Research workbench
Crystal structure of blasticidin S deaminase from coccidioides immitis
Analyse Crystal structure of blasticidin S deaminase from coccidioides immitis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OJ6
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blasticidin-S deaminase
- EC
- 3.5.4.23
- Ligands
- ZN, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 134 | 30% helix, 24% strand | — |
| B | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 134 | 30% helix, 25% strand | — |
| C | Blasticidin-S deaminase (EC 3.5.4.23) | protein | 128 | 31% helix, 30% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.66 | 0.82 | 31 | EDO |
| 2 | 159 | 0.60 | 0.83 | 30 | ZN, EDO |
| 3 | 67 | 0.49 | 0.85 | 17 | empty |
| 4 | 81 | 0.34 | 0.75 | 17 | empty |
| 5 | 56 | 0.32 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1466 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1292 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 998 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 576 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3OJ6 · Crystal structure of Blasticidin S Deaminase from Coccidioides Immitis · 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
- Elsewhere: RCSB PDB 3OJ6 · PDBe 3OJ6
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