empty |
| 3 | 128 | 0.46 | 0.78 | 21 | empty |
| 4 | 123 | 0.42 | 0.76 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1125 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1098 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 684 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 415 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 347 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 2Z3G · PDBe 2Z3G · UniProt P0C2P0
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