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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
5T05
Asym. Unit
Info
Asym.Unit (257 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (127 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 HEPARAN SULFATE 6-O-SULFOTRANSFERASE WITH BOUND PAP AND IDOA2S CONTAINING HEXASACCHARIDE SUBSTRATE
Authors
:
L. C. Pedersen, A. F. Moon, J. M. Krahn, J. Liu
Date
:
15 Aug 16 (Deposition) - 01 Feb 17 (Release) - 01 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Heparan Sulfate, Sulfotransferase, Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Xu, A. F. Moon, S. Xu, J. M. Krahn, J. Liu, L. C. Pedersen
Structure Based Substrate Specificity Analysis Of Heparan Sulfate 6-O-Sulfotransferases.
Acs Chem. Biol. V. 12 73 2017
[
close entry info
]
Hetero Components
(10, 54)
Info
All Hetero Components
01a: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pa)
01b: ADENOSINE-3'-5'-DIPHOSPHATE (A3Pb)
02a: BETA-D-GLUCOPYRANURONIC ACID (BDPa)
02b: BETA-D-GLUCOPYRANURONIC ACID (BDPb)
02c: BETA-D-GLUCOPYRANURONIC ACID (BDPc)
02d: BETA-D-GLUCOPYRANURONIC ACID (BDPd)
03a: CHLORIDE ION (CLa)
03b: CHLORIDE ION (CLb)
03c: CHLORIDE ION (CLc)
03d: CHLORIDE ION (CLd)
04a: 1,2-ETHANEDIOL (EDOa)
04b: 1,2-ETHANEDIOL (EDOb)
04c: 1,2-ETHANEDIOL (EDOc)
04d: 1,2-ETHANEDIOL (EDOd)
04e: 1,2-ETHANEDIOL (EDOe)
04f: 1,2-ETHANEDIOL (EDOf)
04g: 1,2-ETHANEDIOL (EDOg)
04h: 1,2-ETHANEDIOL (EDOh)
04i: 1,2-ETHANEDIOL (EDOi)
04j: 1,2-ETHANEDIOL (EDOj)
04k: 1,2-ETHANEDIOL (EDOk)
04l: 1,2-ETHANEDIOL (EDOl)
04m: 1,2-ETHANEDIOL (EDOm)
04n: 1,2-ETHANEDIOL (EDOn)
04o: 1,2-ETHANEDIOL (EDOo)
05a: ALPHA-D-GLUCOSE (GLCa)
05b: ALPHA-D-GLUCOSE (GLCb)
05c: ALPHA-D-GLUCOSE (GLCc)
05d: ALPHA-D-GLUCOSE (GLCd)
05e: ALPHA-D-GLUCOSE (GLCe)
05f: ALPHA-D-GLUCOSE (GLCf)
05g: ALPHA-D-GLUCOSE (GLCg)
05h: ALPHA-D-GLUCOSE (GLCh)
06a: N-SULFO-ALPHA-D-GLUCOSAMINE (GNSa)
06b: N-SULFO-ALPHA-D-GLUCOSAMINE (GNSb)
06c: N-SULFO-ALPHA-D-GLUCOSAMINE (GNSc)
06d: N-SULFO-ALPHA-D-GLUCOSAMINE (GNSd)
06e: N-SULFO-ALPHA-D-GLUCOSAMINE (GNSe)
06f: N-SULFO-ALPHA-D-GLUCOSAMINE (GNSf)
07a: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSa)
07b: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSb)
08a: SODIUM ION (NAa)
08b: SODIUM ION (NAb)
08c: SODIUM ION (NAc)
08d: SODIUM ION (NAd)
08e: SODIUM ION (NAe)
08f: SODIUM ION (NAf)
08g: SODIUM ION (NAg)
09a: P-NITROPHENOL (NPOa)
09b: P-NITROPHENOL (NPOb)
10a: L(+)-TARTARIC ACID (TLAa)
10b: L(+)-TARTARIC ACID (TLAb)
10c: L(+)-TARTARIC ACID (TLAc)
10d: L(+)-TARTARIC ACID (TLAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A3P
2
Ligand/Ion
ADENOSINE-3'-5'-DIPHOSPHATE
2
BDP
4
Ligand/Ion
BETA-D-GLUCOPYRANURONIC ACID
