Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5A1A

2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003824	molecular_function	catalytic activity
A	0004553	molecular_function	hydrolase activity, hydrolyzing O-glycosyl compounds
A	0004565	molecular_function	beta-galactosidase activity
A	0005975	biological_process	carbohydrate metabolic process
A	0005990	biological_process	lactose catabolic process
A	0008152	biological_process	metabolic process
A	0009341	cellular_component	beta-galactosidase complex
A	0016787	molecular_function	hydrolase activity
A	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
A	0030246	molecular_function	carbohydrate binding
A	0031420	molecular_function	alkali metal ion binding
A	0042802	molecular_function	identical protein binding
A	0046872	molecular_function	metal ion binding
A	1901575	biological_process	organic substance catabolic process
B	0000287	molecular_function	magnesium ion binding
B	0003824	molecular_function	catalytic activity
B	0004553	molecular_function	hydrolase activity, hydrolyzing O-glycosyl compounds
B	0004565	molecular_function	beta-galactosidase activity
B	0005975	biological_process	carbohydrate metabolic process
B	0005990	biological_process	lactose catabolic process
B	0008152	biological_process	metabolic process
B	0009341	cellular_component	beta-galactosidase complex
B	0016787	molecular_function	hydrolase activity
B	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
B	0030246	molecular_function	carbohydrate binding
B	0031420	molecular_function	alkali metal ion binding
B	0042802	molecular_function	identical protein binding
B	0046872	molecular_function	metal ion binding
B	1901575	biological_process	organic substance catabolic process
C	0000287	molecular_function	magnesium ion binding
C	0003824	molecular_function	catalytic activity
C	0004553	molecular_function	hydrolase activity, hydrolyzing O-glycosyl compounds
C	0004565	molecular_function	beta-galactosidase activity
C	0005975	biological_process	carbohydrate metabolic process
C	0005990	biological_process	lactose catabolic process
C	0008152	biological_process	metabolic process
C	0009341	cellular_component	beta-galactosidase complex
C	0016787	molecular_function	hydrolase activity
C	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
C	0030246	molecular_function	carbohydrate binding
C	0031420	molecular_function	alkali metal ion binding
C	0042802	molecular_function	identical protein binding
C	0046872	molecular_function	metal ion binding
C	1901575	biological_process	organic substance catabolic process
D	0000287	molecular_function	magnesium ion binding
D	0003824	molecular_function	catalytic activity
D	0004553	molecular_function	hydrolase activity, hydrolyzing O-glycosyl compounds
D	0004565	molecular_function	beta-galactosidase activity
D	0005975	biological_process	carbohydrate metabolic process
D	0005990	biological_process	lactose catabolic process
D	0008152	biological_process	metabolic process
D	0009341	cellular_component	beta-galactosidase complex
D	0016787	molecular_function	hydrolase activity
D	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
D	0030246	molecular_function	carbohydrate binding
D	0031420	molecular_function	alkali metal ion binding
D	0042802	molecular_function	identical protein binding
D	0046872	molecular_function	metal ion binding
D	1901575	biological_process	organic substance catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PTQ A 2001

Chain	Residue
A	ASN102
A	NA4001
A	HOH5037
A	HOH5079
A	ASP201
A	MET502
A	TYR503
A	GLU537
A	HIS540
A	ASP598
A	PHE601
A	TRP999

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 3001

Chain	Residue
A	GLU416
A	HIS418
A	GLU461
A	HOH5036
A	HOH5037
A	HOH5078

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 3002

Chain	Residue
A	ASP15
A	ASN18
A	VAL21
A	TYR161
A	GLN163
A	ASP193

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 4001

Chain	Residue
A	ASP201
A	PHE601
A	ASN604
A	PTQ2001
A	HOH5013

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 4002

Chain	Residue
A	PHE556
A	TYR559
A	PRO560
A	LEU562
A	HOH5082

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PTQ B 2001

Chain	Residue
B	ASN102
B	ASP201
B	MET502
B	TYR503
B	GLU537
B	HIS540
B	ASP598
B	PHE601
B	TRP999
B	NA4001
B	HOH5037
B	HOH5079

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 3001

Chain	Residue
B	GLU416
B	HIS418
B	GLU461
B	HOH5036
B	HOH5037
B	HOH5078

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 3002

Chain	Residue
B	ASP15
B	ASN18
B	VAL21
B	TYR161
B	GLN163
B	ASP193

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 4001

Chain	Residue
B	ASP201
B	PHE601
B	ASN604
B	PTQ2001
B	HOH5013

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 4002

Chain	Residue
B	PHE556
B	TYR559
B	PRO560
B	LEU562
B	HOH5082

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PTQ C 2001

Chain	Residue
C	ASN102
C	ASP201
C	MET502
C	TYR503
C	GLU537
C	HIS540
C	ASP598
C	PHE601
C	TRP999
C	NA4001
C	HOH5037
C	HOH5079

