Research workbench
Crystal structure analysis of oxidized pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. a pH-induced conformational transition involves a peptide bond flip
Analyse Crystal structure analysis of oxidized pseudomonas aeruginosa azurin at pH 5.5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AZU
- Type
- protein
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Azurin
- UniProt
- P00282
- Ligands
- CU, NO3
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Azurin | protein | 128 | 16% helix, 34% strand | P00282 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.73 | 0.87 | 34 | empty |
| 2 | 57 | 0.67 | 0.96 | 18 | empty |
| 3 | 268 | 0.66 | 0.82 | 36 | empty |
| 4 | 244 | 0.61 | 0.81 | 45 | empty |
| 5 | 255 | 0.60 | 0.80 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–C · 537 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 422 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 419 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4AZU · Crystal structure analysis of oxidized pseudomonas aeruginosa azurin at pH 5.5 and pH… · the same entry in another collection · chain D against D, TM-score 1.00
- P00282 · AlphaFold monomer V2.0 prediction for azurin (P00282) · a predicted model of the same protein · chain B 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 P00282
- Elsewhere: RCSB PDB 4AZU · PDBe 4AZU · UniProt P00282
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