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2AGD
Biol. Unit 3
Info
Asym.Unit (162 KB)
Biol.Unit 1 (55 KB)
Biol.Unit 2 (55 KB)
Biol.Unit 3 (55 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN M340H-BETA-1,4-GALACTOSYLTRANSFERASE-I(M340H-B4GAL-T1) IN COMPLEX WITH GLCNAC-BETA1,4-MAN-ALPHA1,3-MAN-BETA-OR
Authors
:
V. Ramasamy, B. Ramakrishnan, E. Boeggeman, D. M. Ratner, P. H. Seeberg P. K. Qasba
Date
:
26 Jul 05 (Deposition) - 04 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Beta1, 4-Galactosyltransferase-I; Trisaccharide; Closed Conformation; Mutant, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Ramasamy, B. Ramakrishnan, E. Boeggeman, D. M. Ratner, P. H. Seeberger, P. K. Qasba
Oligosaccharide Preferences Of Beta1, 4-Galactosyltransferase-I: Crystal Structures Of Met340His Mutant Of Human Beta1, 4-Galactosyltransferase-I With A Pentasaccharide And Trisaccharides Of The N-Glycan Moiety
J. Mol. Biol. V. 353 53 2005
[
close entry info
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Hetero Components
(8, 12)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: 1,4-DIETHYLENE DIOXIDE (DIOa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
5a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
6a: MANGANESE (II) ION (MNa)
6b: MANGANESE (II) ION (MNb)
6c: MANGANESE (II) ION (MNc)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
8a: SULFATE ION (SO4a)
8b: SULFATE ION (SO4b)
8c: SULFATE ION (SO4c)
8d: SULFATE ION (SO4d)
8e: SULFATE ION (SO4e)
8f: SULFATE ION (SO4f)
8g: SULFATE ION (SO4g)
8h: SULFATE ION (SO4h)
8i: SULFATE ION (SO4i)
8j: SULFATE ION (SO4j)
8k: SULFATE ION (SO4k)
8l: SULFATE ION (SO4l)
8m: SULFATE ION (SO4m)
8n: SULFATE ION (SO4n)
8o: SULFATE ION (SO4o)
8p: SULFATE ION (SO4p)
9a: 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSP... (UDHa)
9b: 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSP... (UDHb)
9c: 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSP... (UDHc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
DIO
1
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
3
GOL
1
Ligand/Ion
GLYCEROL
4
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
5
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
6
MN
-1
Ligand/Ion
MANGANESE (II) ION
7
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
SO4
5
Ligand/Ion
SULFATE ION
9
UDH
1
Ligand/Ion
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC7 (SOFTWARE)
02: AC8 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC9 (SOFTWARE)
06: CC1 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC8 (SOFTWARE)
10: CC9 (SOFTWARE)
11: DC4 (SOFTWARE)
12: DC5 (SOFTWARE)
13: DC6 (SOFTWARE)
14: EC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC7
SOFTWARE
PHE C:276 , TYR C:282 , TYR C:285 , TRP C:310 , GLY C:311 , GLY C:312 , ASP C:314 , ASP C:315 , ARG C:355 , MAN C:412 , GOL C:418 , HOH C:876
BINDING SITE FOR RESIDUE NAG C 411
02
AC8
SOFTWARE
NAG C:411 , BMA C:413
BINDING SITE FOR RESIDUE MAN C 412
03
AC9
SOFTWARE
PHE C:356 , MAN C:412
BINDING SITE FOR RESIDUE BMA C 413
04
BC3
SOFTWARE
ASP C:250 , HIS C:340 , HIS C:343 , UDH C:403 , HOH C:519
BINDING SITE FOR RESIDUE MN C 404
05
BC9
SOFTWARE
ASN C:160 , TYR C:167 , PRO C:169 , ARG C:170 , HOH C:488 , HOH C:489 , HOH C:596 , HOH C:930
BINDING SITE FOR RESIDUE SO4 C 427
06
CC1
SOFTWARE
GLU B:144 , PHE B:145 , ARG B:339 , PRO C:159 , ASN C:160
BINDING SITE FOR RESIDUE SO4 B 428
07
CC3
SOFTWARE
GLU C:144 , PHE C:145 , ASN C:146 , ARG C:339
BINDING SITE FOR RESIDUE SO4 C 430
08
CC4
SOFTWARE
HIS C:343 , SER C:344 , HOH C:781
BINDING SITE FOR RESIDUE SO4 C 431
09
CC8
SOFTWARE
ARG C:267
BINDING SITE FOR RESIDUE SO4 C 435
10
CC9
SOFTWARE
SER C:344 , ARG C:345
BINDING SITE FOR RESIDUE SO4 C 436
11
DC4
SOFTWARE
PRO C:183 , PHE C:184 , ARG C:185 , ARG C:187 , PHE C:222 , ASP C:248 , VAL C:249 , ASP C:250 , LYS C:275 , TRP C:310 , HIS C:340 , ARG C:342 , HIS C:343 , ARG C:345 , ASP C:346 , MN C:404 , GOL C:418 , HOH C:519 , HOH C:686 , HOH C:709 , HOH C:767
BINDING SITE FOR RESIDUE UDH C 403
12
DC5
SOFTWARE
ASN C:306 , TRP C:308 , ARG C:358 , SER C:398
BINDING SITE FOR RESIDUE DIO C 438
13
DC6
SOFTWARE
LYS C:237 , LEU C:374 , THR C:375 , TYR C:376 , GLN C:377 , VAL C:378 , HOH C:717 , HOH C:852
BINDING SITE FOR RESIDUE MES C 439
14
EC2
SOFTWARE
ARG C:224 , TRP C:310 , GLY C:311 , GLU C:313 , ASP C:314 , UDH C:403 , NAG C:411 , HOH C:834 , HOH C:946
BINDING SITE FOR RESIDUE GOL C 418
[
close Site info
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_054020 (H257R, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_054020
H
257
R
B4GT1_HUMAN
Polymorphism
9169
C
H
257
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d2agda_ (A:)
1b: SCOP_d2agdb_ (B:)
1c: SCOP_d2agdc_ (C:)
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(
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(
)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
beta 1,4 galactosyltransferase (b4GalT1)
(39)
Protein domain
:
automated matches
(19)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d2agda_
A:
1b
d2agdb_
B:
1c
d2agdc_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2agdA00 (A:126-398)
1b: CATH_2agdB00 (B:126-398)
1c: CATH_2agdC00 (C:126-398)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Human (Homo sapiens)
(73)
1a
2agdA00
A:126-398
1b
2agdB00
B:126-398
1c
2agdC00
C:126-398
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain C
Asymmetric Unit 1
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