PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2AEC
Asym. Unit
Info
Asym.Unit (161 KB)
Biol.Unit 1 (54 KB)
Biol.Unit 2 (55 KB)
Biol.Unit 3 (54 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN M340H-BETA1,4-GALACTOSYLTRANSFERASE-I (M340H-B4GAL-T1) IN COMPLEX WITH GLCNAC-BETA1,2-MAN-ALPHA1,6-MAN-BETA-OR
Authors
:
V. Ramasamy, B. Ramakrishnan, E. Boeggeman, D. M. Ratner, P. H. Seeberg P. K. Qasba
Date
:
22 Jul 05 (Deposition) - 04 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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, 38)
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)
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)
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
7
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
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
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:627
BINDING SITE FOR RESIDUE NAG A 405
02
AC2
SOFTWARE
TYR A:282 , PHE A:356 , NAG A:405 , BMA A:407 , HOH A:663
BINDING SITE FOR RESIDUE MAN A 406
03
AC3
SOFTWARE
TYR A:282 , MAN A:406 , HOH A:840 , HOH A:899 , HOH B:459
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:620 , HOH B:759 , HOH B:791
BINDING SITE FOR RESIDUE NAG B 408
05
AC5
SOFTWARE
TYR B:282 , PHE B:356 , NAG B:408 , BMA B:410 , HOH B:678 , HOH B:791 , HOH B:814
BINDING SITE FOR RESIDUE MAN B 409
06
AC6
SOFTWARE
GLY A:325 , HOH A:466 , TYR B:282 , MAN B:409
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:919 , HOH C:922
BINDING SITE FOR RESIDUE NAG C 411
08
AC8
SOFTWARE
TYR C:282 , PHE C:356 , NAG C:411 , BMA C:413
BINDING SITE FOR RESIDUE MAN C 412
09
AC9
SOFTWARE
TYR C:282 , GLY C:325 , MAN C:412 , HOH C:690
BINDING SITE FOR RESIDUE BMA C 413
10
BC1
SOFTWARE
ASP A:250 , HIS A:340 , HIS A:343 , UDH A:399 , HOH A:491
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:611
BINDING SITE FOR RESIDUE MN C 404
13
BC4
SOFTWARE
GLU A:144 , PHE A:145 , ASN A:146 , ARG A:339
BINDING SITE FOR RESIDUE SO4 A 421
14
BC5
SOFTWARE
ASN A:160 , TYR A:167 , PRO A:169 , ARG A:170 , HOH A:514 , HOH A:702 , HOH A:726 , HOH A:894
BINDING SITE FOR RESIDUE SO4 A 422
15
BC6
SOFTWARE
ARG A:267 , PRO A:331
BINDING SITE FOR RESIDUE SO4 A 423
16
BC7
SOFTWARE
ARG B:267
BINDING SITE FOR RESIDUE SO4 B 424
17
BC8
SOFTWARE
SER B:344 , ARG B:345
BINDING SITE FOR RESIDUE SO4 B 425
18
BC9
SOFTWARE
ASN C:160 , TYR C:167 , PRO C:169 , ARG C:170 , HOH C:477 , HOH C:512 , HOH C:688 , HOH C:826
BINDING SITE FOR RESIDUE SO4 C 426
19
CC1
SOFTWARE
GLU B:144 , PHE B:145 , ASN B:146 , ARG B:339 , ARG B:342
BINDING SITE FOR RESIDUE SO4 B 427
20
CC2
SOFTWARE
ASN B:160 , TYR B:167 , PRO B:169 , ARG B:170 , HOH B:474 , HOH B:495 , HOH B:632 , HOH B:879
BINDING SITE FOR RESIDUE SO4 B 428
21
CC3
SOFTWARE
GLU C:144 , PHE C:145 , ASN C:146 , ARG C:339
BINDING SITE FOR RESIDUE SO4 C 429
22
CC4
SOFTWARE
HIS C:343 , SER C:344
BINDING SITE FOR RESIDUE SO4 C 430
