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The 2.0 a X-ray structure of guanylate kinase from E.COLI

Analyse The 2.0 a X-ray structure of guanylate kinase 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: 1S96
Type: protein
Length: 409 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanylate kinase
EC: 2.7.4.8
UniProt: P60546
Ligands: PO4, UNX
Pockets: 5 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanylate kinase (EC 2.7.4.8)	protein	205	47% helix, 21% strand	P60546
B	Guanylate kinase (EC 2.7.4.8)	protein	204	47% helix, 20% strand	P60546

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · chains A

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.43	0.74	26	empty
2	148	0.40	0.73	25	empty
3	119	0.37	0.74	26	empty
4	72	0.32	0.75	12	empty
5	62	0.30	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 1621 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

1S96 · The 2.0 A X-ray structure of Guanylate Kinase from E.coli · the same entry in another collection · chain A against A, TM-score 1.00
P60546 · AlphaFold monomer V2.0 prediction for guanylate kinase (P60546) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P60546
Elsewhere: RCSB PDB 1S96 · PDBe 1S96 · UniProt P60546

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