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3VDA
Asym. Unit
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Asym.Unit (701 KB)
Biol.Unit 1 (691 KB)
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(1)
Title
:
E. COLI (LACZ) BETA-GALACTOSIDASE (N460T)
Authors
:
R. W. Wheatley, J. C. Kappelhoff, J. N. Hahn, M. L. Dugdale, M. J. Dutkosk S. D. Tamman, M. E. Fraser, R. E. Huber
Date
:
04 Jan 12 (Deposition) - 11 Apr 12 (Release) - 19 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transition State Stabilization, Substrate Binding, 2-Stage Binding, Tim Barrel (Alpha/Beta Barrel), Jelly-Roll Barrel, Immunoglobulin, Beta Supersandwich, Glycosidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. W. Wheatley, J. C. Kappelhoff, J. N. Hahn, M. L. Dugdale, M. J. Dutkoski, S. D. Tamman, M. E. Fraser, R. E. Huber
Substitution For Asn460 Cripples {Beta}-Galactosidase (Escherichia Coli) By Increasing Substrate Affinity And Decreasing Transition State Stability.
Arch. Biochem. Biophys. V. 521 51 2012
[
close entry info
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Hetero Components
(3, 50)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1aa: DIMETHYL SULFOXIDE (DMSaa)
1ab: DIMETHYL SULFOXIDE (DMSab)
1ac: DIMETHYL SULFOXIDE (DMSac)
1ad: DIMETHYL SULFOXIDE (DMSad)
1ae: DIMETHYL SULFOXIDE (DMSae)
1af: DIMETHYL SULFOXIDE (DMSaf)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
1f: DIMETHYL SULFOXIDE (DMSf)
1g: DIMETHYL SULFOXIDE (DMSg)
1h: DIMETHYL SULFOXIDE (DMSh)
1i: DIMETHYL SULFOXIDE (DMSi)
1j: DIMETHYL SULFOXIDE (DMSj)
1k: DIMETHYL SULFOXIDE (DMSk)
1l: DIMETHYL SULFOXIDE (DMSl)
1m: DIMETHYL SULFOXIDE (DMSm)
1n: DIMETHYL SULFOXIDE (DMSn)
1o: DIMETHYL SULFOXIDE (DMSo)
1p: DIMETHYL SULFOXIDE (DMSp)
1q: DIMETHYL SULFOXIDE (DMSq)
1r: DIMETHYL SULFOXIDE (DMSr)
1s: DIMETHYL SULFOXIDE (DMSs)
1t: DIMETHYL SULFOXIDE (DMSt)
1u: DIMETHYL SULFOXIDE (DMSu)
1v: DIMETHYL SULFOXIDE (DMSv)
1w: DIMETHYL SULFOXIDE (DMSw)
1x: DIMETHYL SULFOXIDE (DMSx)
1y: DIMETHYL SULFOXIDE (DMSy)
1z: DIMETHYL SULFOXIDE (DMSz)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
3i: SODIUM ION (NAi)
3j: SODIUM ION (NAj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
32
Ligand/Ion
DIMETHYL SULFOXIDE
2
MG
8
Ligand/Ion
MAGNESIUM ION
3
NA
10
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(48, 48)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:416 , HIS A:418 , GLU A:461 , HOH A:4376 , HOH A:4402 , HOH A:4417
BINDING SITE FOR RESIDUE MG A 3001
02
AC2
SOFTWARE
ASP A:15 , ASN A:18 , VAL A:21 , GLN A:163 , ASP A:193
