Research workbench

X-ray crystal structure of pseudoazurin MET16GLY variant, reduced form.

Analyse X-ray crystal structure of pseudoazurin MET16GLY variant, reduced form. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YSG
Type: protein
Length: 479 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pseudoazurin
UniProt: P19567
Ligands: CU
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Pseudoazurin	protein	120	21% helix, 36% strand	P19567
C	Pseudoazurin	protein	119	21% helix, 34% strand	P19567

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 7 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1163	0.76	0.78	105	GOL
2	238	0.59	0.80	31	GOL

Interfaces

5 interfaces between chains.

A–D · 435 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 324 Å² buried · 1 hydrogen bond · protein-protein
C–D · 316 Å² buried · 1 hydrogen bond · protein-protein
B–D · 261 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 224 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5YSG · X-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced Form. · the same entry in another collection · chain D against D, TM-score 1.00
P19567 · AlphaFold monomer V2.0 prediction for pseudoazurin (P19567) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P19567
Elsewhere: RCSB PDB 5YSG · PDBe 5YSG · UniProt P19567

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