Research workbench
Crystal structure of blasticidin S deaminase (bsd) complexed with deaminohydroxy blasticidin S
Analyse Crystal structure of blasticidin S deaminase (bsd) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z3H
- Type
- protein
- Length
- 491 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
- BLO, ZN
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 122 | 34% helix, 27% strand | P0C2P0 |
| B | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 126 | 31% helix, 25% strand | P0C2P0 |
| D | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 121 | 33% helix, 26% strand | P0C2P0 |
Ligands and binding sites
- BLO · 1-(4-{[(3R)-3-amino-5-{[(Z)-amino(imino)methyl](methyl)amino}pentanoyl]amino}-2,3,4-trideoxy-D-erythro-hex-2-enopyranuronosyl)-4-hydroxypyrimidin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
- 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 | 146 | 0.56 | 0.82 | 29 | BLO |
| 2 | 163 | 0.48 | 0.77 | 23 | BLO |
| 3 | 118 | 0.45 | 0.78 | 21 | ZN, BLO |
| 4 | 119 | 0.44 | 0.77 | 20 | BLO |
Interfaces
6 interfaces between chains.
- B–C · 1123 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1093 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 629 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 409 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2Z3H · Crystal structure of blasticidin S deaminase (BSD) complexed with deaminohydroxy… · the same entry in another collection · chain D against D, 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 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 P0C2P0
- Elsewhere: RCSB PDB 2Z3H · PDBe 2Z3H · UniProt P0C2P0
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