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3VD7
Asym. Unit
Info
Asym.Unit (678 KB)
Biol.Unit 1 (668 KB)
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(1)
Title
:
E. COLI (LACZ) BETA-GALACTOSIDASE (N460S) IN COMPLEX WITH GALACTOTETRAZOLE
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
:
2.87
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
(4, 47)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1aa: DIMETHYL SULFOXIDE (DMSaa)
1ab: DIMETHYL SULFOXIDE (DMSab)
1ac: DIMETHYL SULFOXIDE (DMSac)
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: (5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6... (GTZa)
2b: (5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6... (GTZb)
2c: (5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6... (GTZc)
2d: (5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6... (GTZd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
4f: SODIUM ION (NAf)
4g: SODIUM ION (NAg)
4h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
29
Ligand/Ion
DIMETHYL SULFOXIDE
2
GTZ
4
Ligand/Ion
(5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6,7,8-TRIHYDROXY-TETRAZOLO[1,5-A]PIPERIDINE
3
MG
6
Ligand/Ion
MAGNESIUM ION
4
NA
8
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(47, 47)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:201 , GLU A:461 , MET A:502 , TYR A:503 , GLU A:537 , HIS A:540 , TRP A:568 , ASN A:604 , TRP A:999 , NA A:3101 , HOH A:4060
BINDING SITE FOR RESIDUE GTZ A 2001
02
AC2
SOFTWARE
GLU A:416 , HIS A:418 , GLU A:461 , HOH A:4058 , HOH A:4059 , HOH A:4060
BINDING SITE FOR RESIDUE MG A 3001
03
AC3
SOFTWARE
ASP A:201 , PHE A:601 , ASN A:604 , GTZ A:2001
BINDING SITE FOR RESIDUE NA A 3101
04
AC4
SOFTWARE
PHE A:556 , TYR A:559 , PRO A:560 , LEU A:562 , HOH A:4064
BINDING SITE FOR RESIDUE NA A 2102
05
AC5
SOFTWARE
LYS A:380 , ASN A:383 , PHE A:384 , PHE A:626 , TYR A:642 , TRP A:708
BINDING SITE FOR RESIDUE DMS A 8001
06
AC6
SOFTWARE
TRP A:36 , ASP A:45 , ARG A:310 , ALA A:327
BINDING SITE FOR RESIDUE DMS A 8002
07
AC7
SOFTWARE
THR A:271 , LEU A:291 , ARG A:292
BINDING SITE FOR RESIDUE DMS A 8003
08
AC8
SOFTWARE
HIS A:316 , GLY A:320 , LEU A:322
BINDING SITE FOR RESIDUE DMS A 8004
09
AC9
SOFTWARE
VAL A:84 , VAL A:85 , HIS A:93
BINDING SITE FOR RESIDUE DMS A 8005
10
BC1
SOFTWARE
ASP A:428 , PRO A:430 , GLN D:445
BINDING SITE FOR RESIDUE DMS A 8006
11
BC2
SOFTWARE
ASN B:102 , ASP B:201 , HIS B:391 , GLU B:461 , MET B:502 , TYR B:503 , GLU B:537 , HIS B:540 , TRP B:568 , ASN B:604 , TRP B:999 , NA B:3101 , HOH B:4002 , HOH B:4092
BINDING SITE FOR RESIDUE GTZ B 2001
12
BC3
SOFTWARE
GLU B:416 , HIS B:418 , GLU B:461 , HOH B:4002 , HOH B:4077 , HOH B:4092
BINDING SITE FOR RESIDUE MG B 3001
13
BC4
SOFTWARE
