Research workbench
Crystal structure of circularly permutated azurin 3
Analyse Crystal structure of circularly permutated azurin 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YT7
- Type
- protein
- Length
- 528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Azurin
- UniProt
- P00282
- Ligands
- CU, CA, NA, NO3, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Azurin | protein | 133 | 18% helix, 34% strand | P00282 |
| B | Azurin | protein | 132 | 16% helix, 34% strand | P00282 |
| C | Azurin | protein | 130 | 16% helix, 35% strand | P00282 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, C
- NO3 · Nitrate ion · ion · 4 copies · chains A, B, D, C
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.69 | 0.81 | 58 | NA |
| 2 | 315 | 0.53 | 0.75 | 39 | empty |
| 3 | 234 | 0.48 | 0.74 | 28 | NO3 |
| 4 | 250 | 0.48 | 0.73 | 41 | NO3 |
| 5 | 96 | 0.37 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 450 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 307 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 120 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 5YT7 · PDBe 5YT7 · UniProt P00282
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