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 3001

Chain	Residue
C	GLU416
C	HIS418
C	GLU461
C	HOH5036
C	HOH5037
C	HOH5078

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 3002

Chain	Residue
C	ASP15
C	ASN18
C	VAL21
C	TYR161
C	GLN163
C	ASP193

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA C 4001

Chain	Residue
C	ASP201
C	PHE601
C	ASN604
C	PTQ2001
C	HOH5013

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA C 4002

Chain	Residue
C	PRO560
C	LEU562
C	HOH5082
C	PHE556
C	TYR559

site_id	BC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PTQ D 2001

Chain	Residue
D	ASN102
D	ASP201
D	MET502
D	TYR503
D	GLU537
D	HIS540
D	ASP598
D	PHE601
D	TRP999
D	NA4001
D	HOH5037
D	HOH5079

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 3001

Chain	Residue
D	GLU416
D	HIS418
D	GLU461
D	HOH5036
D	HOH5037
D	HOH5078

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 3002

Chain	Residue
D	ASP15
D	ASN18
D	VAL21
D	TYR161
D	GLN163
D	ASP193

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA D 4001

Chain	Residue
D	ASP201
D	PHE601
D	ASN604
D	PTQ2001
D	HOH5013

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA D 4002

Chain	Residue
D	PHE556
D	TYR559
D	PRO560
D	LEU562
D	HOH5082

Functional Information from PROSITE/UniProt

site_id	PS00608
Number of Residues	15
Details	GLYCOSYL_HYDROL_F2_2 Glycosyl hydrolases family 2 acid/base catalyst. DRNHPSVIIWSlg.NE

Chain	Residue	Details
A	ASP447-GLU461

site_id	PS00719
Number of Residues	26
Details	GLYCOSYL_HYDROL_F2_1 Glycosyl hydrolases family 2 signature 1. NaVRCSHYPnhplWYtlcDryGLYVV

Chain	Residue	Details
A	ASN385-VAL410

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton donor => ECO:0000269\|PubMed:6420154

Chain	Residue	Details
A	GLU461
B	GLU461
C	GLU461
D	GLU461

site_id	SWS_FT_FI2
Number of Residues	4
Details	ACT_SITE: Nucleophile => ECO:0000269\|PubMed:1350782

Chain	Residue	Details
A	GLU537
B	GLU537
C	GLU537
D	GLU537

site_id	SWS_FT_FI3
Number of Residues	28
Details	BINDING:

Chain	Residue	Details
A	ASN102
B	GLU461
B	GLU537
B	PHE601
B	ASN604
B	TRP999
C	ASN102
C	ASP201
C	GLU461
C	GLU537
C	PHE601
A	ASP201
C	ASN604
C	TRP999
D	ASN102
D	ASP201
D	GLU461
D	GLU537
D	PHE601
D	ASN604
D	TRP999
A	GLU461
A	GLU537
A	PHE601
A	ASN604
A	TRP999
B	ASN102
B	ASP201

site_id	SWS_FT_FI4
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:11045615

Chain	Residue	Details
A	GLU416
D	GLU416
D	HIS418
D	ASN597
A	HIS418
A	ASN597
B	GLU416
B	HIS418
B	ASN597
C	GLU416
C	HIS418
C	ASN597

site_id	SWS_FT_FI5
Number of Residues	8
Details	SITE: Transition state stabilizer

Chain	Residue	Details
A	HIS357
A	HIS391
B	HIS357
B	HIS391
C	HIS357
C	HIS391
D	HIS357
D	HIS391

site_id	SWS_FT_FI6
Number of Residues	4
Details	SITE: Important for ensuring that an appropriate proportion of lactose is converted to allolactose

Chain	Residue	Details
A	TRP999
B	TRP999
C	TRP999
D	TRP999

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	10
Details	M-CSA 422

Chain	Residue	Details
A	ASP201
A	ASN604
A	HIS357
A	HIS391
A	GLU416
A	HIS418
A	GLU461
A	GLU537
A	ASN597
A	PHE601

site_id	MCSA2
Number of Residues	10
Details	M-CSA 422

Chain	Residue	Details
B	ASP201
B	ASN604
B	HIS357
B	HIS391
B	GLU416
B	HIS418
B	GLU461
B	GLU537
B	ASN597
B	PHE601

site_id	MCSA3
Number of Residues	10
Details	M-CSA 422

Chain	Residue	Details
C	ASP201
C	ASN604
C	HIS357
C	HIS391
C	GLU416
C	HIS418
C	GLU461
C	GLU537
C	ASN597
C	PHE601

site_id	MCSA4
Number of Residues	10
Details	M-CSA 422

Chain	Residue	Details
D	ASP201
D	ASN604
D	HIS357
D	HIS391
D	GLU416
D	HIS418
D	GLU461
D	GLU537
D	ASN597
D	PHE601

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)