MolNFT v1 · #134245 · protein
Circularly permutated azurin (cpaz) based on P. aeruginosa azurin sequence
5SYD · Azurin, chimeric construct: “Circularly permutated azurin (cpaz) based on P. aeruginosa azurin sequence”. X-ray diffraction, 1 ligand (CU), 2 pockets (best druggability 0.46). MolNFT v1 #134245 on GenesisL1: 3D structure, binding…
- PDB
- 5SYD
- Type
- protein
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Azurin, chimeric construct
- UniProt
- P00282, B3EWN9
- Ligands
- CU
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Azurin, chimeric construct | protein | 130 | 15% helix, 35% strand | P00282, B3EWN9 |
| B | Azurin, chimeric construct | protein | 131 | 15% helix, 33% strand | P00282, B3EWN9 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.46 | 0.79 | 21 | empty |
| 2 | 66 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 426 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5SYD · Circularly permutated azurin (cpAz) based on P. aeruginosa azurin sequence · the same entry in another collection · chain A against A, TM-score 1.00
- B3EWN9 · AlphaFold monomer V2.0 prediction for azurin (B3EWN9) · a predicted model of the same protein · chain B against A, TM-score 0.66
- P00282 · AlphaFold monomer V2.0 prediction for azurin (P00282) · a predicted model of the same protein · chain B against A, TM-score 0.66
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
- Every structure of UniProt B3EWN9
- Elsewhere: RCSB PDB 5SYD · PDBe 5SYD · UniProt P00282 · UniProt B3EWN9
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