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2AGD
Biol. Unit 2
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
(6, 15)
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
4
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
7
Ligand/Ion
SULFATE ION
9
UDH
1
Ligand/Ion
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC4 (SOFTWARE)
06: BC7 (SOFTWARE)
07: BC8 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC5 (SOFTWARE)
11: CC7 (SOFTWARE)
12: DC1 (SOFTWARE)
13: DC3 (SOFTWARE)
14: DC7 (SOFTWARE)
15: DC8 (SOFTWARE)
16: DC9 (SOFTWARE)
17: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
PHE B:276 , TYR B:282 , TYR B:285 , TRP B:310 , GLY B:311 , GLY B:312 , ASP B:314 , ASP B:315 , ARG B:355 , MAN B:409 , GOL B:414 , HOH B:538 , HOH B:551 , HOH B:720
BINDING SITE FOR RESIDUE NAG B 408
02
AC5
SOFTWARE
NAG B:408 , BMA B:410
BINDING SITE FOR RESIDUE MAN B 409
03
AC6
SOFTWARE
PHE B:356 , MAN B:409 , HOH B:538
BINDING SITE FOR RESIDUE BMA B 410
04
BC2
SOFTWARE
ASP B:250 , HIS B:340 , HIS B:343 , UDH B:401 , HOH B:453
BINDING SITE FOR RESIDUE MN B 402
05
BC4
SOFTWARE
GLU A:144 , PHE A:145 , ASN A:146 , ARG A:339 , HOH B:916
BINDING SITE FOR RESIDUE SO4 A 422
06
BC7
SOFTWARE
ARG B:267
BINDING SITE FOR RESIDUE SO4 B 425
07
BC8
SOFTWARE
SER B:344 , ARG B:345 , UDH B:401
BINDING SITE FOR RESIDUE SO4 B 426
08
CC1
SOFTWARE
GLU B:144 , PHE B:145 , ARG B:339 , PRO C:159 , ASN C:160
BINDING SITE FOR RESIDUE SO4 B 428
09
CC2
SOFTWARE
ASN B:160 , TYR B:167 , PRO B:169 , ARG B:170 , HOH B:466 , HOH B:525 , HOH B:656 , HOH B:860
BINDING SITE FOR RESIDUE SO4 B 429
10
CC5
SOFTWARE
HIS B:343 , SER B:344 , HOH B:629
BINDING SITE FOR RESIDUE SO4 B 432
11
CC7
SOFTWARE
ASP B:150 , LEU B:151 , LYS B:192 , HOH B:739
BINDING SITE FOR RESIDUE SO4 B 434
12
DC1
SOFTWARE
VAL B:381 , ARG B:383 , HOH B:927
BINDING SITE FOR RESIDUE SO4 B 437
13
DC3
SOFTWARE
HOH A:465 , PRO B:183 , PHE B:184 , ARG B:185 , ARG B:187 , PHE B:222 , ASP B:248 , VAL B:249 , ASP B:250 , LYS B:275 , TRP B:310 , HIS B:340 , HIS B:343 , ARG B:345 , ASP B:346 , MN B:402 , GOL B:414 , SO4 B:426 , HOH B:453 , HOH B:480 , HOH B:720 , HOH B:923
BINDING SITE FOR RESIDUE UDH B 401
14
DC7
SOFTWARE
ARG B:224 , TRP B:310 , GLY B:311 , GLU B:313 , ASP B:314 , UDH B:401 , NAG B:408 , HOH B:478 , HOH B:510
BINDING SITE FOR RESIDUE GOL B 414
15
DC8
SOFTWARE
VAL A:322 , MET A:326 , SER A:327 , ILE A:328 , PHE B:318 , SER B:327 , ILE B:328 , HOH B:599
BINDING SITE FOR RESIDUE GOL B 415
16
DC9
SOFTWARE
SER A:368 , ASP A:369 , PHE B:184 , ARG B:185 , ASN B:186 , ASN B:215 , HOH B:491 , HOH B:769
BINDING SITE FOR RESIDUE GOL B 416
17
EC3
SOFTWARE
ASN B:306 , TRP B:308 , ARG B:358 , PRO B:397 , SER B:398
BINDING SITE FOR RESIDUE GOL B 419
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_054020 (H257R, chain B, )
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
B
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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All Exon Boundaries
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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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Superfamilies
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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:
[
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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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(
)
(
)
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 B
Asymmetric Unit 1
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