3
CL
4
Ligand/Ion
CHLORIDE ION
4
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
5
GLC
8
Ligand/Ion
ALPHA-D-GLUCOSE
6
GNS
6
Ligand/Ion
N-SULFO-ALPHA-D-GLUCOSAMINE
7
IDS
2
Ligand/Ion
2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
8
NA
7
Ligand/Ion
SODIUM ION
9
NPO
2
Ligand/Ion
P-NITROPHENOL
10
TLA
4
Ligand/Ion
L(+)-TARTARIC ACID
[
close Hetero Component info
]
Sites
(36, 36)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:1101 , LYS A:1104 , THR A:1105 , GLY A:1106 , GLY A:1107 , THR A:1108 , THR A:1109 , ARG A:1191 , SER A:1199 , THR A:1300 , GLN A:1303 , THR A:1323 , ILE A:1325 , THR A:1328 , ARG A:1329 , ALA A:1330 , EDO A:1420 , HOH A:1636 , HOH A:1714 , HOH A:1715 , HOH A:1721 , HOH A:1811 , HOH A:1915
binding site for residue A3P A 1401
02
AC2
SOFTWARE
VAL A:35 , THR A:36 , VAL A:37 , BDP A:1407 , NPO A:1408 , HOH A:1734 , HOH A:1827
binding site for residue EDO A 1413
03
AC3
SOFTWARE
ARG A:354 , HOH A:1779 , LEU B:1227 , SER B:1249 , EDO B:1415 , HOH B:1647
binding site for residue EDO A 1414
04
AC4
SOFTWARE
ARG A:1116 , GLN A:1130 , LYS A:1131 , CYS A:1133
binding site for residue EDO A 1415
05
AC5
SOFTWARE
ARG A:1191 , THR A:1328 , HOH A:1524 , HOH A:1593
binding site for residue EDO A 1416
06
AC6
SOFTWARE
ARG A:1258 , CYS A:1268 , TYR A:1269 , ARG A:1279 , HOH A:1534
binding site for residue EDO A 1417
07
AC7
SOFTWARE
TYR A:17 , ASN A:18 , ASP A:296 , LYS A:297
binding site for residue EDO A 1418
08
AC8
SOFTWARE
TYR A:176 , MET A:330 , PRO A:331 , ASN A:332 , HOH A:1730 , HOH A:1885
binding site for residue EDO A 1419
09
AC9
SOFTWARE
ARG A:1329 , A3P A:1401 , NA A:1427 , HOH A:1715
binding site for residue EDO A 1420
10
AD1
SOFTWARE
PRO A:1281 , LEU A:1349 , GLN A:1352 , GLU B:1278
binding site for residue EDO A 1421
11
AD2
SOFTWARE
PHE A:1302 , ARG A:1304 , LYS A:1305 , HOH A:1644
binding site for residue CL A 1422
12
AD3
SOFTWARE
LYS A:1132 , TRP A:1153 , GNS A:1404 , HOH A:1972
binding site for residue CL A 1423
13
AD4
SOFTWARE
HIS A:1315 , ARG A:1317 , HOH A:1794
binding site for residue CL A 1424
14
AD5
SOFTWARE
ASN A:1232 , ASP A:1235 , HOH A:1883 , HOH A:1920 , HOH A:1954 , HOH A:1990
binding site for residue NA A 1425
15
AD6
SOFTWARE
GNS A:1404 , IDS A:1405 , HOH A:1850 , HOH A:1923 , HOH A:1964
binding site for residue NA A 1426
16
AD7
SOFTWARE
LYS A:1104 , HIS A:1203 , ARG A:1206 , EDO A:1420 , TLA A:1430 , HOH A:1811
binding site for residue NA A 1427
17
AD8
SOFTWARE
BDP A:1403 , TLA A:1430
binding site for residue NA A 1428
18
AD9
SOFTWARE
ALA A:1331 , VAL A:1333 , HOH A:1928 , HOH A:1935
binding site for residue NA A 1429
19
AE1
SOFTWARE
HIS A:1203 , ARG A:1206 , GNS A:1402 , NA A:1427 , NA A:1428 , HOH A:1786 , HOH A:1925
