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Crystal structure of ZN(II)-bound yjia GTPase from E. COLI

Analyse Crystal structure of ZN(II)-bound yjia GTPase from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IXM
Type: protein
Length: 635 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized GTP-binding protein yjia
UniProt: P24203
Ligands: ZN, SO4
Pockets: 12 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized GTP-binding protein yjia	protein	318	30% helix, 30% strand	P24203
B	Uncharacterized GTP-binding protein yjia	protein	317	29% helix, 30% strand	P24203

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	557	0.87	0.92	61	empty
2	120	0.59	0.85	28	empty
3	213	0.53	0.77	33	empty
4	160	0.49	0.78	27	empty
5	171	0.49	0.77	26	empty

Interfaces

1 interface between chains.

A–B · 1184 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

4IXM · Crystal structure of Zn(II)-bound YjiA GTPase from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
P24203 · AlphaFold monomer V2.0 prediction for P-loop guanosine triphosphatase yjia (P24203) · a predicted model of the same protein · chain A 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 P24203
Elsewhere: RCSB PDB 4IXM · PDBe 4IXM · UniProt P24203

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