Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6CVM

Atomic resolution cryo-EM structure of beta-galactosidase

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	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
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	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
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	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
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	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

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	binding site for residue PTQ A 2001

Chain	Residue
A	ASN102
A	ASP598
A	PHE601
A	VAL795
A	TRP999
A	NA2004
A	HOH2136
A	HOH2283
A	ASP201
A	HIS391
A	GLU461
A	MET502
A	TYR503
A	GLU537
A	HIS540
A	TRP568

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 2002

Chain	Residue
A	GLU416
A	HIS418
A	GLU461
A	HOH2136
A	HOH2226
A	HOH2283

site_id	AC3
Number of Residues	5
Details	binding site for residue MG A 2003

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

site_id	AC4
Number of Residues	6
Details	binding site for residue NA A 2004

Chain	Residue
A	TYR100
A	ASP201
A	PHE601
A	ASN604
A	PTQ2001
A	HOH2633

site_id	AC5
Number of Residues	6
Details	binding site for residue NA A 2005

Chain	Residue
A	PHE556
A	TYR559
A	PRO560
A	LEU562
A	HOH2432
A	HOH2643

site_id	AC6
Number of Residues	16
Details	binding site for residue PTQ B 2001

Chain	Residue
B	ASN102
B	ASP201
B	HIS391
B	GLU461
B	MET502
B	TYR503
B	GLU537
B	HIS540
B	TRP568
B	ASP598
B	PHE601
B	VAL795
B	TRP999
B	NA2004
B	HOH2139
B	HOH2282

site_id	AC7
Number of Residues	6
Details	binding site for residue MG B 2002

Chain	Residue
B	GLU416
B	HIS418
B	GLU461
B	HOH2139
B	HOH2227
B	HOH2282

site_id	AC8
Number of Residues	5
Details	binding site for residue MG B 2003

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

site_id	AC9
Number of Residues	6
Details	binding site for residue NA B 2004

Chain	Residue
B	TYR100
B	ASP201
B	PHE601
B	ASN604
B	PTQ2001
B	HOH2633

site_id	AD1
Number of Residues	6
Details	binding site for residue NA B 2005

Chain	Residue
B	PHE556
B	TYR559
B	PRO560
B	LEU562
B	HOH2432
B	HOH2643

site_id	AD2
Number of Residues	16
Details	binding site for residue PTQ C 2001

Chain	Residue
C	ASN102
C	ASP201
C	HIS391
C	GLU461
C	MET502
C	TYR503
C	GLU537
C	HIS540
C	TRP568
C	ASP598
C	PHE601
C	VAL795
C	TRP999
C	NA2004
C	HOH2139
C	HOH2283

site_id	AD3
Number of Residues	6
Details	binding site for residue MG C 2002

Chain	Residue
C	HOH2283
C	GLU416
C	HIS418
C	GLU461
C	HOH2139
C	HOH2225

site_id	AD4
Number of Residues	5
Details	binding site for residue MG C 2003

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

site_id	AD5
Number of Residues	6
Details	binding site for residue NA C 2004

Chain	Residue
C	TYR100
C	ASP201
C	PHE601
C	ASN604
C	PTQ2001
C	HOH2634

site_id	AD6
Number of Residues	6
Details	binding site for residue NA C 2005

Chain	Residue
C	PHE556
C	TYR559
C	PRO560
C	LEU562
C	HOH2433
C	HOH2644

site_id	AD7
Number of Residues	16
Details	binding site for residue PTQ D 2001

Chain	Residue
D	ASN102
D	ASP201
D	HIS391
D	GLU461
D	MET502
D	TYR503
D	GLU537
D	HIS540
D	TRP568
D	ASP598
D	PHE601
D	VAL795
D	TRP999
D	NA2004
D	HOH2135
D	HOH2281

site_id	AD8
Number of Residues	6
Details	binding site for residue MG D 2002

Chain	Residue
D	GLU416
D	HIS418
D	GLU461
D	HOH2135
D	HOH2225
D	HOH2281

site_id	AD9
Number of Residues	5
Details	binding site for residue MG D 2003

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

site_id	AE1
Number of Residues	6
Details	binding site for residue NA D 2004

Chain	Residue
D	TYR100
D	ASP201
D	PHE601
D	ASN604
D	PTQ2001
D	HOH2633

site_id	AE2
Number of Residues	6
Details	binding site for residue NA D 2005

Chain	Residue
D	PHE556
D	TYR559
D	PRO560
D	LEU562
D	HOH2433
D	HOH2644

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	Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"6420154","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"1350782","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	36
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11045615","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Site: {"description":"Transition state stabilizer"}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Site: {"description":"Important for ensuring that an appropriate proportion of lactose is converted to allolactose"}

Chain

Residue

Details

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)