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Crystal structure of refined tetragonal crystal of yoda from escherichia COLI

Analyse Crystal structure of refined tetragonal crystal of yoda from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1S7D
Type: protein
Length: 187 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metal-binding protein yoda
UniProt: P76344
Ligands: ZN
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metal-binding protein yoda	protein	187	28% helix, 28% strand	P76344

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	480	0.66	0.78	46	ZN
2	74	0.34	0.76	20	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

1S7D · Crystal structure of refined tetragonal crystal of YodA from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
P76344 · AlphaFold monomer V2.0 prediction for metal-binding protein zint (P76344) · 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 P76344
Elsewhere: RCSB PDB 1S7D · PDBe 1S7D · UniProt P76344

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