MolNFT v1 · #111980 · protein

Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with inorganic pyrophosphate

4Z74: “Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with inorganic…”. X-ray diffraction, 2 ligands (POP, CA), 20 pockets (best druggability 0.81). MolNFT v1 #111980 on GenesisL1: 3D structure…

PDB: 4Z74
Type: protein
Length: 1,921 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic pyrophosphatase
EC: 3.6.1.1
UniProt: P9WI55
Ligands: POP, CA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, E, H, I, K, L	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	160	21% helix, 38% strand	P9WI55
J	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	161	22% helix, 35% strand	P9WI55

Ligands and binding sites

POP · Pyrophosphate 2- · ligand · 12 copies · chains A, B, C, D, F, G, E, H, I, J, K, L
CA · Calcium ion · metal · 44 copies · chains A, B, C, D, F, G, E, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	726	0.81	0.84	64	empty
2	882	0.80	0.83	72	empty
3	978	0.79	0.81	77	empty
4	682	0.79	0.83	54	empty
5	667	0.78	0.83	65	empty

Interfaces

26 interfaces between chains.

G–I · 700 Å² buried · 13 hydrogen bonds · protein-protein
J–L · 690 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 689 Å² buried · 11 hydrogen bonds · protein-protein
J–K · 689 Å² buried · 12 hydrogen bonds · protein-protein
K–L · 683 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4Z74 · Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex… · the same entry in another collection · chain L against L, 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 P9WI55
Elsewhere: RCSB PDB 4Z74 · PDBe 4Z74 · UniProt P9WI55

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