BINDING SITE FOR RESIDUE MG A 3002
03
AC3
SOFTWARE
ASP A:201 , PHE A:601 , ASN A:604 , HOH A:4311
BINDING SITE FOR RESIDUE NA A 3101
04
AC4
SOFTWARE
PHE A:556 , TYR A:559 , PRO A:560 , LEU A:562 , HOH A:4041 , HOH A:4312
BINDING SITE FOR RESIDUE NA A 3102
05
AC5
SOFTWARE
PHE A:931 , PRO A:932 , LEU A:967 , THR A:970 , HOH A:4014 , HOH A:4065
BINDING SITE FOR RESIDUE NA A 3103
06
AC6
SOFTWARE
THR A:229 , VAL A:330 , GLY A:331 , ARG A:333 , HIS A:450 , PRO A:451 , ARG A:482
BINDING SITE FOR RESIDUE DMS A 8001
07
AC7
SOFTWARE
ARG A:557 , HIS A:622 , GLN A:625 , GLN A:628
BINDING SITE FOR RESIDUE DMS A 8002
08
AC8
SOFTWARE
LYS A:380 , ASN A:383 , PHE A:384 , PHE A:626 , TYR A:642 , TRP A:708 , HOH A:4128
BINDING SITE FOR RESIDUE DMS A 8003
09
AC9
SOFTWARE
PRO A:32 , PHE A:33 , TRP A:36 , ASP A:45 , ALA A:327 , HOH A:4414
BINDING SITE FOR RESIDUE DMS A 8004
10
BC1
SOFTWARE
LEU A:291 , ARG A:292
BINDING SITE FOR RESIDUE DMS A 8005
11
BC2
SOFTWARE
ILE A:576 , PRO A:584 , TRP A:585 , SER A:586 , ARG A:973
BINDING SITE FOR RESIDUE DMS A 8006
12
BC3
SOFTWARE
ASP A:428 , PRO A:430 , HIS D:226 , GLN D:445
BINDING SITE FOR RESIDUE DMS A 8007
13
BC4
SOFTWARE
GLU B:416 , HIS B:418 , GLU B:461 , HOH B:4019 , HOH B:4367 , HOH B:4394
BINDING SITE FOR RESIDUE MG B 3001
14
BC5
SOFTWARE
ASP B:15 , ASN B:18 , VAL B:21 , GLN B:163 , ASP B:193
BINDING SITE FOR RESIDUE MG B 3002
15
BC6
SOFTWARE
ASP B:201 , PHE B:601 , ASN B:604 , HOH B:4274 , HOH B:4372
BINDING SITE FOR RESIDUE NA B 3101
16
BC7
SOFTWARE
PHE B:556 , TYR B:559 , PRO B:560 , LEU B:562 , HOH B:4079 , HOH B:4275
BINDING SITE FOR RESIDUE NA B 3102
17
BC8
SOFTWARE
THR B:229 , VAL B:330 , GLY B:331 , ARG B:333 , ASN B:449 , PRO B:451 , ARG B:482
BINDING SITE FOR RESIDUE DMS B 8001
18
BC9
SOFTWARE
ARG B:557 , HIS B:622 , GLN B:623 , HOH B:4261
BINDING SITE FOR RESIDUE DMS B 8002
19
CC1
SOFTWARE
LYS B:380 , ASN B:383 , PHE B:384 , PHE B:626 , TYR B:642 , TRP B:708 , HOH B:4087
BINDING SITE FOR RESIDUE DMS B 8003
20
CC2
SOFTWARE
PRO B:32 , PHE B:33 , ALA B:34 , ASP B:45 , DMS B:8008
BINDING SITE FOR RESIDUE DMS B 8004
21
CC3
SOFTWARE
GLY B:270 , LEU B:291 , ARG B:292
BINDING SITE FOR RESIDUE DMS B 8005
22
CC4
SOFTWARE
VAL B:289 , THR B:290 , ARG B:292 , HOH B:4288
BINDING SITE FOR RESIDUE DMS B 8007
23
CC5
SOFTWARE
TRP B:36 , ASP B:45 , ARG B:46 , PRO B:47 , DMS B:8004
BINDING SITE FOR RESIDUE DMS B 8008
24
CC6
SOFTWARE
GLU C:416 , HIS C:418 , GLU C:461 , HOH C:4314 , HOH C:4364 , HOH C:4382
BINDING SITE FOR RESIDUE MG C 3001
25
CC7
SOFTWARE
