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3NKM
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (152 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MOUSE AUTOTAXIN
Authors
:
H. Nishimasu, R. Ishitani, E. Mihara, J. Takagi, J. Aoki, O. Nureki
Date
:
20 Jun 10 (Deposition) - 19 Jan 11 (Release) - 19 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Lysophospholipase D, Autotaxin, Enpp2, Lysophosphatidic Acid, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Nishimasu, S. Okudaira, K. Hama, E. Mihara, N. Dohmae, A. Inoue, R. Ishitani, J. Takagi, J. Aoki, O. Nureki
Crystal Structure Of Autotaxin And Insight Into Gpcr Activation By Lipid Mediators
Nat. Struct. Mol. Biol. V. 18 205 2011
[
close entry info
]
Hetero Components
(11, 36)
Info
All Hetero Components
01a: BETA-D-MANNOSE (BMAa)
02a: CALCIUM ION (CAa)
03a: 1,2-ETHANEDIOL (EDOa)
03b: 1,2-ETHANEDIOL (EDOb)
03c: 1,2-ETHANEDIOL (EDOc)
03d: 1,2-ETHANEDIOL (EDOd)
03e: 1,2-ETHANEDIOL (EDOe)
03f: 1,2-ETHANEDIOL (EDOf)
03g: 1,2-ETHANEDIOL (EDOg)
03h: 1,2-ETHANEDIOL (EDOh)
03i: 1,2-ETHANEDIOL (EDOi)
03j: 1,2-ETHANEDIOL (EDOj)
03k: 1,2-ETHANEDIOL (EDOk)
03l: 1,2-ETHANEDIOL (EDOl)
03m: 1,2-ETHANEDIOL (EDOm)
03n: 1,2-ETHANEDIOL (EDOn)
03o: 1,2-ETHANEDIOL (EDOo)
03p: 1,2-ETHANEDIOL (EDOp)
03q: 1,2-ETHANEDIOL (EDOq)
04a: POTASSIUM ION (Ka)
05a: ALPHA-D-MANNOSE (MANa)
05b: ALPHA-D-MANNOSE (MANb)
05c: ALPHA-D-MANNOSE (MANc)
07a: N-ACETYL-D-GLUCOSAMINE (NAGa)
07b: N-ACETYL-D-GLUCOSAMINE (NAGb)
07c: N-ACETYL-D-GLUCOSAMINE (NAGc)
07d: N-ACETYL-D-GLUCOSAMINE (NAGd)
07e: N-ACETYL-D-GLUCOSAMINE (NAGe)
07f: N-ACETYL-D-GLUCOSAMINE (NAGf)
06a: SODIUM ION (NAa)
08a: (2R)-2-HYDROXY-3-(PHOSPHONOOXY)PRO... (NKPa)
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
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
4
K
1
Ligand/Ion
POTASSIUM ION
5
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
6
NA
1
Ligand/Ion
SODIUM ION
7
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
NKP
1
Ligand/Ion
(2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL (9E)-OCTADEC-9-ENOATE
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
(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: 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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:53 , SER A:55 , NAG A:899
BINDING SITE FOR RESIDUE NAG A 898
02
AC2
SOFTWARE
NAG A:898
BINDING SITE FOR RESIDUE NAG A 899
03
AC3
SOFTWARE
HOH A:19 , LEU A:220 , PRO A:522 , ASN A:524 , LEU A:741 , HIS A:827 , HOH A:875 , HOH A:894 , NAG A:901 , HOH A:941 , HOH A:1077 , HOH A:1102 , HOH A:1511
BINDING SITE FOR RESIDUE NAG A 900
04
AC4
SOFTWARE
HOH A:33 , SER A:224 , NAG A:900 , BMA A:902 , MAN A:903 , MAN A:905 , HOH A:1367
BINDING SITE FOR RESIDUE NAG A 901
05
AC5
SOFTWARE
NAG A:901 , MAN A:903
BINDING SITE FOR RESIDUE BMA A 902
06
AC6
SOFTWARE
NAG A:901 , BMA A:902 , MAN A:904 , HOH A:1394
BINDING SITE FOR RESIDUE MAN A 903
07
AC7
SOFTWARE
SER A:224 , GLY A:255 , MAN A:903 , MAN A:905 , EDO A:1025 , HOH A:1099 , HOH A:1390 , HOH A:1471 , HOH A:1548
BINDING SITE FOR RESIDUE MAN A 904
08
AC8
SOFTWARE
HOH A:33 , GLU A:223 , SER A:224 , ASN A:436 , ASN A:437 , NAG A:901 , MAN A:904 , HOH A:917 , HOH A:1373 , HOH A:1419
BINDING SITE FOR RESIDUE MAN A 905
09
AC9
SOFTWARE
LEU A:376 , THR A:377 , ASN A:410 , NAG A:908 , HOH A:1125 , HOH A:1249 , HOH A:1290 , HOH A:1428
BINDING SITE FOR RESIDUE NAG A 907
10
BC1
SOFTWARE
NAG A:907 , HOH A:1371 , HOH A:1428 , HOH A:1474
BINDING SITE FOR RESIDUE NAG A 908
11
BC2
SOFTWARE
ASP A:171 , THR A:209 , ASP A:311 , ASP A:358 , HIS A:359 , SO4 A:1006
BINDING SITE FOR RESIDUE ZN A 1001
12
BC3
SOFTWARE
ASP A:311 , HIS A:315 , HIS A:474 , SO4 A:1006
BINDING SITE FOR RESIDUE ZN A 1002
13
BC4
SOFTWARE
