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3EE5
Biol. Unit 3
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
(8, 9)
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
1
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
2
Ligand/Ion
SULFATE ION
9
UDH
1
Ligand/Ion
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
[
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Sites
(10, 10)
Info
All Sites
01: DC2 (SOFTWARE)
02: DC3 (SOFTWARE)
03: DC4 (SOFTWARE)
04: DC5 (SOFTWARE)
05: DC6 (SOFTWARE)
06: DC7 (SOFTWARE)
07: DC8 (SOFTWARE)
08: DC9 (SOFTWARE)
09: EC1 (SOFTWARE)
10: EC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
DC2
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 , HIS C:343 , ARG C:345 , ASP C:346 , MN C:400 , GOL C:418 , HOH C:3275 , HOH C:3281 , HOH C:3389 , HOH C:3429
BINDING SITE FOR RESIDUE UDH C2399
02
DC3
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 , GOL C:418 , GAL C:2401 , HOH C:3474
BINDING SITE FOR RESIDUE NAG C2400
03
DC4
SOFTWARE
2NA C:102 , TYR C:282 , NAG C:2400 , HOH C:3397 , HOH C:3474
BINDING SITE FOR RESIDUE GAL C2401
04
DC5
SOFTWARE
TYR C:282 , GLN C:284 , PHE C:323 , ARG C:324 , GLY C:325 , GAL C:2401
BINDING SITE FOR RESIDUE 2NA C 102
05
DC6
SOFTWARE
ARG C:224 , ASP C:248 , GLY C:288 , TRP C:310 , GLY C:311 , GLU C:313 , ASP C:314 , UDH C:2399 , NAG C:2400 , HOH C:3471
BINDING SITE FOR RESIDUE GOL C 418
06
DC7
SOFTWARE
TRP C:308 , ARG C:358 , PRO C:397 , SER C:398
BINDING SITE FOR RESIDUE DIO C 435
07
DC8
SOFTWARE
LYS C:237 , LEU C:374 , THR C:375 , TYR C:376 , GLN C:377 , VAL C:378 , HOH C:3358 , HOH C:3472
BINDING SITE FOR RESIDUE MES C 436
08
DC9
SOFTWARE
GLU C:144 , PHE C:145 , ASN C:146 , ARG C:339
BINDING SITE FOR RESIDUE SO4 C 608
09
EC1
SOFTWARE
HIS C:343 , SER C:344
BINDING SITE FOR RESIDUE SO4 C 612
10
EC2
SOFTWARE
ASP C:250 , HIS C:340 , HIS C:343 , UDH C:2399 , HOH C:3275
BINDING SITE FOR RESIDUE MN C 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 C, )
View:
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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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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_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 C
Asymmetric Unit 1
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