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3VD5
Asym. Unit
Info
Asym.Unit (689 KB)
Biol.Unit 1 (679 KB)
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(1)
Title
:
E. COLI (LACZ) BETA-GALACTOSIDASE (N460S)
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
:
2.70
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
[
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Hetero Components
(3, 43)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
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)
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)
3k: SODIUM ION (NAk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
24
Ligand/Ion
DIMETHYL SULFOXIDE
2
MG
8
Ligand/Ion
MAGNESIUM ION
3
NA
11
Ligand/Ion
SODIUM ION
[
close Hetero Component info
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Sites
(41, 41)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:416 , HIS A:418 , GLU A:461 , HOH A:4041 , HOH A:4194 , HOH A:4195
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:4266 , HOH A:4267
BINDING SITE FOR RESIDUE NA A 3101
04
AC4
SOFTWARE
PHE A:556 , TYR A:559 , PRO A:560 , LEU A:562 , HOH A:4112 , HOH A:4268
BINDING SITE FOR RESIDUE NA A 3102
05
AC5
SOFTWARE
PRO A:932 , LEU A:967 , THR A:970
BINDING SITE FOR RESIDUE NA A 3103
06
AC6
SOFTWARE
LYS A:380 , ASN A:383 , PHE A:626 , TYR A:642 , TRP A:708 , HOH A:4275
BINDING SITE FOR RESIDUE DMS A 8001
07
AC7
SOFTWARE
ARG A:557 , HIS A:622 , GLN A:623 , GLN A:628
BINDING SITE FOR RESIDUE DMS A 8002
08
AC8
SOFTWARE
THR A:229 , VAL A:330 , GLY A:331 , ARG A:333 , ASN A:449 , PRO A:451 , ARG A:482
BINDING SITE FOR RESIDUE DMS A 8003
09
AC9
SOFTWARE
GLY A:270 , THR A:271 , LEU A:291 , ARG A:292
BINDING SITE FOR RESIDUE DMS A 8004
10
BC1
SOFTWARE
ASP A:45 , PRO A:47 , SER A:48 , DMS A:8007
BINDING SITE FOR RESIDUE DMS A 8005
11
BC2
SOFTWARE
GLU A:57 , LEU A:125 , THR A:126 , GLU C:819
BINDING SITE FOR RESIDUE DMS A 8006
12
BC3
SOFTWARE
PHE A:33 , ALA A:34 , ASP A:45 , ALA A:327 , DMS A:8005
BINDING SITE FOR RESIDUE DMS A 8007
13
BC4
SOFTWARE
GLU C:416 , HIS C:418 , GLU C:461 , HOH C:4017 , HOH C:4109 , HOH C:4171
BINDING SITE FOR RESIDUE MG C 3001
14
BC5
SOFTWARE
ASP C:15 , ASN C:18 , VAL C:21 , GLN C:163 , ASP C:193
BINDING SITE FOR RESIDUE MG C 3002
15
BC6
SOFTWARE
TYR C:100 , ASP C:201 , PHE C:601 , ASN C:604 , HOH C:4173
BINDING SITE FOR RESIDUE NA C 3101
16
BC7
SOFTWARE
PHE C:556 , TYR C:559 , PRO C:560 , LEU C:562 , HOH C:4074
BINDING SITE FOR RESIDUE NA C 3102
17
BC8
SOFTWARE
PHE C:931 , PRO C:932 , LEU C:967 , THR C:970
BINDING SITE FOR RESIDUE NA C 3103
18
BC9
SOFTWARE
ILE C:576 , PRO C:584 , TRP C:585 , SER C:586 , ARG C:973
BINDING SITE FOR RESIDUE DMS C 8001
19
CC1
SOFTWARE
THR C:229 , GLY C:331 , ARG C:333 , PRO C:451 , ARG C:482 , HOH C:4081
BINDING SITE FOR RESIDUE DMS C 8002
20
CC2
SOFTWARE
GLY C:275 , VAL C:289 , THR C:290
BINDING SITE FOR RESIDUE DMS C 8003
21
CC3
SOFTWARE
HIS C:622 , GLN C:623 , GLN C:625 , GLN C:628
BINDING SITE FOR RESIDUE DMS C 8004
22
CC4
SOFTWARE
PHE C:629 , ARG C:630 , HOH C:4107
BINDING SITE FOR RESIDUE DMS C 8005
23
CC5
SOFTWARE
GLU D:416 , HIS D:418 , GLU D:461 , HOH D:4134 , HOH D:4231 , HOH D:4232
BINDING SITE FOR RESIDUE MG D 3001
24
CC6
SOFTWARE
ASP D:15 , ASN D:18 , VAL D:21 , GLN D:163 , ASP D:193