ASP C:15 , ASN C:18 , VAL C:21 , GLN C:163 , ASP C:193
BINDING SITE FOR RESIDUE MG C 3002
26
CC8
SOFTWARE
ASP C:201 , PHE C:601 , ASN C:604 , HOH C:4279 , HOH C:4368
BINDING SITE FOR RESIDUE NA C 3101
27
CC9
SOFTWARE
PHE C:556 , TYR C:559 , PRO C:560 , LEU C:562 , HOH C:4275 , HOH C:4280
BINDING SITE FOR RESIDUE NA C 3102
28
DC1
SOFTWARE
ARG C:557 , HIS C:622 , GLN C:623 , GLN C:628
BINDING SITE FOR RESIDUE DMS C 8001
29
DC2
SOFTWARE
LYS C:380 , ASN C:383 , PHE C:626 , TYR C:642 , TRP C:708 , HOH C:4081 , HOH C:4200
BINDING SITE FOR RESIDUE DMS C 8002
30
DC3
SOFTWARE
THR C:290 , LEU C:291 , ARG C:292
BINDING SITE FOR RESIDUE DMS C 8003
31
DC4
SOFTWARE
ARG C:52 , LEU C:54 , LEU C:125 , THR C:126
BINDING SITE FOR RESIDUE DMS C 8004
32
DC5
SOFTWARE
GLY C:275 , VAL C:289 , THR C:290 , ARG C:292
BINDING SITE FOR RESIDUE DMS C 8005
33
DC6
SOFTWARE
THR C:83 , VAL C:84 , VAL C:85 , HIS C:93
BINDING SITE FOR RESIDUE DMS C 8006
34
DC7
SOFTWARE
SER C:48
BINDING SITE FOR RESIDUE DMS C 8007
35
DC8
SOFTWARE
GLU D:416 , HIS D:418 , GLU D:461 , HOH D:4263 , HOH D:4349 , HOH D:4392
BINDING SITE FOR RESIDUE MG D 3001
36
DC9
SOFTWARE
ASP D:15 , ASN D:18 , VAL D:21 , GLN D:163 , ASP D:193
BINDING SITE FOR RESIDUE MG D 3002
37
EC1
SOFTWARE
ASP D:201 , PHE D:601 , ASN D:604 , HOH D:4049 , HOH D:4212
BINDING SITE FOR RESIDUE NA D 3101
38
EC2
SOFTWARE
PHE D:556 , TYR D:559 , PRO D:560 , LEU D:562 , HOH D:4124 , HOH D:4244
BINDING SITE FOR RESIDUE NA D 3102
39
EC3
SOFTWARE
PHE D:931 , PRO D:932 , LEU D:967 , THR D:970 , HOH D:4134 , HOH D:4217
BINDING SITE FOR RESIDUE NA D 3103
40
EC4
SOFTWARE
THR D:229 , VAL D:330 , GLY D:331 , ARG D:448 , ASN D:449 , ARG D:482
BINDING SITE FOR RESIDUE DMS D 8001
41
EC5
SOFTWARE
ARG D:557 , HIS D:622 , GLN D:623 , GLN D:628 , HOH D:4076
BINDING SITE FOR RESIDUE DMS D 8002
42
EC6
SOFTWARE
LYS D:380 , ASN D:383 , PHE D:626 , TYR D:642 , TRP D:708
BINDING SITE FOR RESIDUE DMS D 8003
43
EC7
SOFTWARE
ARG D:505 , GLU D:508 , PRO D:1001 , VAL D:1003 , HOH D:4045
BINDING SITE FOR RESIDUE DMS D 8004
44
EC8
SOFTWARE
SER D:53 , LEU D:54 , ASN D:55
BINDING SITE FOR RESIDUE DMS D 8005
45
EC9
SOFTWARE
HOH D:4012
BINDING SITE FOR RESIDUE DMS D 8006
46
FC1
SOFTWARE
ILE D:576 , PRO D:584 , TRP D:585 , SER D:586 , ARG D:973
BINDING SITE FOR RESIDUE DMS D 8007
47
FC2
SOFTWARE
GLY D:276 , THR D:290 , ARG D:292
BINDING SITE FOR RESIDUE DMS D 8008
48
FC3
SOFTWARE
GLY D:270 , THR D:290 , LEU D:291 , ARG D:292
BINDING SITE FOR RESIDUE DMS D 8010
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F2_1 (A:385-410,B:385-410,C:385-410,D:38...)
