Research workbench
Crystal structure of native pseudoazurin from hyphomicrobium denitrificans
Analyse Crystal structure of native pseudoazurin from hyphomicrobium denitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EF4
- Type
- protein
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue copper protein
- UniProt
- A7VL37
- Ligands
- CU, PO4
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Blue copper protein | protein | 124 | 16% helix, 34% strand | A7VL37 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.45 | 0.80 | 24 | PO4 |
| 2 | 65 | 0.37 | 0.79 | 13 | PO4 |
| 3 | 53 | 0.29 | 0.75 | 16 | empty |
| 4 | 59 | 0.27 | 0.73 | 17 | PO4 |
Interfaces
2 interfaces between chains.
- A–B · 395 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3EF4 · Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans · 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 A7VL37
- Elsewhere: RCSB PDB 3EF4 · PDBe 3EF4 · UniProt A7VL37
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