MolNFT v1 · #11742 · protein
Azurin dimer, crosslinked via disulfide bridge
1JVO: “Azurin dimer, crosslinked via disulfide bridge”. X-ray diffraction, 1 ligand (CU), 10 pockets (best druggability 0.72). MolNFT v1 #11742 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JVO
- Type
- protein
- Length
- 1,536 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Azurin
- UniProt
- P00282
- Ligands
- CU
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Azurin | protein | 128 | 19% helix, 34% strand | P00282 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.72 | 0.78 | 80 | empty |
| 2 | 480 | 0.70 | 0.80 | 50 | empty |
| 3 | 358 | 0.66 | 0.80 | 39 | empty |
| 4 | 296 | 0.56 | 0.76 | 38 | empty |
| 5 | 281 | 0.55 | 0.76 | 37 | empty |
Interfaces
15 interfaces between chains.
- A–D · 484 Ų buried · 1 hydrogen bond · protein-protein
- E–H · 482 Ų buried · 0 hydrogen bonds · protein-protein
- I–L · 472 Ų buried · 0 hydrogen bonds · protein-protein
- G–H · 235 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 232 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1JVO · Azurin dimer, crosslinked via disulfide bridge · the same entry in another collection · chain L against L, TM-score 1.00
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 1JVO · PDBe 1JVO · UniProt P00282
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