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Asym. Unit
Info
Asym.Unit (150 KB)
Biol.Unit 1 (142 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AUTOTAXIN IN COMPLEX WITH 2BOA
Authors
:
H. Nishimasu, R. Ishitani, O. Nureki
Date
:
09 May 13 (Deposition) - 31 Jul 13 (Release) - 16 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kawaguchi, T. Okabe, S. Okudaira, H. Nishimasu, R. Ishitani, H. Kojima, O. Nureki, J. Aoki, T. Nagano
Screening And X-Ray Crystal Structure-Based Optimization Of Autotaxin (Enpp2) Inhibitors, Using A Newly Developed Fluorescence Probe
Acs Chem. Biol. V. 8 1713 2013
[
close entry info
]
Hetero Components
(11, 37)
Info
All Hetero Components
01a: BETA-D-MANNOSE (BMAa)
02a: CALCIUM ION (CAa)
03a: [2-({4-[(5Z)-5-(3,4-DICHLOROBENZYL... (DWWa)
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)
04p: 1,2-ETHANEDIOL (EDOp)
05a: POTASSIUM ION (Ka)
06a: ALPHA-D-MANNOSE (MANa)
06b: ALPHA-D-MANNOSE (MANb)
06c: ALPHA-D-MANNOSE (MANc)
06d: ALPHA-D-MANNOSE (MANd)
08a: N-ACETYL-D-GLUCOSAMINE (NAGa)
08b: N-ACETYL-D-GLUCOSAMINE (NAGb)
08c: N-ACETYL-D-GLUCOSAMINE (NAGc)
08d: N-ACETYL-D-GLUCOSAMINE (NAGd)
08e: N-ACETYL-D-GLUCOSAMINE (NAGe)
08f: N-ACETYL-D-GLUCOSAMINE (NAGf)
07a: SODIUM ION (NAa)
09a: THIOCYANATE ION (SCNa)
09b: THIOCYANATE ION (SCNb)
09c: THIOCYANATE ION (SCNc)
10a: SULFATE ION (SO4a)
11a: ZINC ION (ZNa)
11b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
1
Ligand/Ion
CALCIUM ION
3
DWW
1
Ligand/Ion
[2-({4-[(5Z)-5-(3,4-DICHLOROBENZYLIDENE)-4-OXO-4,5-DIHYDRO-1,3-THIAZOL-2-YL]PIPERAZIN-1-YL}METHYL)PHENYL]BORONIC ACID
4
EDO
16
Ligand/Ion
1,2-ETHANEDIOL
5
K
1
Ligand/Ion
POTASSIUM ION
6
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
7
NA
1
Ligand/Ion
SODIUM ION
8
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
9
SCN
3
Ligand/Ion
THIOCYANATE ION
10
SO4
1
Ligand/Ion
SULFATE ION
11
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:171 , THR A:209 , ASP A:358 , HIS A:359
BINDING SITE FOR RESIDUE ZN A 912
02
AC2
SOFTWARE
ASP A:311 , HIS A:315 , HIS A:474 , SO4 A:917
BINDING SITE FOR RESIDUE ZN A 913
03
AC3
SOFTWARE
ASP A:735 , ASN A:737 , ASN A:739 , LEU A:741 , ASP A:743 , HOH A:1327
BINDING SITE FOR RESIDUE CA A 914
04
AC4
SOFTWARE
ASN A:797 , SER A:800 , SER A:803 , HOH A:1369 , HOH A:1370 , HOH A:1371
BINDING SITE FOR RESIDUE NA A 915
05
AC5
SOFTWARE
TYR A:665 , ASP A:668 , MET A:671 , HOH A:1372 , HOH A:1373
BINDING SITE FOR RESIDUE K A 916
06
AC6
SOFTWARE
THR A:209 , ASN A:230 , LEU A:243 , ASP A:311 , HIS A:474 , ZN A:913 , HOH A:1265
BINDING SITE FOR RESIDUE SO4 A 917
07
AC7
SOFTWARE
THR A:761
BINDING SITE FOR RESIDUE SCN A 918
08
AC8
SOFTWARE
ARG A:393
BINDING SITE FOR RESIDUE SCN A 919
09
AC9
SOFTWARE
GLY A:229 , ARG A:391
BINDING SITE FOR RESIDUE SCN A 920
10
BC1
SOFTWARE
ARG A:823 , GLU A:826 , ASP A:832 , TYR A:841 , LYS A:848
BINDING SITE FOR RESIDUE EDO A 921
11
BC2
SOFTWARE
ILE A:151 , CYS A:194 , GLY A:491 , LYS A:495 , TYR A:496 , ARG A:535 , HOH A:1020