BINDING SITE FOR RESIDUE MG D 3002
25
CC7
SOFTWARE
TYR D:100 , ASP D:201 , PHE D:601 , ASN D:604 , HOH D:4233
BINDING SITE FOR RESIDUE NA D 3101
26
CC8
SOFTWARE
PHE D:556 , TYR D:559 , PRO D:560 , LEU D:562
BINDING SITE FOR RESIDUE NA D 3102
27
CC9
SOFTWARE
GLY D:275 , GLY D:276 , VAL D:289 , THR D:290
BINDING SITE FOR RESIDUE DMS D 8001
28
DC1
SOFTWARE
GLY D:270 , THR D:290 , LEU D:291 , ARG D:292
BINDING SITE FOR RESIDUE DMS D 8002
29
DC2
SOFTWARE
ASP D:45
BINDING SITE FOR RESIDUE DMS D 8003
30
DC3
SOFTWARE
LEU D:54 , ASN D:55 , GLU D:57 , LEU D:125
BINDING SITE FOR RESIDUE DMS D 8004
31
DC4
SOFTWARE
ARG D:557 , HIS D:622 , GLN D:623 , GLN D:628 , GLN D:718 , HOH D:4008 , HOH D:4041
BINDING SITE FOR RESIDUE DMS D 8005
32
DC5
SOFTWARE
ARG D:230
BINDING SITE FOR RESIDUE DMS D 8006
33
DC6
SOFTWARE
GLU B:416 , HIS B:418 , GLU B:461 , HOH B:4027 , HOH B:4111 , HOH B:4211
BINDING SITE FOR RESIDUE MG B 3001
34
DC7
SOFTWARE
ASP B:15 , ASN B:18 , VAL B:21 , GLN B:163 , ASP B:193
BINDING SITE FOR RESIDUE MG B 3002
35
DC8
SOFTWARE
TYR B:100 , ASP B:201 , PHE B:601 , ASN B:604 , HOH B:4244 , HOH B:4245
BINDING SITE FOR RESIDUE NA B 3101
36
DC9
SOFTWARE
PHE B:556 , TYR B:559 , PRO B:560 , LEU B:562 , HOH B:4217
BINDING SITE FOR RESIDUE NA B 3102
37
EC1
SOFTWARE
SER B:647 , GLU B:650 , LEU B:670 , HOH B:4013 , HOH B:4155
BINDING SITE FOR RESIDUE NA B 3103
38
EC2
SOFTWARE
LEU B:291 , ARG B:292
BINDING SITE FOR RESIDUE DMS B 8001
39
EC3
SOFTWARE
LYS B:380 , ASN B:383 , PHE B:384 , PHE B:626 , TYR B:642 , TRP B:708
BINDING SITE FOR RESIDUE DMS B 8002
40
EC4
SOFTWARE
VAL B:335 , PRO B:480 , SER B:481
BINDING SITE FOR RESIDUE DMS B 8003
41
EC5
SOFTWARE
THR B:229 , VAL B:330 , GLY B:331 , ASN B:449
BINDING SITE FOR RESIDUE DMS B 8004
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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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
View:
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_d3vd5a1 (A:13-219)
1b: SCOP_d3vd5b1 (B:13-219)
1c: SCOP_d3vd5c1 (C:13-219)
1d: SCOP_d3vd5d1 (D:13-219)
2a: SCOP_d3vd5a2 (A:220-333)
2b: SCOP_d3vd5a4 (A:626-730)
2c: SCOP_d3vd5b2 (B:220-333)
2d: SCOP_d3vd5b4 (B:626-730)
2e: SCOP_d3vd5c2 (C:220-333)
2f: SCOP_d3vd5c4 (C:626-730)
2g: SCOP_d3vd5d2 (D:220-333)
2h: SCOP_d3vd5d4 (D:626-730)
3a: SCOP_d3vd5a5 (A:731-1023)
3b: SCOP_d3vd5b5 (B:731-1023)
3c: SCOP_d3vd5c5 (C:731-1023)
3d: SCOP_d3vd5d5 (D:731-1023)
4a: SCOP_d3vd5a3 (A:334-625)
4b: SCOP_d3vd5b3 (B:334-625)
4c: SCOP_d3vd5c3 (C:334-625)
4d: SCOP_d3vd5d3 (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
d3vd5a1
A:13-219
1b
d3vd5b1
B:13-219
1c
d3vd5c1
C:13-219
1d
d3vd5d1
D:13-219
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
d3vd5a2
A:220-333
2b
d3vd5a4
A:626-730
2c
d3vd5b2
B:220-333
2d
d3vd5b4
B:626-730
2e
d3vd5c2
C:220-333
2f
d3vd5c4
C:626-730
2g
d3vd5d2
D:220-333
2h
d3vd5d4
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
d3vd5a5
A:731-1023
3b
d3vd5b5
B:731-1023
3c
d3vd5c5
C:731-1023
3d
d3vd5d5
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
d3vd5a3
A:334-625
4b
d3vd5b3
B:334-625
4c
d3vd5c3
C:334-625
4d
d3vd5d3
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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Asym.Unit (689 KB)
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