Research workbench

Mercury metallated pseudomonas aeruginosa azurin at 1.54 a

Analyse Mercury metallated pseudomonas aeruginosa azurin at 1.54 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JKN
Type: protein
Length: 512 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
EC: 1.20.9.1
UniProt: P00282
Ligands: HG, NO3, SO4
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Azurin (EC 1.20.9.1)	protein	128	19% helix, 34% strand	P00282

Ligands and binding sites

HG · Mercury (II) ion · metal · 5 copies · chains A, B, C, D
NO3 · Nitrate ion · ion · 7 copies · chains A, D, B
SO4 · Sulfate ion · ion · chains D

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	326	0.73	0.85	37	HG, NO3
2	264	0.71	0.86	37	NO3
3	80	0.64	0.91	21	empty
4	260	0.63	0.81	45	empty
5	248	0.61	0.81	41	empty

Interfaces

6 interfaces between chains.

A–C · 553 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 523 Å² buried · 1 hydrogen bond · protein-protein
C–D · 411 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 409 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 363 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4JKN · Mercury Metallated Pseudomonas aeruginosa Azurin at 1.54 A · 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 4JKN · PDBe 4JKN · UniProt P00282

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.