Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3VD5

E. coli (lacZ) beta-galactosidase (N460S)

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	6
Details	BINDING SITE FOR RESIDUE MG A 3001

Chain	Residue
A	GLU416
A	HIS418
A	GLU461
A	HOH4041
A	HOH4194
A	HOH4195

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 3002

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

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 3101

Chain	Residue
A	ASP201
A	PHE601
A	ASN604
A	HOH4266
A	HOH4267

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA A 3102

Chain	Residue
A	PHE556
A	TYR559
A	PRO560
A	LEU562
A	HOH4112
A	HOH4268

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA A 3103

Chain	Residue
A	PRO932
A	LEU967
A	THR970

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS A 8001

Chain	Residue
A	LYS380
A	ASN383
A	PHE626
A	TYR642
A	TRP708
A	HOH4275

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS A 8002

Chain	Residue
A	ARG557
A	HIS622
A	GLN623
A	GLN628

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DMS A 8003

Chain	Residue
A	THR229
A	VAL330
A	GLY331
A	ARG333
A	ASN449
A	PRO451
A	ARG482

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS A 8004

Chain	Residue
A	GLY270
A	THR271
A	LEU291
A	ARG292

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS A 8005

Chain	Residue
A	ASP45
A	PRO47
A	SER48
A	DMS8007

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS A 8006

Chain	Residue
A	GLU57
A	LEU125
A	THR126
C	GLU819

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DMS A 8007

Chain	Residue
A	PHE33
A	ALA34
A	ASP45
A	ALA327
A	DMS8005

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 3001

Chain	Residue
C	GLU416
C	HIS418
C	GLU461
C	HOH4017
C	HOH4109
C	HOH4171

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 3002

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

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA C 3101

Chain	Residue
C	TYR100
C	ASP201
C	PHE601
C	ASN604
C	HOH4173

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA C 3102

Chain	Residue
C	PHE556
C	TYR559
C	PRO560
C	LEU562
C	HOH4074

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA C 3103

Chain	Residue
C	PHE931
C	PRO932
C	LEU967
C	THR970

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DMS C 8001

Chain	Residue
C	ILE576
C	PRO584
C	TRP585
C	SER586
C	ARG973

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS C 8002

Chain	Residue
C	THR229
C	GLY331
C	ARG333
C	PRO451
C	ARG482
C	HOH4081

site_id	CC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE DMS C 8003

Chain	Residue
C	GLY275
C	VAL289
C	THR290

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS C 8004

Chain	Residue
C	GLN623
C	GLN625
C	GLN628
C	HIS622

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE DMS C 8005

Chain	Residue
C	PHE629
C	ARG630
C	HOH4107

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 3001

Chain	Residue
D	GLU416
D	HIS418
D	GLU461
D	HOH4134
D	HOH4231
D	HOH4232

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 3002

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

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA D 3101

Chain	Residue
D	TYR100
D	ASP201
D	PHE601
D	ASN604
D	HOH4233

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA D 3102

Chain	Residue
D	PHE556
D	TYR559
D	PRO560
D	LEU562

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS D 8001

Chain	Residue
D	GLY275
D	GLY276
D	VAL289
D	THR290

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS D 8002

Chain	Residue
D	GLY270
D	THR290
D	LEU291
D	ARG292

site_id	DC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE DMS D 8003

Chain	Residue
D	ASP45

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS D 8004

Chain	Residue
D	LEU54
D	ASN55
D	GLU57
D	LEU125

site_id	DC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DMS D 8005

Chain	Residue
D	ARG557
D	HIS622
D	GLN623
D	GLN628
D	GLN718
D	HOH4008
D	HOH4041

site_id	DC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE DMS D 8006

Chain	Residue
D	ARG230

site_id	DC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 3001

Chain	Residue
B	GLU416
B	HIS418
B	GLU461
B	HOH4027
B	HOH4111
B	HOH4211

site_id	DC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 3002

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

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 3101

Chain	Residue
B	TYR100
B	ASP201
B	PHE601
B	ASN604
B	HOH4244
B	HOH4245

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 3102

Chain	Residue
B	PHE556
B	TYR559
B	PRO560
B	LEU562
B	HOH4217

site_id	EC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 3103

Chain	Residue
B	SER647
B	GLU650
B	LEU670
B	HOH4013
B	HOH4155

site_id	EC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE DMS B 8001

Chain	Residue
B	LEU291
B	ARG292

site_id	EC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS B 8002

Chain	Residue
B	LYS380
B	ASN383
B	PHE384
B	PHE626
B	TYR642
B	TRP708

site_id	EC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE DMS B 8003

Chain	Residue
B	VAL335
B	PRO480
B	SER481

site_id	EC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS B 8004

Chain	Residue
B	THR229
B	VAL330
B	GLY331
B	ASN449

Functional Information from PROSITE/UniProt

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)
		EDMap 2fo-fc (MTZ)