binding site for residue TLA A 1430
20
AE2
SOFTWARE
SER A:270 , PRO A:271 , ASN A:272 , LYS A:273 , GLU A:274 , HOH A:1501 , HOH A:1656
binding site for residue TLA A 1431
21
AE3
SOFTWARE
HIS B:1101 , LYS B:1104 , THR B:1105 , GLY B:1106 , GLY B:1107 , THR B:1108 , THR B:1109 , ARG B:1191 , SER B:1199 , THR B:1300 , GLN B:1303 , THR B:1323 , GLN B:1324 , ILE B:1325 , THR B:1328 , ARG B:1329 , ALA B:1330 , TLA B:1423 , HOH B:1581 , HOH B:1604 , HOH B:1645 , HOH B:1652 , HOH B:1661 , HOH B:1668 , HOH B:1683 , HOH B:1798
binding site for residue A3P B 1401
22
AE4
SOFTWARE
ARG B:1191 , THR B:1328 , HOH B:1522 , HOH B:1616
binding site for residue EDO B 1413
23
AE5
SOFTWARE
TYR B:176 , MET B:330 , PRO B:331 , ASN B:332 , HOH B:1542 , HOH B:1808 , HOH B:1819
binding site for residue EDO B 1414
24
AE6
SOFTWARE
EDO A:1414 , ARG B:1258 , CYS B:1268 , TYR B:1269 , ARG B:1279 , HOH B:1610 , HOH B:1723
binding site for residue EDO B 1415
25
AE7
SOFTWARE
HOH A:1577 , LYS B:1292 , PHE B:1356 , HOH B:1540 , HOH B:1665
binding site for residue EDO B 1416
26
AE8
SOFTWARE
TYR B:90 , GNS B:1406 , HOH B:1550
binding site for residue EDO B 1417
27
AE9
SOFTWARE
ASN B:1280 , PRO B:1281 , LEU B:1349 , GLN B:1352 , HOH B:1511
binding site for residue EDO B 1418
28
AF1
SOFTWARE
GLU B:1276
binding site for residue CL B 1419
29
AF2
SOFTWARE
ASN B:1232 , ASP B:1235 , HOH B:1772 , HOH B:1881 , HOH B:1941 , HOH B:1942
binding site for residue NA B 1420
30
AF3
SOFTWARE
GLN B:325 , GLY B:327 , HOH B:1874 , HOH B:1940
binding site for residue NA B 1421
31
AF4
SOFTWARE
HIS B:1203 , ARG B:1206 , GNS B:1402 , HOH B:1544 , HOH B:1658 , HOH B:1778 , HOH B:1924
binding site for residue TLA B 1422
32
AF5
SOFTWARE
THR B:1108 , THR B:1109 , ARG B:1112 , A3P B:1401 , HOH B:1581 , HOH B:1645 , HOH B:1658 , HOH B:1668
binding site for residue TLA B 1423
33
AF6
SOFTWARE
TYR A:17 , ASN A:18 , ALA A:21 , VAL A:37 , GLU A:38 , HIS A:39 , LYS A:1131 , LYS A:1132 , ARG A:1148 , TRP A:1153 , LEU A:1157 , HIS A:1158 , HIS A:1203 , ALA A:1208 , THR A:1209 , TRP A:1210 , EDO A:1413 , CL A:1423 , NA A:1426 , NA A:1428 , TLA A:1430 , HOH A:1525 , HOH A:1570 , HOH A:1649 , HOH A:1699 , HOH A:1702 , HOH A:1714 , HOH A:1720 , HOH A:1734 , HOH A:1842 , HOH A:1850 , HOH A:1896 , HOH A:1923 , HOH A:1927 , HOH A:1931
binding site for Poly-Saccharide residues GNS A 1402 through NPO A 1408
34
AF7
SOFTWARE
