MolNFT v1 · #11857 · protein

E. COLI (lacz) beta-galactosidase in complex with galacto- tetrazole

1JZ6: “E. COLI (lacz) beta-galactosidase in complex with galacto- tetrazole”. X-ray diffraction, 3 ligands (GTZ, MG, NA), 20 pockets (best druggability 0.79). MolNFT v1 #11857 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JZ6
Type: protein
Length: 4,044 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: P00722
Ligands: GTZ, MG, NA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-galactosidase (EC 3.2.1.23)	protein	1011	14% helix, 41% strand	P00722

Ligands and binding sites

GTZ · (5R, 6S, 7S, 8S)-5-hydroxymethyl-6,7,8-trihydroxy-tetrazolo[1,5-a]piperidine · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
NA · Sodium ion · metal · 11 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 74 copies · chains A, D, B, C

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	809	0.79	0.83	102	empty
2	678	0.77	0.82	94	empty
3	1066	0.77	0.79	98	DMS
4	1126	0.76	0.78	105	DMS
5	533	0.74	0.82	69	DMS

Interfaces

6 interfaces between chains.

A–D · 2331 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 2284 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2010 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2007 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 131 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1JZ6 · E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH GALACTO-TETRAZOLE · the same entry in another collection · chain D against D, TM-score 1.00
P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain D 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 P00722
Elsewhere: RCSB PDB 1JZ6 · PDBe 1JZ6 · UniProt P00722

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