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4DHL
Biol. Unit 1
Info
Asym.Unit (337 KB)
Biol.Unit 1 (167 KB)
Biol.Unit 2 (166 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RED KIDNEY BEAN PURPLE ACID PHOSPHATASE IN COMPLEX WITH MAYBRIDGE FRAGMENT MO07123
Authors
:
D. Feder, D. J. Clayton, W. M. Hussein, G. Schenk, R. Mcgeary, L. W. Gudda
Date
:
29 Jan 12 (Deposition) - 12 Dec 12 (Release) - 02 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Catalytic C Domain, N Terminal Domain, Phosphatase, Acid Phosphatase, Phosphoric Monoester Hydrolases, Hydrolase, Mo07123, Maybridge, Fragment, Lysosome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Feder, W. M. Hussein, D. J. Clayton, M. W. Kan, G. Schenk, R. P. Mcgeary, L. W. Guddat
Identification Of Purple Acid Phosphatase Inhibitors By Fragment-Based Screening: Promising New Leads For Osteoporosis Therapeutics.
Chem. Biol. Drug Des. V. 80 665 2012
[
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Hetero Components
(6, 30)
Info
All Hetero Components
1a: 2-(4-METHYLPHENYL)-1,3-THIAZOLE-4-... (0K7a)
1b: 2-(4-METHYLPHENYL)-1,3-THIAZOLE-4-... (0K7b)
1c: 2-(4-METHYLPHENYL)-1,3-THIAZOLE-4-... (0K7c)
1d: 2-(4-METHYLPHENYL)-1,3-THIAZOLE-4-... (0K7d)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
4a: ALPHA-L-FUCOSE (FUCa)
4b: ALPHA-L-FUCOSE (FUCb)
4c: ALPHA-L-FUCOSE (FUCc)
4d: ALPHA-L-FUCOSE (FUCd)
4e: ALPHA-L-FUCOSE (FUCe)
4f: ALPHA-L-FUCOSE (FUCf)
4g: ALPHA-L-FUCOSE (FUCg)
4h: ALPHA-L-FUCOSE (FUCh)
4i: ALPHA-L-FUCOSE (FUCi)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6m: N-ACETYL-D-GLUCOSAMINE (NAGm)
6n: N-ACETYL-D-GLUCOSAMINE (NAGn)
6o: N-ACETYL-D-GLUCOSAMINE (NAGo)
6p: N-ACETYL-D-GLUCOSAMINE (NAGp)
6q: N-ACETYL-D-GLUCOSAMINE (NAGq)
6r: N-ACETYL-D-GLUCOSAMINE (NAGr)
6s: N-ACETYL-D-GLUCOSAMINE (NAGs)
6t: N-ACETYL-D-GLUCOSAMINE (NAGt)
6u: N-ACETYL-D-GLUCOSAMINE (NAGu)
6v: N-ACETYL-D-GLUCOSAMINE (NAGv)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
7e: SULFATE ION (SO4e)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
8c: ZINC ION (ZNc)
8d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0K7
2
Ligand/Ion
2-(4-METHYLPHENYL)-1,3-THIAZOLE-4-CARBOXYLIC ACID
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
FE
-1
Ligand/Ion
FE (III) ION
4
FUC
5
Ligand/Ion
ALPHA-L-FUCOSE
5
GOL
2
Ligand/Ion
GLYCEROL
6
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
3
Ligand/Ion
SULFATE ION
8
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(37, 37)
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: CC6 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC3 (SOFTWARE)
21: DC4 (SOFTWARE)
22: DC5 (SOFTWARE)
23: DC6 (SOFTWARE)
24: DC7 (SOFTWARE)
25: DC8 (SOFTWARE)