ASP A:735 , ASN A:737 , ASN A:739 , LEU A:741 , ASP A:743 , HOH A:880
BINDING SITE FOR RESIDUE CA A 1003
14
BC5
SOFTWARE
HOH A:2 , ASN A:797 , SER A:800 , SER A:803 , HOH A:980 , HOH A:986
BINDING SITE FOR RESIDUE NA A 1004
15
BC6
SOFTWARE
TYR A:665 , ASP A:668 , MET A:671
BINDING SITE FOR RESIDUE K A 1005
16
BC7
SOFTWARE
ASP A:171 , THR A:209 , ASN A:230 , ASP A:311 , HIS A:315 , HIS A:359 , HIS A:474 , LYS A:579 , ZN A:1001 , ZN A:1002
BINDING SITE FOR RESIDUE SO4 A 1006
17
BC8
SOFTWARE
TYR A:214 , PRO A:258 , HOH A:1048
BINDING SITE FOR RESIDUE NKP A 1007
18
BC9
SOFTWARE
MET A:232 , ARG A:393 , HOH A:1527
BINDING SITE FOR RESIDUE SCN A 1008
19
CC1
SOFTWARE
LYS A:208 , GLY A:229 , ASN A:230 , SER A:231 , VAL A:385
BINDING SITE FOR RESIDUE SCN A 1009
20
CC2
SOFTWARE
PRO A:544 , ARG A:823 , GLU A:826 , ASP A:832 , TYR A:841 , LEU A:845 , LYS A:848
BINDING SITE FOR RESIDUE EDO A 1010
21
CC3
SOFTWARE
HOH A:25 , ILE A:151 , CYS A:194 , GLY A:195 , GLY A:491 , LYS A:495 , TYR A:496
BINDING SITE FOR RESIDUE EDO A 1011
22
CC4
SOFTWARE
PHE A:675 , TYR A:680 , TRP A:708 , GLN A:712 , HOH A:939
BINDING SITE FOR RESIDUE EDO A 1012
23
CC5
SOFTWARE
HOH A:5 , TYR A:601 , PHE A:621 , PHE A:734 , ARG A:742 , ASP A:743 , HOH A:921
BINDING SITE FOR RESIDUE EDO A 1013
24
CC6
SOFTWARE
ARG A:192 , HIS A:197 , LYS A:499
BINDING SITE FOR RESIDUE EDO A 1014
25
CC7
SOFTWARE
TYR A:701 , TYR A:736 , GLN A:750 , VAL A:759 , PRO A:760 , THR A:761 , HIS A:793
BINDING SITE FOR RESIDUE EDO A 1015
26
CC8
SOFTWARE
LEU A:446 , VAL A:447 , GLU A:448 , HOH A:872 , HOH A:1171 , HOH A:1289
BINDING SITE FOR RESIDUE EDO A 1016
27
CC9
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 1017
28
DC1
SOFTWARE
PRO A:520 , ALA A:521 , PRO A:522 , ASN A:523 , HOH A:949 , HOH A:1033 , HOH A:1361 , HOH A:1403
BINDING SITE FOR RESIDUE EDO A 1018
29
DC2
SOFTWARE
ILE A:620 , PHE A:621 , GLU A:745 , TYR A:751 , SER A:756 , HOH A:1328
BINDING SITE FOR RESIDUE EDO A 1019
30
DC3
SOFTWARE
LEU A:771 , SER A:785 , VAL A:786 , TYR A:850 , HOH A:1284
BINDING SITE FOR RESIDUE EDO A 1020
31
DC4
SOFTWARE
LEU A:600 , ARG A:742 , GLY A:830
BINDING SITE FOR RESIDUE EDO A 1021
32
DC5
SOFTWARE
GLY A:267 , ASN A:374 , LYS A:415 , HOH A:1426
BINDING SITE FOR RESIDUE EDO A 1022
33
DC6
SOFTWARE
PHE A:704 , PRO A:792 , ARG A:794 , ASP A:796 , ASN A:797 , HOH A:869
BINDING SITE FOR RESIDUE EDO A 1023
34
DC7
SOFTWARE
HOH A:17 , GLU A:799 , GLU A:813 , HOH A:872 , HOH A:972 , HOH A:1525
BINDING SITE FOR RESIDUE EDO A 1024
35
DC8
SOFTWARE
GLY A:226 , ASN A:437 , ARG A:439 , MAN A:904 , HOH A:917 , HOH A:1099
BINDING SITE FOR RESIDUE EDO A 1025
36
DC9
SOFTWARE
ASP A:363 , THR A:365 , ARG A:368 , ARG A:450 , GLN A:471 , HOH A:954 , HOH A:1569
BINDING SITE FOR RESIDUE EDO A 1026
[
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
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
(3, 5)
Info
all PFAM domains
1a: PFAM_Phosphodiest_3nkmA01 (A:279-477)
1b: PFAM_Phosphodiest_3nkmA02 (A:279-477)
2a: PFAM_Endonuclease_NS_3nkmA03 (A:609-840)
3a: PFAM_Somatomedin_B_3nkmA04 (A:99-142)
3b: PFAM_Somatomedin_B_3nkmA05 (A:99-142)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Alk_phosphatase
(47)
Family
:
Phosphodiest
(9)
Mus musculus (Mouse)
(6)
1a
Phosphodiest-3nkmA01
A:279-477
1b
Phosphodiest-3nkmA02
A:279-477
Clan
:
His-Me_finger
(38)
Family
:
Endonuclease_NS
(14)
Mus musculus (Mouse)
(6)
2a
Endonuclease_NS-3nkmA03
A:609-840
Clan
:
no clan defined [family: Somatomedin_B]
(13)
Family
:
Somatomedin_B
(13)
Mus musculus (Mouse)
(6)
3a
Somatomedin_B-3nkmA04
A:99-142
3b
Somatomedin_B-3nkmA05
A:99-142
[
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]
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Asymmetric Unit 1
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