Research workbench
Crystal structure of pseudomonas aeruginosa azurin with IRON(II) at the copper-binding site.
Analyse Crystal structure of pseudomonas aeruginosa azurin with IRON(II) at the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HZ1
- Type
- protein
- Length
- 509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Azurin
- UniProt
- P00282
- Ligands
- FE2
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Azurin | protein | 127 | 15% helix, 34% strand | P00282 |
| B | Azurin | protein | 127 | 18% helix, 32% strand | P00282 |
| D | Azurin | protein | 128 | 15% helix, 34% strand | P00282 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 2 copies · chains B, C
- ACT · Acetate ion · additive · 5 copies · chains A, D, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.76 | 0.87 | 51 | ACT |
| 2 | 303 | 0.70 | 0.84 | 40 | ACT |
| 3 | 208 | 0.53 | 0.77 | 32 | ACT |
| 4 | 166 | 0.51 | 0.78 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–D · 555 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 414 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 380 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 377 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HZ1 · Crystal Structure of Pseudomonas aeruginosa azurin with iron(II) at the copper-binding… · 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 4HZ1 · PDBe 4HZ1 · UniProt P00282
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