ASP B:15 , ASN B:18 , VAL B:21 , GLN B:163 , ASP B:193
BINDING SITE FOR RESIDUE MG B 3002
14
BC5
SOFTWARE
ASP B:201 , PHE B:601 , ASN B:604 , GTZ B:2001 , HOH B:4093
BINDING SITE FOR RESIDUE NA B 3101
15
BC6
SOFTWARE
PHE B:556 , TYR B:559 , PRO B:560 , LEU B:562 , HOH B:4016
BINDING SITE FOR RESIDUE NA B 3102
16
BC7
SOFTWARE
THR B:229 , VAL B:330 , GLY B:331 , ARG B:333 , PRO B:451 , ARG B:482
BINDING SITE FOR RESIDUE DMS B 8001
17
BC8
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
18
BC9
SOFTWARE
PHE B:33 , ALA B:34 , ASP B:45 , ARG B:310 , ALA B:327
BINDING SITE FOR RESIDUE DMS B 8003
19
CC1
SOFTWARE
THR B:271 , LEU B:291 , ARG B:292
BINDING SITE FOR RESIDUE DMS B 8004
20
CC2
SOFTWARE
ILE B:576 , PRO B:584 , TRP B:585 , SER B:586
BINDING SITE FOR RESIDUE DMS B 8005
21
CC3
SOFTWARE
GLY B:275 , VAL B:289 , THR B:290
BINDING SITE FOR RESIDUE DMS B 8006
22
CC4
SOFTWARE
VAL B:84 , VAL B:85 , HIS B:93
BINDING SITE FOR RESIDUE DMS B 8007
23
CC5
SOFTWARE
LEU B:293 , ASN B:294
BINDING SITE FOR RESIDUE DMS B 8008
24
CC6
SOFTWARE
ASN C:102 , ASP C:201 , HIS C:391 , GLU C:461 , MET C:502 , TYR C:503 , GLU C:537 , HIS C:540 , TRP C:568 , ASN C:604 , TRP C:999 , NA C:3101 , HOH C:4003
BINDING SITE FOR RESIDUE GTZ C 2001
25
CC7
SOFTWARE
GLU C:416 , HIS C:418 , GLU C:461 , HOH C:4003 , HOH C:4075 , HOH C:4076
BINDING SITE FOR RESIDUE MG C 3001
26
CC8
SOFTWARE
ASP C:15 , ASN C:18 , VAL C:21 , GLN C:163 , ASP C:193
BINDING SITE FOR RESIDUE MG C 3002
27
CC9
SOFTWARE
TYR C:100 , ASP C:201 , PHE C:601 , ASN C:604 , GTZ C:2001 , HOH C:4077
BINDING SITE FOR RESIDUE NA C 3101
28
DC1
SOFTWARE
PHE C:556 , TYR C:559 , PRO C:560 , LEU C:562 , HOH C:4078
BINDING SITE FOR RESIDUE NA C 3102
29
DC2
SOFTWARE
THR C:229 , VAL C:330 , GLY C:331 , ARG C:333 , ASN C:449 , HIS C:450 , PRO C:451 , ARG C:482
BINDING SITE FOR RESIDUE DMS C 8001
30
DC3
SOFTWARE
ARG C:557 , HIS C:622 , GLN C:623 , GLN C:628 , HOH C:4042
BINDING SITE FOR RESIDUE DMS C 8002
31
DC4
SOFTWARE
LYS C:380 , ASN C:383 , PHE C:384 , PHE C:626 , TYR C:642 , TRP C:708
BINDING SITE FOR RESIDUE DMS C 8003
32
DC5
SOFTWARE
THR C:271 , LEU C:291 , ARG C:292
BINDING SITE FOR RESIDUE DMS C 8004
33
DC6
SOFTWARE
ILE C:576 , PRO C:584 , TRP C:585 , SER C:586 , ARG C:973
BINDING SITE FOR RESIDUE DMS C 8005
34
DC7
SOFTWARE
VAL C:85 , HIS C:93
BINDING SITE FOR RESIDUE DMS C 8006
35
DC8
SOFTWARE
ASP C:45 , ARG C:46 , HOH C:4024
BINDING SITE FOR RESIDUE DMS C 8007
36
DC9
SOFTWARE
GLN C:50 , SER C:132 , TRP C:133 , HIS C:216
BINDING SITE FOR RESIDUE DMS C 8008
37
EC1
SOFTWARE
ASP D:201 , GLU D:461 , MET D:502 , TYR D:503 , GLU D:537 , HIS D:540 , TRP D:568 , PHE D:601 , ASN D:604 , TRP D:999 , NA D:3101
BINDING SITE FOR RESIDUE GTZ D 2001
38
EC2
SOFTWARE
GLU D:416 , HIS D:418 , GLU D:461 , HOH D:4003 , HOH D:4121 , HOH D:4122
