MolNFT v1 · #114026 · protein
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
5AZU: “Crystal structure analysis of oxidized pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. a pH-induced…”. X-ray diffraction, 2 ligands (CU, NO3), 5 pockets (best druggability 0.71). MolNFT v1 #114026 on GenesisL1: 3D structure…
- PDB
- 5AZU
- 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 0.71
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Azurin | protein | 128 | 17% 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 | 224 | 0.71 | 0.87 | 29 | empty |
| 2 | 58 | 0.66 | 0.95 | 20 | empty |
| 3 | 231 | 0.65 | 0.83 | 36 | empty |
| 4 | 246 | 0.59 | 0.80 | 43 | empty |
| 5 | 195 | 0.58 | 0.81 | 40 | empty |
Interfaces
6 interfaces between chains.
- B–D · 546 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 538 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 413 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 404 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 391 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5AZU · Crystal structure analysis of oxidized pseudomonas aeruginosa azurin at pH 5.5 and pH… · the same entry in another collection · chain B against B, TM-score 1.00
- P00282 · AlphaFold monomer V2.0 prediction for azurin (P00282) · a predicted model of the same protein · chain C 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 5AZU · PDBe 5AZU · UniProt P00282
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