ASP A:14 , LYS A:15 , TYR A:17 , ASN A:18 , ALA A:21 , VAL A:37 , GLU A:38 , HIS A:39 , GLU A:44 , GLU A:45 , TRP A:62 , ALA A:63 , ASP A:65 , ARG A:66 , GLU A:111 , GLU A:153 , PRO A:154 , TYR A:155 , TRP A:230 , TRP A:340 , TYR A:341 , ARG A:344 , LYS A:1131 , LYS A:1132 , ARG A:1148 , TRP A:1153 , LEU A:1157 , GNS A:1402 , EDO A:1413 , CL A:1423 , NA A:1426 , NA A:1428 , HOH A:1506 , HOH A:1525 , HOH A:1530 , HOH A:1553 , HOH A:1570 , HOH A:1691 , HOH A:1699 , HOH A:1705 , HOH A:1720 , HOH A:1734 , HOH A:1774 , HOH A:1839 , HOH A:1842 , HOH A:1850 , HOH A:1923 , HOH A:1931
binding site for Poly-Saccharide residues GLC A 1409 through GLC A 1412
35
AF8
SOFTWARE
ASP A:14 , LYS A:15 , TYR A:17 , ASN A:18 , ALA A:21 , VAL A:37 , GLU A:38 , HIS A:39 , GLU A:44 , GLU A:45 , TRP A:62 , ALA A:63 , ASP A:65 , ARG A:66 , GLU A:111 , GLU A:153 , PRO A:154 , TYR A:155 , TRP A:230 , TRP A:340 , TYR A:341 , ARG A:344 , LYS A:1131 , LYS A:1132 , ARG A:1148 , TRP A:1153 , LEU A:1157 , HIS A:1158 , HIS A:1203 , ALA A:1208 , THR A:1209 , TRP A:1210 , GLC A:1409 , EDO A:1413 , CL A:1423 , NA A:1426 , NA A:1428 , TLA A:1430 , HOH A:1525 , HOH A:1530 , HOH A:1553 , HOH A:1570 , HOH A:1649 , HOH A:1691 , HOH A:1699 , HOH A:1702 , HOH A:1705 , HOH A:1714 , HOH A:1720 , HOH A:1734 , HOH A:1774 , HOH A:1839 , HOH A:1842 , HOH A:1850 , HOH A:1896 , HOH A:1923 , HOH A:1927 , HOH A:1931 , ASP B:14 , LYS B:15 , GLU B:44 , TRP B:62 , ALA B:63 , ASP B:65 , ARG B:66 , PHE B:92 , GLU B:111 , GLU B:153 , PRO B:154 , TYR B:155 , TRP B:230 , MET B:321 , TRP B:340 , TYR B:341 , ARG B:344 , LYS B:1131 , LYS B:1132 , ARG B:1148 , GLY B:1152 , TRP B:1153 , LEU B:1157 , HIS B:1158 , HIS B:1203 , ALA B:1208 , THR B:1209 , TRP B:1210 , GLC B:1409 , EDO B:1417 , TLA B:1422 , HOH B:1510 , HOH B:1521 , HOH B:1544 , HOH B:1573 , HOH B:1577 , HOH B:1584 , HOH B:1596 , HOH B:1601 , HOH B:1652 , HOH B:1653 , HOH B:1678 , HOH B:1697 , HOH B:1728 , HOH B:1777 , HOH B:1786 , HOH B:1800 , HOH B:1856 , HOH B:1886 , HOH B:1891
binding site for Poly-Saccharide residues GNS B 1402 through NPO B 1408
36
AF9
SOFTWARE
ASP B:14 , LYS B:15 , LYS B:42 , GLU B:44 , GLU B:45 , TRP B:62 , ALA B:63 , ASP B:65 , ARG B:66 , PHE B:92 , GLU B:111 , GLU B:153 , PRO B:154 , TYR B:155 , TRP B:230 , MET B:321 , TRP B:340 , TYR B:341 , ARG B:344 , LYS B:1131 , LYS B:1132 , ARG B:1148 , GLY B:1152 , TRP B:1153 , LEU B:1157 , GNS B:1402 , EDO B:1417 , HOH B:1510 , HOH B:1521 , HOH B:1523 , HOH B:1544 , HOH B:1577 , HOH B:1584 , HOH B:1596 , HOH B:1653 , HOH B:1678 , HOH B:1697 , HOH B:1728 , HOH B:1777 , HOH B:1800 , HOH B:1886 , HOH B:1891
binding site for Poly-Saccharide residues GLC B 1409 through GLC B 1412
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (257 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (127 KB)
Header - Biol.Unit 2
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
5T05
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help