MolNFT v1 · #82136 · protein

E. COLI (lacz) beta-galactosidase (N460T) in complex with iptg

3VDC: “E. COLI (lacz) beta-galactosidase (N460T) in complex with iptg”. X-ray diffraction, 3 ligands (IPT, NA, MG), 20 pockets (best druggability 0.82). MolNFT v1 #82136 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VDC
Type: protein
Length: 4,060 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: IPT, NA, MG
Pockets: 20 · best druggability 0.82

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	1015	14% helix, 41% strand	P00722

Ligands and binding sites

IPT · 1-methylethyl 1-thio-beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 10 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 46 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	1016	0.82	0.83	113	empty
2	1018	0.82	0.83	116	empty
3	876	0.78	0.81	91	DMS
4	1085	0.76	0.79	106	DMS
5	400	0.75	0.85	67	DMS

Interfaces

6 interfaces between chains.

A–D · 2559 Å² buried · 35 hydrogen bonds · protein-protein
B–C · 2554 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2141 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2128 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 156 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3VDC · E. coli (lacZ) beta-galactosidase (N460T) in complex with IPTG · 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 3VDC · PDBe 3VDC · UniProt P00722

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