MolNFT v1 · #107756 · protein

Structure of inorganic pyrophosphatase from escherichia COLI in complex with sulfate

4UM4: “Structure of inorganic pyrophosphatase from escherichia COLI in complex with sulfate”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.85). MolNFT v1 #107756 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4UM4
Type: protein
Length: 525 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic pyrophosphatase
EC: 3.6.1.1
UniProt: P0A7A9
Ligands: SO4
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	175	18% helix, 33% strand	P0A7A9

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	335	0.85	0.94	33	empty
2	308	0.62	0.79	39	SO4
3	399	0.62	0.77	35	empty
4	230	0.58	0.79	32	SO4
5	203	0.57	0.80	33	SO4

Interfaces

3 interfaces between chains.

A–B · 704 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 701 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 694 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4UM4 · Structure of inorganic pyrophosphatase from escherichia COLI in complex with sulfate · the same entry in another collection · chain A against A, TM-score 1.00
P0A7A9 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (P0A7A9) · 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 P0A7A9
Elsewhere: RCSB PDB 4UM4 · PDBe 4UM4 · UniProt P0A7A9

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