26: DC9 (SOFTWARE)
27: EC1 (SOFTWARE)
28: EC2 (SOFTWARE)
29: EC3 (SOFTWARE)
30: EC4 (SOFTWARE)
31: EC5 (SOFTWARE)
32: EC6 (SOFTWARE)
33: EC7 (SOFTWARE)
34: EC8 (SOFTWARE)
35: EC9 (SOFTWARE)
36: FC7 (SOFTWARE)
37: FC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:135 , ASP A:164 , ASN A:201 , HIS A:286 , HIS A:323 , FE A:502 , 0K7 A:503
BINDING SITE FOR RESIDUE ZN A 501
02
AC2
SOFTWARE
ASP A:135 , ASP A:164 , TYR A:167 , HIS A:325 , ZN A:501 , 0K7 A:503
BINDING SITE FOR RESIDUE FE A 502
03
AC3
SOFTWARE
ASP A:164 , TYR A:167 , ASN A:201 , HIS A:202 , HIS A:295 , HIS A:296 , HIS A:323 , HIS A:325 , TYR A:365 , ZN A:501 , FE A:502 , HOH A:937 , ARG D:258
BINDING SITE FOR RESIDUE 0K7 A 503
04
AC4
SOFTWARE
THR A:305 , ASN A:335 , ILE A:336 , ALA A:337 , TYR A:338 , HOH A:640 , HOH A:976 , HOH D:602
BINDING SITE FOR RESIDUE GOL A 504
05
AC5
SOFTWARE
SER A:61 , ASN A:64 , ARG A:68 , LYS A:96 , TYR A:101 , HOH A:666
BINDING SITE FOR RESIDUE SO4 A 505
06
AC6
SOFTWARE
LYS A:274 , ARG A:275 , SER A:276 , HOH A:712 , GLN D:374
BINDING SITE FOR RESIDUE SO4 A 506
07
AC7
SOFTWARE
PRO A:153 , LYS A:154 , HOH A:690 , HOH A:922 , HOH A:987 , PRO B:427
BINDING SITE FOR RESIDUE EDO A 507
08
AC8
SOFTWARE
ASP A:16 , PHE A:140 , ASN A:143 , SER A:147
BINDING SITE FOR RESIDUE NAG A 508
09
AC9
SOFTWARE
ASN A:81 , ASN A:173 , NAG A:510 , FUC A:511 , HOH A:932 , TYR C:24 , ASP C:50
BINDING SITE FOR RESIDUE NAG A 509
10
BC1
SOFTWARE
NAG A:509
BINDING SITE FOR RESIDUE NAG A 510
11
BC2
SOFTWARE
NAG A:509
BINDING SITE FOR RESIDUE FUC A 511
12
BC3
SOFTWARE
TYR A:24 , ARG A:108 , ASN A:109 , FUC A:513 , NAG A:514 , HOH A:807
BINDING SITE FOR RESIDUE NAG A 512
13
BC4
SOFTWARE
NAG A:512 , NAG A:514
BINDING SITE FOR RESIDUE FUC A 513
14
BC5
SOFTWARE
NAG A:512 , FUC A:513
BINDING SITE FOR RESIDUE NAG A 514
15
BC6
SOFTWARE
ASN A:396 , HIS A:399 , NAG A:516 , FUC A:517 , HOH A:857 , HOH A:991
BINDING SITE FOR RESIDUE NAG A 515
16
BC7
SOFTWARE
TRP A:419 , NAG A:515 , FUC A:517 , HOH A:892 , HOH A:897
BINDING SITE FOR RESIDUE NAG A 516
17
BC8
SOFTWARE
NAG A:515 , NAG A:516
BINDING SITE FOR RESIDUE FUC A 517
18
CC6
SOFTWARE
ASN B:81 , ASN B:173 , HOH B:764 , TYR D:24 , ASP D:50
BINDING SITE FOR RESIDUE NAG B 507
19
DC2
SOFTWARE
ASP D:135 , ASP D:164 , ASN D:201 , HIS D:286 , HIS D:323 , FE D:502 , 0K7 D:503
BINDING SITE FOR RESIDUE ZN D 501
20
DC3
SOFTWARE
ASP D:135 , ASP D:164 , TYR D:167 , HIS D:325 , ZN D:501 , 0K7 D:503
BINDING SITE FOR RESIDUE FE D 502
21
DC4
SOFTWARE
ASP D:164 , ASN D:201 , HIS D:202 , HIS D:296 , HIS D:323 , HIS D:325 , TYR D:365 , ZN D:501 , FE D:502 , HOH D:977
BINDING SITE FOR RESIDUE 0K7 D 503
22
DC5
SOFTWARE
LYS C:313 , TYR D:314 , HOH D:975 , HOH D:976
