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Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (146 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AUTOTAXIN IN COMPLEX WITH COMPOUND 10
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
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
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: (5Z)-5-(3,4-DICHLOROBENZYLIDENE)-2... (DWVa)
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)
04q: 1,2-ETHANEDIOL (EDOq)
04r: 1,2-ETHANEDIOL (EDOr)
05a: POTASSIUM ION (Ka)
06a: ALPHA-D-MANNOSE (MANa)
06b: ALPHA-D-MANNOSE (MANb)
06c: ALPHA-D-MANNOSE (MANc)
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)
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
DWV
1
Ligand/Ion
(5Z)-5-(3,4-DICHLOROBENZYLIDENE)-2-(4-METHYLPIPERAZIN-1-YL)-1,3-THIAZOL-4(5H)-ONE
4
EDO
18
Ligand/Ion
1,2-ETHANEDIOL
5
K
1
Ligand/Ion
POTASSIUM ION
6
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
7
NA
1
Ligand/Ion
SODIUM ION
8
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
9
SCN
2
Ligand/Ion
THIOCYANATE ION
10
SO4
1
Ligand/Ion
SULFATE ION
11
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(30, 30)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:171 , THR A:209 , ASP A:358 , HIS A:359 , SO4 A:936
BINDING SITE FOR RESIDUE ZN A 911
02
AC2
SOFTWARE
ASP A:311 , HIS A:315 , HIS A:474 , SO4 A:936
BINDING SITE FOR RESIDUE ZN A 912
03
AC3
SOFTWARE
ASP A:735 , ASN A:737 , ASN A:739 , LEU A:741 , ASP A:743 , HOH A:1045
BINDING SITE FOR RESIDUE CA A 913
04
AC4
SOFTWARE
ASN A:797 , SER A:800 , SER A:803 , HOH A:1417 , HOH A:1418 , HOH A:1419
BINDING SITE FOR RESIDUE NA A 914
05
AC5
SOFTWARE
TYR A:665 , ASP A:668 , MET A:671 , HOH A:1420
BINDING SITE FOR RESIDUE K A 915
06
AC6
SOFTWARE
MET A:232 , ARG A:393
BINDING SITE FOR RESIDUE SCN A 916
07
AC7
SOFTWARE
GLY A:229 , ASN A:230 , ARG A:391 , HOH A:1237
BINDING SITE FOR RESIDUE SCN A 917
08
AC8
SOFTWARE
ARG A:823 , GLU A:826 , ASP A:832 , TYR A:841 , LYS A:848
BINDING SITE FOR RESIDUE EDO A 918
09
AC9
SOFTWARE
ILE A:151 , CYS A:194 , TYR A:490 , GLY A:491 , PHE A:494 , LYS A:495 , TYR A:496 , HOH A:1022
BINDING SITE FOR RESIDUE EDO A 919
10
BC1
SOFTWARE
PHE A:675 , PRO A:679 , TYR A:680 , TRP A:708 , GLN A:712 , HOH A:1088
BINDING SITE FOR RESIDUE EDO A 920
11
BC2
SOFTWARE
TYR A:601 , PHE A:621 , PHE A:734 , ARG A:742 , ASP A:743 , HOH A:1004 , HOH A:1071
BINDING SITE FOR RESIDUE EDO A 921
12
BC3
SOFTWARE
HIS A:197 , LYS A:499
BINDING SITE FOR RESIDUE EDO A 922
13
BC4
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 923
14
BC5
SOFTWARE
LEU A:446 , GLU A:448 , HOH A:1037 , HOH A:1282
BINDING SITE FOR RESIDUE EDO A 924
15
BC6
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 925
16
BC7
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 926
17
BC8
SOFTWARE
SER A:785 , VAL A:786 , TYR A:850 , EDO A:933
BINDING SITE FOR RESIDUE EDO A 927
18
BC9
SOFTWARE
LEU A:600 , ARG A:742 , GLY A:830 , HOH A:1014
BINDING SITE FOR RESIDUE EDO A 928
19
CC1
SOFTWARE
GLY A:267 , ASN A:374 , LYS A:414 , LYS A:415 , HOH A:1310
BINDING SITE FOR RESIDUE EDO A 929
20
CC2
SOFTWARE
PHE A:704 , PRO A:792 , ARG A:794 , ASP A:796 , ASN A:797 , HOH A:1034
BINDING SITE FOR RESIDUE EDO A 930
21
CC3
SOFTWARE
GLU A:799 , SER A:800 , GLU A:813 , HOH A:1015 , HOH A:1037 , HOH A:1116 , HOH A:1334
BINDING SITE FOR RESIDUE EDO A 931
22
CC4
SOFTWARE
GLY A:226 , ASN A:437 , ARG A:438 , ARG A:439 , MAN A:907 , MAN A:908 , HOH A:1069 , HOH A:1197
BINDING SITE FOR RESIDUE EDO A 932
23
CC5
SOFTWARE
ARG A:723 , SER A:785 , VAL A:786 , HIS A:852 , EDO A:927
BINDING SITE FOR RESIDUE EDO A 933
24
CC6
SOFTWARE
HIS A:427 , THR A:761 , HIS A:762 , HIS A:793 , HOH A:1172
BINDING SITE FOR RESIDUE EDO A 934
25
CC7
SOFTWARE
LYS A:495 , TYR A:496 , ARG A:535
BINDING SITE FOR RESIDUE EDO A 935
26
CC8
SOFTWARE
THR A:209 , ASN A:230 , ASP A:311 , HIS A:315 , HIS A:474 , LEU A:577 , LYS A:579 , ZN A:911 , ZN A:912
BINDING SITE FOR RESIDUE SO4 A 936
27
CC9
SOFTWARE
SER A:169 , LEU A:213 , LEU A:243 , PHE A:273 , PHE A:274 , TRP A:275 , TYR A:306 , LYS A:579
BINDING SITE FOR RESIDUE DWV A 937
28
DC1
SOFTWARE
ASN A:53 , SER A:55
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 53 RESIDUES 901 TO 902
29
DC2
SOFTWARE
LEU A:376 , THR A:377 , ASN A:410 , HOH A:1214 , HOH A:1320 , HOH A:1405
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 410 RESIDUES 909 TO 910
30
DC3
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:932 , HOH A:1016 , HOH A:1030 , HOH A:1040 , HOH A:1058 , HOH A:1069 , HOH A:1090 , HOH A:1165 , HOH A:1179 , HOH A:1197 , HOH A:1297 , HOH A:1302 , HOH A:1327 , HOH A:1340
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 524 RESIDUES 903 TO 908
[
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
(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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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Asymmetric Unit 1
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