2: GLYCOSYL_HYDROL_F2_2 (A:447-461,B:447-461,C:447-461,D:44...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F2_1
PS00719
Glycosyl hydrolases family 2 signature 1.
BGAL_ECOLI
386-411
4
A:385-410
B:385-410
C:385-410
D:385-410
2
GLYCOSYL_HYDROL_F2_2
PS00608
Glycosyl hydrolases family 2 acid/base catalyst.
BGAL_ECOLI
448-462
4
A:447-461
B:447-461
C:447-461
D:447-461
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 20)
Info
All SCOP Domains
1a: SCOP_d3vdaa1 (A:9-219)
1b: SCOP_d3vdab1 (B:9-219)
1c: SCOP_d3vdac1 (C:9-219)
1d: SCOP_d3vdad1 (D:9-219)
2a: SCOP_d3vdaa2 (A:220-333)
2b: SCOP_d3vdaa4 (A:626-730)
2c: SCOP_d3vdab2 (B:220-333)
2d: SCOP_d3vdab4 (B:626-730)
2e: SCOP_d3vdac2 (C:220-333)
2f: SCOP_d3vdac4 (C:626-730)
2g: SCOP_d3vdad2 (D:220-333)
2h: SCOP_d3vdad4 (D:626-730)
3a: SCOP_d3vdaa5 (A:731-1023)
3b: SCOP_d3vdab5 (B:731-1023)
3c: SCOP_d3vdac5 (C:731-1023)
3d: SCOP_d3vdad5 (D:731-1023)
4a: SCOP_d3vdaa3 (A:334-625)
4b: SCOP_d3vdab3 (B:334-625)
4c: SCOP_d3vdac3 (C:334-625)
4d: SCOP_d3vdad3 (D:334-625)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
beta-Galactosidase/glucuronidase, N-terminal domain
(49)
Protein domain
:
beta-Galactosidase
(42)
Escherichia coli [TaxId: 562]
(41)
1a
d3vdaa1
A:9-219
1b
d3vdab1
B:9-219
1c
d3vdac1
C:9-219
1d
d3vdad1
D:9-219
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
beta-Galactosidase/glucuronidase domain
(79)
Family
:
beta-Galactosidase/glucuronidase domain
(49)
Protein domain
:
beta-Galactosidase, domains 2 and 4
(42)
Escherichia coli [TaxId: 562]
(41)
2a
d3vdaa2
A:220-333
2b
d3vdaa4
A:626-730
2c
d3vdab2
B:220-333
2d
d3vdab4
B:626-730
2e
d3vdac2
C:220-333
2f
d3vdac4
C:626-730
2g
d3vdad2
D:220-333
2h
d3vdad4
D:626-730
Fold
:
Supersandwich
(271)
Superfamily
:
Galactose mutarotase-like
(205)
Family
:
beta-Galactosidase, domain 5
(42)
Protein domain
:
beta-Galactosidase, domain 5
(42)
Escherichia coli [TaxId: 562]
(41)
3a
d3vdaa5
A:731-1023
3b
d3vdab5
B:731-1023
3c
d3vdac5
C:731-1023
3d
d3vdad5
D:731-1023
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
beta-Galactosidase, domain 3
(42)
Escherichia coli [TaxId: 562]
(41)
4a
d3vdaa3
A:334-625
4b
d3vdab3
B:334-625
4c
d3vdac3
C:334-625
4d
d3vdad3
D:334-625
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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all PFAM domains
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Sorry, no Info available
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