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2AGD
Asym. Unit
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
]
Hetero Components
(9, 41)
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
3
Ligand/Ion
BETA-D-MANNOSE
2
DIO
1
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
3
GOL
8
Ligand/Ion
GLYCEROL
4
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
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
16
Ligand/Ion
SULFATE ION
9
UDH
3
Ligand/Ion
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(41, 41)
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)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
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 , MAN A:406 , GOL A:417 , HOH A:561 , HOH A:581
BINDING SITE FOR RESIDUE NAG A 405
02
AC2
SOFTWARE
NAG A:405 , BMA A:407 , HOH A:848 , HOH A:877
BINDING SITE FOR RESIDUE MAN A 406
03
AC3
SOFTWARE
PHE A:356 , MAN A:406 , HOH A:581
BINDING SITE FOR RESIDUE BMA A 407
04
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
05
AC5
SOFTWARE
NAG B:408 , BMA B:410
BINDING SITE FOR RESIDUE MAN B 409
06
AC6
SOFTWARE
PHE B:356 , MAN B:409 , HOH B:538
BINDING SITE FOR RESIDUE BMA B 410
07
AC7
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 , MAN C:412 , GOL C:418 , HOH C:876
BINDING SITE FOR RESIDUE NAG C 411
08
AC8
SOFTWARE
NAG C:411 , BMA C:413
BINDING SITE FOR RESIDUE MAN C 412
09
AC9
SOFTWARE
PHE C:356 , MAN C:412
BINDING SITE FOR RESIDUE BMA C 413
10
BC1
SOFTWARE
ASP A:250 , HIS A:340 , HIS A:343 , UDH A:399 , HOH A:468
BINDING SITE FOR RESIDUE MN A 400
11
BC2
SOFTWARE
ASP B:250 , HIS B:340 , HIS B:343 , UDH B:401 , HOH B:453
BINDING SITE FOR RESIDUE MN B 402
12
BC3
SOFTWARE
ASP C:250 , HIS C:340 , HIS C:343 , UDH C:403 , HOH C:519
BINDING SITE FOR RESIDUE MN C 404
13
BC4
SOFTWARE
GLU A:144 , PHE A:145 , ASN A:146 , ARG A:339 , HOH B:916
BINDING SITE FOR RESIDUE SO4 A 422
14
BC5
SOFTWARE
ASN A:160 , TYR A:167 , PRO A:169 , ARG A:170 , HOH A:518 , HOH A:712 , HOH A:804 , HOH A:908
BINDING SITE FOR RESIDUE SO4 A 423
15
BC6
SOFTWARE
ARG A:267
BINDING SITE FOR RESIDUE SO4 A 424
16
BC7
SOFTWARE
ARG B:267
BINDING SITE FOR RESIDUE SO4 B 425
17
BC8
SOFTWARE
SER B:344 , ARG B:345 , UDH B:401
BINDING SITE FOR RESIDUE SO4 B 426
18
BC9
SOFTWARE
ASN C:160 , TYR C:167 , PRO C:169 , ARG C:170 , HOH C:488 , HOH C:489 , HOH C:596 , HOH C:930
BINDING SITE FOR RESIDUE SO4 C 427
19
CC1
SOFTWARE
GLU B:144 , PHE B:145 , ARG B:339 , PRO C:159 , ASN C:160
BINDING SITE FOR RESIDUE SO4 B 428
20
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
21
CC3
SOFTWARE
GLU C:144 , PHE C:145 , ASN C:146 , ARG C:339
BINDING SITE FOR RESIDUE SO4 C 430
22
CC4
SOFTWARE
HIS C:343 , SER C:344 , HOH C:781
BINDING SITE FOR RESIDUE SO4 C 431
23
CC5
SOFTWARE
HIS B:343 , SER B:344 , HOH B:629
BINDING SITE FOR RESIDUE SO4 B 432
24
CC6
SOFTWARE
HIS A:343 , SER A:344 , HOH A:644
BINDING SITE FOR RESIDUE SO4 A 433
25
CC7
SOFTWARE
ASP B:150 , LEU B:151 , LYS B:192 , HOH B:739
BINDING SITE FOR RESIDUE SO4 B 434
26
CC8
SOFTWARE
ARG C:267
BINDING SITE FOR RESIDUE SO4 C 435
27
CC9
SOFTWARE
SER C:344 , ARG C:345
BINDING SITE FOR RESIDUE SO4 C 436
28
DC1
SOFTWARE
VAL B:381 , ARG B:383 , HOH B:927
BINDING SITE FOR RESIDUE SO4 B 437
29
DC2
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 , ASP A:346 , MN A:400 , GOL A:417 , HOH A:468 , HOH A:561 , HOH A:571 , HOH A:587 , HOH A:635
BINDING SITE FOR RESIDUE UDH A 399
30
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
31
DC4
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 , ARG C:342 , HIS C:343 , ARG C:345 , ASP C:346 , MN C:404 , GOL C:418 , HOH C:519 , HOH C:686 , HOH C:709 , HOH C:767
BINDING SITE FOR RESIDUE UDH C 403
32
DC5
SOFTWARE
ASN C:306 , TRP C:308 , ARG C:358 , SER C:398
BINDING SITE FOR RESIDUE DIO C 438
33
DC6
SOFTWARE
LYS C:237 , LEU C:374 , THR C:375 , TYR C:376 , GLN C:377 , VAL C:378 , HOH C:717 , HOH C:852
BINDING SITE FOR RESIDUE MES C 439
34
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
35
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
36
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
37
EC1
SOFTWARE
TRP A:310 , GLY A:311 , GLU A:313 , ASP A:314 , UDH A:399 , NAG A:405 , HOH A:685 , HOH A:912
BINDING SITE FOR RESIDUE GOL A 417
38
EC2
SOFTWARE
ARG C:224 , TRP C:310 , GLY C:311 , GLU C:313 , ASP C:314 , UDH C:403 , NAG C:411 , HOH C:834 , HOH C:946
BINDING SITE FOR RESIDUE GOL C 418
39
EC3
SOFTWARE
ASN B:306 , TRP B:308 , ARG B:358 , PRO B:397 , SER B:398
BINDING SITE FOR RESIDUE GOL B 419
40
EC4
SOFTWARE
ALA A:217 , THR A:220 , ASP A:393 , GLY A:395 , HOH A:471
BINDING SITE FOR RESIDUE GOL A 420
41
EC5
SOFTWARE
THR A:299 , HOH A:574 , HOH A:620 , HOH A:671
BINDING SITE FOR RESIDUE GOL A 421
[
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:
Select:
Label:
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_d2agda_ (A:)
1b: SCOP_d2agdb_ (B:)
1c: SCOP_d2agdc_ (C:)
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Protein Domains
(
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(
)
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:
[
close SCOP info
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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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(
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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
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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