MolNFT v1 · #141097 · protein

X-ray crystal structure of pseudoazurin THR36LYS variant

5YW3: “X-ray crystal structure of pseudoazurin THR36LYS variant”. X-ray diffraction, 2 ligands (CU, CL), 3 pockets (best druggability 0.75). MolNFT v1 #141097 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YW3
Type: protein
Length: 496 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pseudoazurin
UniProt: P19567
Ligands: CU, CL
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Pseudoazurin	protein	124	19% helix, 36% strand	P19567

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains B, C, D

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

Pockets

3 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	904	0.75	0.78	90	CL
2	415	0.61	0.76	42	empty
3	118	0.41	0.76	20	empty

Interfaces

4 interfaces between chains.

B–D · 571 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 393 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 331 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 259 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5YW3 · X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant · 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 A 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 P19567
Elsewhere: RCSB PDB 5YW3 · PDBe 5YW3 · UniProt P19567

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