MolNFT v1 · #113126 · protein

Crystal structure of full-length E. COLI ygif in complex with tripolyphosphate and two magnesium ions

5A60 · Inorganic triphosphatase: “Crystal structure of full-length E. COLI ygif in complex with tripolyphosphate and two magnesium ions”. X-ray diffraction, 2 ligands (3PO, MG), 4 pockets (best druggability 0.67). MolNFT v1 #113126 on…

PDB: 5A60
Type: protein
Length: 429 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic triphosphatase
EC: 3.6.1.25
UniProt: V8FJJ2
Ligands: 3PO, MG
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inorganic triphosphatase (EC 3.6.1.25)	protein	429	48% helix, 23% strand	V8FJJ2

Ligands and binding sites

3PO · Triphosphate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

4 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	470	0.67	0.79	61	MG, 3PO
2	223	0.53	0.77	26	empty
3	118	0.45	0.78	18	empty
4	50	0.26	0.74	19	EDO

Compared structures

5A60 · Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two… · the same entry in another collection · chain A against A, TM-score 1.00

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 V8FJJ2
Elsewhere: RCSB PDB 5A60 · PDBe 5A60 · UniProt V8FJJ2

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