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3EE5
Biol. Unit 1
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, 11)
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
2
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
5
Ligand/Ion
SULFATE ION
9
UDH
1
Ligand/Ion
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
[
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]
Sites
(16, 16)
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: BC3 (SOFTWARE)
12: BC6 (SOFTWARE)
13: BC7 (SOFTWARE)
14: BC9 (SOFTWARE)
15: CC1 (SOFTWARE)
16: CC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:183 , PHE A:184 , ARG A:185 , ARG A:187 , PHE A:222 , ASP A:248 , VAL A:249 , ASP A:250 , LYS A:275 , TRP A:310 , HIS A:340 , HIS A:343 , ARG A:345 , ASP A:346 , GOL A:417 , MN A:611 , HOH A:3012 , HOH A:3040 , HOH A:3058 , HOH A:3071
BINDING SITE FOR RESIDUE UDH A 399
02
AC2
SOFTWARE
PHE A:276 , TYR A:282 , TYR A:285 , TRP A:310 , GLY A:311 , GLY A:312 , ASP A:314 , ASP A:315 , ARG A:355 , GAL A:401 , GOL A:417 , HOH A:3052
BINDING SITE FOR RESIDUE NAG A 400
03
AC3
SOFTWARE
2NA A:100 , NAG A:400 , HOH A:3052
BINDING SITE FOR RESIDUE GAL A 401
04
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
05
AC5
SOFTWARE
ASN A:160 , TYR A:167 , PRO A:169 , ARG A:170 , HOH A:3021 , HOH A:3074 , HOH A:3080 , HOH A:3136
BINDING SITE FOR RESIDUE SO4 A 602
06
AC6
SOFTWARE
GLU A:144 , PHE A:145 , ASN A:146 , ARG A:339
BINDING SITE FOR RESIDUE SO4 A 604
07
AC7
SOFTWARE
THR A:375 , TYR A:376
BINDING SITE FOR RESIDUE SO4 A 607
08
AC8
SOFTWARE
ARG A:267 , PRO A:331
BINDING SITE FOR RESIDUE SO4 A 609
09
AC9
SOFTWARE
SER A:344 , HOH A:3404
BINDING SITE FOR RESIDUE SO4 A 610
10
BC1
SOFTWARE
ASP A:250 , HIS A:340 , HIS A:343 , UDH A:399 , HOH A:3012
BINDING SITE FOR RESIDUE MN A 611
11
BC3
SOFTWARE
TRP A:310 , GLY A:311 , GLU A:313 , ASP A:314 , UDH A:399 , NAG A:400 , HOH A:3261 , HOH A:3325
BINDING SITE FOR RESIDUE GOL A 417
12
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
13
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
14
BC9
SOFTWARE
SER A:327 , ILE A:328 , PHE B:318 , SER B:327 , ILE B:328
BINDING SITE FOR RESIDUE GOL B 415
15
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
16
CC9
SOFTWARE
GLY A:395 , THR A:396 , GOL A:420 , LYS B:348 , HOH B:3430
BINDING SITE FOR RESIDUE SO4 B 614
[
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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 A, )
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
A
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
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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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(
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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 A
Asymmetric Unit 1
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