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3EE5
Biol. Unit 2
Info
Asym.Unit (161 KB)
Biol.Unit 1 (54 KB)
Biol.Unit 2 (55 KB)
Biol.Unit 3 (54 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN M340H-BETA1,4-GALACTOSYLTRANSFERASE-I (M340H-B4GAL-T1) IN COMPLEX WITH GLCNAC-BETA1,3-GAL-BETA-NAPHTHALENEMETHANOL
Authors
:
B. Ramakrishnan, P. K. Qasba
Date
:
04 Sep 08 (Deposition) - 06 Jan 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Closed Conformation, Carbohydrate Acceptor Binding, Alternative Initiation, Cell Membrane, Congenital Disorder Of Glycosylation, Glycoprotein, Glycosyltransferase, Golgi Apparatus, Manganese, Membrane, Metal-Binding, Secreted, Signal-Anchor, Transferase, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Brown, F. Yang, A. Sinha, B. Ramakrishnan, Y. Tor, P. K. Qasba, J. D. Esko
Deoxygenated Disaccharide Analogs As Specific Inhibitors Of {Beta}1-4-Galactosyltransferase 1 And Selectin-Mediated Tumor Metastasis
J. Biol. Chem. V. 284 4952 2009
[
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Hetero Components
(6, 15)
Info
All Hetero Components
1a: NAPHTHALEN-2-YLMETHANOL (2NAa)
1b: NAPHTHALEN-2-YLMETHANOL (2NAb)
1c: NAPHTHALEN-2-YLMETHANOL (2NAc)
2a: 1,4-DIETHYLENE DIOXIDE (DIOa)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
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)
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
2NA
1
Ligand/Ion
NAPHTHALEN-2-YLMETHANOL
2
DIO
-1
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
3
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
4
GOL
4
Ligand/Ion
GLYCEROL
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
[
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]
Sites
(18, 18)
Info
All Sites
01: AC4 (SOFTWARE)
02: BC2 (SOFTWARE)
03: BC4 (SOFTWARE)
04: BC5 (SOFTWARE)
05: BC6 (SOFTWARE)
06: BC7 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
TYR A:282 , GLN A:284 , GAL A:401 , PHE B:323 , ARG B:324 , GLY B:325
BINDING SITE FOR RESIDUE 2NA A 100
02
BC2
SOFTWARE
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:400 , SO4 B:611 , HOH B:3154 , HOH B:3155 , HOH B:3185
BINDING SITE FOR RESIDUE UDH B1399
03
BC4
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 , GOL B:414 , GAL B:1401 , HOH B:3279 , HOH B:3368 , HOH B:3392
BINDING SITE FOR RESIDUE NAG B1400
04
BC5
SOFTWARE
2NA B:101 , NAG B:1400 , HOH B:3279 , HOH B:3354
BINDING SITE FOR RESIDUE GAL B1401
05
BC6
SOFTWARE
ALA A:217 , THR A:220 , ASP A:393 , GLY A:395 , THR A:396 , HOH A:3158 , HOH A:3191 , SO4 B:614
BINDING SITE FOR RESIDUE GOL A 420
06
BC7
SOFTWARE
PHE A:323 , ARG A:324 , GLY A:325 , TYR B:282 , GLN B:284 , GAL B:1401
BINDING SITE FOR RESIDUE 2NA B 101
07
BC8
SOFTWARE
TRP B:310 , GLY B:311 , GLU B:313 , ASP B:314 , NAG B:1400 , HOH B:3169 , HOH B:3188
BINDING SITE FOR RESIDUE GOL B 414
08
BC9
SOFTWARE
SER A:327 , ILE A:328 , PHE B:318 , SER B:327 , ILE B:328
BINDING SITE FOR RESIDUE GOL B 415
09
CC1
SOFTWARE
SER A:368 , ASP A:369 , PHE B:184 , ARG B:185 , ASN B:186 , ASN B:215
BINDING SITE FOR RESIDUE GOL B 416
10
CC2
SOFTWARE
ASN B:306 , TRP B:308 , ARG B:358 , PRO B:397 , SER B:398
BINDING SITE FOR RESIDUE GOL B 419
11
CC3
SOFTWARE
GLU B:144 , PHE B:145 , ASN B:146 , ARG B:339 , ARG B:342
BINDING SITE FOR RESIDUE SO4 B 601
12
CC4
SOFTWARE
ASN B:160 , TYR B:167 , PRO B:169 , ARG B:170 , HOH B:3172 , HOH B:3189 , HOH B:3286 , HOH B:3443
BINDING SITE FOR RESIDUE SO4 B 603
13
CC5
SOFTWARE
HIS B:343 , SER B:344 , HOH B:3246
BINDING SITE FOR RESIDUE SO4 B 605
14
CC6
SOFTWARE
ASP B:150 , LEU B:151 , GLU B:152
BINDING SITE FOR RESIDUE SO4 B 606
15
CC7
SOFTWARE
SER B:344 , ARG B:345 , UDH B:1399
BINDING SITE FOR RESIDUE SO4 B 611
16
CC8
SOFTWARE
ARG B:267 , HOH B:3258
BINDING SITE FOR RESIDUE SO4 B 613
17
CC9
SOFTWARE
GLY A:395 , THR A:396 , GOL A:420 , LYS B:348 , HOH B:3430
BINDING SITE FOR RESIDUE SO4 B 614
18
DC1
SOFTWARE
ASP B:250 , HIS B:340 , HIS B:343 , UDH B:1399 , HOH B:3155
BINDING SITE FOR RESIDUE MN B 400
[
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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 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
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;
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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_d3ee5a_ (A:)
1b: SCOP_d3ee5b_ (B:)
1c: SCOP_d3ee5c_ (C:)
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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
d3ee5a_
A:
1b
d3ee5b_
B:
1c
d3ee5c_
C:
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_3ee5A00 (A:126-398)
1b: CATH_3ee5B00 (B:126-398)
1c: CATH_3ee5C00 (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
3ee5A00
A:126-398
1b
3ee5B00
B:126-398
1c
3ee5C00
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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