23
CC5
SOFTWARE
HIS B:343 , SER B:344 , HOH B:573
BINDING SITE FOR RESIDUE SO4 B 431
24
CC6
SOFTWARE
HIS A:343 , SER A:344 , HOH A:805
BINDING SITE FOR RESIDUE SO4 A 432
25
CC7
SOFTWARE
VAL B:149 , ASP B:150 , LEU B:151 , LYS B:192
BINDING SITE FOR RESIDUE SO4 B 433
26
CC8
SOFTWARE
SER C:344 , ARG C:345 , UDH C:403
BINDING SITE FOR RESIDUE SO4 C 434
27
CC9
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 , HOH A:491 , HOH A:600 , HOH A:644 , HOH A:689
BINDING SITE FOR RESIDUE UDH A 399
28
DC1
SOFTWARE
HOH A:452 , 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 , HOH B:453 , HOH B:489
BINDING SITE FOR RESIDUE UDH B 401
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:404 , GOL C:418 , SO4 C:434 , HOH C:611 , HOH C:622 , HOH C:788 , HOH C:844
BINDING SITE FOR RESIDUE UDH C 403
30
DC3
SOFTWARE
ASN C:306 , TRP C:308 , ARG C:358 , PRO C:397 , SER C:398
BINDING SITE FOR RESIDUE DIO C 435
31
DC4
SOFTWARE
LYS C:237 , LEU C:374 , THR C:375 , TYR C:376 , GLN C:377 , VAL C:378 , HOH C:887 , HOH C:920
BINDING SITE FOR RESIDUE MES C 436
32
DC5
SOFTWARE
ARG B:224 , TRP B:310 , GLY B:311 , GLU B:313 , ASP B:314 , UDH B:401 , NAG B:408 , HOH B:471 , HOH B:494
BINDING SITE FOR RESIDUE GOL B 414
33
DC6
SOFTWARE
MET A:326 , SER A:327 , ILE A:328 , PHE B:318 , SER B:327 , ILE B:328 , HOH B:610
BINDING SITE FOR RESIDUE GOL B 415
34
DC7
SOFTWARE
SER A:368 , ASP A:369 , PHE B:184 , ARG B:185 , ASN B:186 , ASN B:215 , HOH B:526
BINDING SITE FOR RESIDUE GOL B 416
35
DC8
SOFTWARE
ARG A:224 , TRP A:310 , GLY A:311 , GLU A:313 , ASP A:314 , NAG A:405 , HOH A:591 , HOH A:691
BINDING SITE FOR RESIDUE GOL A 417
36
DC9
SOFTWARE
ARG C:224 , TRP C:310 , GLY C:311 , GLU C:313 , ASP C:314 , UDH C:403 , NAG C:411
BINDING SITE FOR RESIDUE GOL C 418
37
EC1
SOFTWARE
ASN B:306 , TRP B:308 , ARG B:358 , PRO B:397 , SER B:398 , HOH B:914
BINDING SITE FOR RESIDUE GOL B 419
38
EC2
SOFTWARE
THR A:220 , ASP A:393 , GLY A:395 , HOH A:456 , HOH A:499
BINDING SITE FOR RESIDUE GOL A 420
[
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:127-138 | B:127-138 | C:127-138)
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:127-138
B:127-138
C:127-138
12
12
12
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_d2aeca_ (A:)
1b: SCOP_d2aecb_ (B:)
1c: SCOP_d2aecc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2aeca_
A:
1b
d2aecb_
B:
1c
d2aecc_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2aecA00 (A:127-398)
1b: CATH_2aecB00 (B:127-398)
1c: CATH_2aecC00 (C:127-398)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
2aecA00
A:127-398
1b
2aecB00
B:127-398
1c
2aecC00
C:127-398
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (161 KB)
Header - Asym.Unit
Biol.Unit 1 (54 KB)
Header - Biol.Unit 1
Biol.Unit 2 (55 KB)
Header - Biol.Unit 2
Biol.Unit 3 (54 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2AEC
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help