BINDING SITE FOR RESIDUE EDO A 922
12
BC3
SOFTWARE
GLY A:674 , PHE A:675 , PRO A:678 , PRO A:679 , TYR A:680 , TRP A:708 , GLN A:712
BINDING SITE FOR RESIDUE EDO A 923
13
BC4
SOFTWARE
TYR A:601 , PHE A:621 , PHE A:734 , ARG A:742 , ASP A:743 , HOH A:1004 , HOH A:1068
BINDING SITE FOR RESIDUE EDO A 924
14
BC5
SOFTWARE
ARG A:192 , HIS A:197 , LYS A:499
BINDING SITE FOR RESIDUE EDO A 925
15
BC6
SOFTWARE
TYR A:701 , TYR A:736 , GLN A:750 , VAL A:759 , PRO A:760 , HIS A:793
BINDING SITE FOR RESIDUE EDO A 926
16
BC7
SOFTWARE
LEU A:446 , VAL A:447 , GLU A:448 , HOH A:1035 , HOH A:1231 , HOH A:1296
BINDING SITE FOR RESIDUE EDO A 927
17
BC8
SOFTWARE
ILE A:392 , ARG A:393 , TYR A:402 , GLU A:441 , ASP A:442 , LEU A:443
BINDING SITE FOR RESIDUE EDO A 928
18
BC9
SOFTWARE
PRO A:520 , ALA A:521 , ASN A:523 , HOH A:1135 , HOH A:1245 , HOH A:1350
BINDING SITE FOR RESIDUE EDO A 929
19
CC1
SOFTWARE
ILE A:620 , PHE A:621 , GLU A:745 , TYR A:751 , SER A:756 , PRO A:758
BINDING SITE FOR RESIDUE EDO A 930
20
CC2
SOFTWARE
SER A:785 , VAL A:786 , TYR A:850 , HOH A:1233
BINDING SITE FOR RESIDUE EDO A 931
21
CC3
SOFTWARE
ARG A:742 , GLY A:830
BINDING SITE FOR RESIDUE EDO A 932
22
CC4
SOFTWARE
ASN A:374 , LYS A:415
BINDING SITE FOR RESIDUE EDO A 933
23
CC5
SOFTWARE
PHE A:704 , PRO A:792 , ARG A:794 , ASP A:796 , ASN A:797 , HOH A:1032
BINDING SITE FOR RESIDUE EDO A 934
24
CC6
SOFTWARE
GLU A:799 , LEU A:814 , HOH A:1035 , HOH A:1109 , HOH A:1264
BINDING SITE FOR RESIDUE EDO A 935
25
CC7
SOFTWARE
GLY A:226 , ASN A:437 , ARG A:438 , ARG A:439 , MAN A:907 , HOH A:1173
BINDING SITE FOR RESIDUE EDO A 936
26
CC8
SOFTWARE
SER A:169 , PHE A:210 , LEU A:213 , LEU A:243 , PHE A:273 , PHE A:274 , TRP A:275 , TYR A:306
BINDING SITE FOR RESIDUE DWW A 937
27
CC9
SOFTWARE
ASN A:53
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 53 RESIDUES 901 TO 902
28
DC1
SOFTWARE
LEU A:376 , THR A:377 , ASN A:410 , HOH A:1187 , HOH A:1339
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 410 RESIDUES 910 TO 911
29
DC2
SOFTWARE
LEU A:220 , GLU A:223 , SER A:224 , GLY A:255 , ASN A:436 , ASN A:437 , PRO A:522 , ASN A:524 , LEU A:741 , HIS A:827 , EDO A:936 , HOH A:1015 , HOH A:1028 , HOH A:1038 , HOH A:1056 , HOH A:1065 , HOH A:1088 , HOH A:1149 , HOH A:1160 , HOH A:1173 , HOH A:1260 , HOH A:1268 , HOH A:1298
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 524 RESIDUES 903 TO 909
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: SMB_2 (A:54-97|A:98-142)
2: SMB_1 (A:73-93|A:117-137)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SMB_2
PS50958
Somatomedin B (SMB) domain profile.
ENPP2_MOUSE
54-97
98-142
2
A:54-97
A:98-142
2
SMB_1
PS00524
Somatomedin B domain (SMB) signature.
ENPP2_MOUSE
73-93
117-137
2
A:73-93
A:117-137
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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Chain A
Asymmetric Unit 1
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