BINDING SITE FOR RESIDUE MG D 3001
39
EC3
SOFTWARE
ASP D:201 , PHE D:601 , ASN D:604 , GTZ D:2001 , HOH D:4123
BINDING SITE FOR RESIDUE NA D 3101
40
EC4
SOFTWARE
PHE D:556 , TYR D:559 , PRO D:560 , LEU D:562 , HOH D:4086 , HOH D:4114
BINDING SITE FOR RESIDUE NA D 3102
41
EC5
SOFTWARE
THR D:229 , VAL D:330 , GLY D:331 , ARG D:333 , ASN D:449 , PRO D:451 , ARG D:482
BINDING SITE FOR RESIDUE DMS D 8001
42
EC6
SOFTWARE
LYS D:380 , ASN D:383 , PHE D:384 , PHE D:626 , TYR D:642 , TRP D:708
BINDING SITE FOR RESIDUE DMS D 8002
43
EC7
SOFTWARE
THR D:271 , LEU D:291 , ARG D:292
BINDING SITE FOR RESIDUE DMS D 8003
44
EC8
SOFTWARE
GLU D:314 , HIS D:316 , GLY D:320
BINDING SITE FOR RESIDUE DMS D 8004
45
EC9
SOFTWARE
SER D:53 , LEU D:54 , ASN D:55 , LEU D:125
BINDING SITE FOR RESIDUE DMS D 8005
46
FC1
SOFTWARE
ILE D:576 , PRO D:584 , TRP D:585 , SER D:586 , ARG D:973
BINDING SITE FOR RESIDUE DMS D 8006
47
FC2
SOFTWARE
ASP D:45
BINDING SITE FOR RESIDUE DMS D 8007
[
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_d3vd7a1 (A:13-219)
1b: SCOP_d3vd7b1 (B:13-219)
1c: SCOP_d3vd7c1 (C:13-219)
1d: SCOP_d3vd7d1 (D:13-219)
2a: SCOP_d3vd7a2 (A:220-333)
2b: SCOP_d3vd7a4 (A:626-730)
2c: SCOP_d3vd7b2 (B:220-333)
2d: SCOP_d3vd7b4 (B:626-730)
2e: SCOP_d3vd7c2 (C:220-333)
2f: SCOP_d3vd7c4 (C:626-730)
2g: SCOP_d3vd7d2 (D:220-333)
2h: SCOP_d3vd7d4 (D:626-730)
3a: SCOP_d3vd7a5 (A:731-1023)
3b: SCOP_d3vd7b5 (B:731-1023)
3c: SCOP_d3vd7c5 (C:731-1023)
3d: SCOP_d3vd7d5 (D:731-1023)
4a: SCOP_d3vd7a3 (A:334-625)
4b: SCOP_d3vd7b3 (B:334-625)
4c: SCOP_d3vd7c3 (C:334-625)
4d: SCOP_d3vd7d3 (D:334-625)
View:
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Classes
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)
(
)
Folds
(
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(
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Superfamilies
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(
)
Families
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(
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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
d3vd7a1
A:13-219
1b
d3vd7b1
B:13-219
1c
d3vd7c1
C:13-219
1d
d3vd7d1
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
d3vd7a2
A:220-333
2b
d3vd7a4
A:626-730
2c
d3vd7b2
B:220-333
2d
d3vd7b4
B:626-730
2e
d3vd7c2
C:220-333
2f
d3vd7c4
C:626-730
2g
d3vd7d2
D:220-333
2h
d3vd7d4
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
d3vd7a5
A:731-1023
3b
d3vd7b5
B:731-1023
3c
d3vd7c5
C:731-1023
3d
d3vd7d5
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
d3vd7a3
A:334-625
4b
d3vd7b3
B:334-625
4c
d3vd7c3
C:334-625
4d
d3vd7d3
D:334-625
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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