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3EE5
Asym. Unit
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
[
close entry info
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Hetero Components
(9, 38)
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
3
Ligand/Ion
NAPHTHALEN-2-YLMETHANOL
2
DIO
1
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
3
GAL
3
Ligand/Ion
BETA-D-GALACTOSE
4
GOL
7
Ligand/Ion
GLYCEROL
5
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
6
MN
3
Ligand/Ion
MANGANESE (II) ION
7
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
SO4
14
Ligand/Ion
SULFATE ION
9
UDH
3
Ligand/Ion
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(38, 38)
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: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
View:
Select:
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
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
12
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
13
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
14
BC5
SOFTWARE
2NA B:101 , NAG B:1400 , HOH B:3279 , HOH B:3354
BINDING SITE FOR RESIDUE GAL B1401
15
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
16
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
17
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
18
BC9
SOFTWARE
SER A:327 , ILE A:328 , PHE B:318 , SER B:327 , ILE B:328
BINDING SITE FOR RESIDUE GOL B 415
19
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
20
CC2
SOFTWARE
ASN B:306 , TRP B:308 , ARG B:358 , PRO B:397 , SER B:398
BINDING SITE FOR RESIDUE GOL B 419
21
CC3
SOFTWARE
GLU B:144 , PHE B:145 , ASN B:146 , ARG B:339 , ARG B:342
BINDING SITE FOR RESIDUE SO4 B 601
22
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
23
CC5
SOFTWARE
HIS B:343 , SER B:344 , HOH B:3246
BINDING SITE FOR RESIDUE SO4 B 605
24
CC6
SOFTWARE
ASP B:150 , LEU B:151 , GLU B:152
BINDING SITE FOR RESIDUE SO4 B 606
25
CC7
SOFTWARE
SER B:344 , ARG B:345 , UDH B:1399
BINDING SITE FOR RESIDUE SO4 B 611
26
CC8
SOFTWARE
ARG B:267 , HOH B:3258
BINDING SITE FOR RESIDUE SO4 B 613
27
CC9
SOFTWARE
GLY A:395 , THR A:396 , GOL A:420 , LYS B:348 , HOH B:3430
BINDING SITE FOR RESIDUE SO4 B 614
28
DC1
SOFTWARE
ASP B:250 , HIS B:340 , HIS B:343 , UDH B:1399 , HOH B:3155
BINDING SITE FOR RESIDUE MN B 400
29
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
30
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
31
DC4
SOFTWARE
2NA C:102 , TYR C:282 , NAG C:2400 , HOH C:3397 , HOH C:3474
BINDING SITE FOR RESIDUE GAL C2401
32
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
33
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
34
DC7
SOFTWARE
TRP C:308 , ARG C:358 , PRO C:397 , SER C:398
BINDING SITE FOR RESIDUE DIO C 435
35
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
36
DC9
SOFTWARE
GLU C:144 , PHE C:145 , ASN C:146 , ARG C:339
BINDING SITE FOR RESIDUE SO4 C 608
37
EC1
SOFTWARE
HIS C:343 , SER C:344
BINDING SITE FOR RESIDUE SO4 C 612
38
EC2
SOFTWARE
ASP C:250 , HIS C:340 , HIS C:343 , UDH C:2399 , HOH C:3275
BINDING SITE FOR RESIDUE MN C 400
[
close Site info
]
SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_054020 (H257R, chain A/B/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
A/B/C
H
257
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(6, 18)
Info
All Exons
Exon 1.1 (A:126-138 | B:126-138 | C:126-138)
Exon 1.2 (A:138-216 | B:138-216 | C:138-216)
Exon 1.3 (A:217-279 | B:217-279 | C:217-279)
Exon 1.4 (A:279-320 | B:279-320 | C:279-320)
Exon 1.5 (A:320-355 | B:320-355 | C:320-355)
Exon 1.6 (A:355-398 | B:355-398 | C:355-398)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000379731
1
ENSE00001482335
chr9:
33167354-33166756
599
B4GT1_HUMAN
1-138
138
3
A:126-138
B:126-138
C:126-138
13
13
13
1.2
ENST00000379731
2
ENSE00000695817
chr9:
33135422-33135187
236
B4GT1_HUMAN
138-216
79
3
A:138-216
B:138-216
C:138-216
79
79
79
1.3
ENST00000379731
3
ENSE00000695815
chr9:
33120604-33120417
188
B4GT1_HUMAN
217-279
63
3
A:217-279
B:217-279
C:217-279
63
63
63
1.4
ENST00000379731
4
ENSE00000695812
chr9:
33116111-33115989
123
B4GT1_HUMAN
279-320
42
3
A:279-320
B:279-320
C:279-320
42
42
42
1.5
ENST00000379731
5
ENSE00000695809
chr9:
33113876-33113772
105
B4GT1_HUMAN
320-355
36
3
A:320-355
B:320-355
C:320-355
36
36
36
1.6
ENST00000379731
6
ENSE00001482317
chr9:
33113584-33110635
2950
B4GT1_HUMAN
355-398
44
3
A:355-398
B:355-398
C:355-398
44
44
44
[
close EXON info
]
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:
[
close SCOP info
]
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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Sorry, no Info available
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