BINDING SITE FOR RESIDUE GOL D 504
23
DC6
SOFTWARE
LYS D:274 , ARG D:275 , SER D:276
BINDING SITE FOR RESIDUE SO4 D 505
24
DC7
SOFTWARE
HOH A:999 , THR D:305 , ASN D:335 , ILE D:336 , TYR D:338 , EDO D:508
BINDING SITE FOR RESIDUE EDO D 506
25
DC8
SOFTWARE
ASP D:169 , ASN D:201 , HIS D:202
BINDING SITE FOR RESIDUE EDO D 507
26
DC9
SOFTWARE
TYR A:338 , HOH A:999 , ARG D:304 , ASN D:335 , TYR D:338 , EDO D:506
BINDING SITE FOR RESIDUE EDO D 508
27
EC1
SOFTWARE
ASP D:16 , PHE D:140 , ASN D:143 , SER D:147 , HOH D:695 , HOH D:745
BINDING SITE FOR RESIDUE NAG D 509
28
EC2
SOFTWARE
TYR D:171 , ASN D:173 , HIS D:174 , GLU D:209
BINDING SITE FOR RESIDUE EDO D 510
29
EC3
SOFTWARE
SER D:220 , TYR D:221 , HIS D:224 , HOH D:771 , HOH D:835
BINDING SITE FOR RESIDUE EDO D 511
30
EC4
SOFTWARE
GLN B:374 , ASN D:396 , ARG D:397 , THR D:398 , HIS D:399 , NAG D:513 , FUC D:514
BINDING SITE FOR RESIDUE NAG D 512
31
EC5
SOFTWARE
TRP D:419 , NAG D:512 , FUC D:514 , HOH D:891 , HOH D:951
BINDING SITE FOR RESIDUE NAG D 513
32
EC6
SOFTWARE
NAG D:512 , NAG D:513
BINDING SITE FOR RESIDUE FUC D 514
33
EC7
SOFTWARE
TYR D:24 , ARG D:108 , ASN D:109 , FUC D:516
BINDING SITE FOR RESIDUE NAG D 515
34
EC8
SOFTWARE
FUC C:507 , NAG D:515
BINDING SITE FOR RESIDUE FUC D 516
35
EC9
SOFTWARE
TYR B:24 , ASP B:50 , ASN D:81 , ASN D:173
BINDING SITE FOR RESIDUE NAG D 517
36
FC7
SOFTWARE
NAG C:506 , FUC D:516
BINDING SITE FOR RESIDUE FUC C 507
37
FC8
SOFTWARE
TYR A:24 , ASP A:50 , ASN C:81
BINDING SITE FOR RESIDUE NAG C 508
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d4dhla1 (A:8-120)
1b: SCOP_d4dhlb1 (B:8-120)
1c: SCOP_d4dhlc1 (C:7-120)
1d: SCOP_d4dhld1 (D:8-120)
2a: SCOP_d4dhla2 (A:121-431)
2b: SCOP_d4dhlb2 (B:121-432)
2c: SCOP_d4dhlc2 (C:121-430)
2d: SCOP_d4dhld2 (D:121-430)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Purple acid phosphatase, N-terminal domain
(9)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
French bean (Phaseolus vulgaris) [TaxId: 3885]
(5)
1a
d4dhla1
A:8-120
1b
d4dhlb1
B:8-120
1c
d4dhlc1
C:7-120
1d
d4dhld1
D:8-120
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-dependent phosphatases
(115)
Superfamily
:
Metallo-dependent phosphatases
(115)
Family
:
Purple acid phosphatase-like
(14)
Protein domain
:
automated matches
(7)
French bean (Phaseolus vulgaris) [TaxId: 3885]
(5)
2a
d4dhla2
A:121-431
2b
d4dhlb2
B:121-432
2c
d4dhlc2
C:121-430
2d
d4dhld2
D:121-430
[
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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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Sorry, no Info available
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Asym.Unit (337 KB)
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