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Getting 'Exon' information from database.
3SL6
Asym. Unit
Info
Asym.Unit (232 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (59 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 WITH COMPOUND 12C
Authors
:
S. F. Feil
Date
:
24 Jun 11 (Deposition) - 26 Oct 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.44
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Catalytic Domain, Camp Hydrolysis, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Nankervis, S. C. Feil, N. C. Hancock, Z. Zheng, H. L. Ng, C. J. Morton, J. K. Holien, P. W. Ho, M. M. Frazzetto, I. G. Jennings, D. T. Manallack, T. J. Martin, P. E. Thompson, M. W. Parker
Thiophene Inhibitors Of Pde4: Crystal Structures Show A Second Binding Mode At The Catalytic Domain Of Pde4D2.
Bioorg. Med. Chem. Lett. V. 21 7089 2011
[
close entry info
]
Hetero Components
(5, 44)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
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)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8a)
4b: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8b)
4c: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8c)
4d: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8d)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
30
Ligand/Ion
1,2-ETHANEDIOL
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
JN8
4
Ligand/Ion
CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[(THIOPHEN-2-YLACETYL)AMINO]-4,5,6,7-TETRAHYDROTHIENO[2,3-C]PYRIDINE-3-CARBOXYLATE
5
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(44, 44)
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)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ZN A:11 , HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:452
BINDING SITE FOR RESIDUE ZN A 10
02
AC2
SOFTWARE
ZN A:10 , ASP A:201 , HOH A:448 , HOH A:449 , HOH A:450
BINDING SITE FOR RESIDUE ZN A 11
03
AC3
SOFTWARE
GLU A:218 , LYS C:239
BINDING SITE FOR RESIDUE EDO A 2
04
AC4
SOFTWARE
THR A:134 , LYS A:136 , EDO D:7 , PRO D:179 , ASP D:391
BINDING SITE FOR RESIDUE EDO A 4
05
AC5
SOFTWARE
LEU A:175 , THR A:178 , TRP A:384 , ASP A:391
BINDING SITE FOR RESIDUE EDO A 5
06
AC6
SOFTWARE
ASN A:115 , ARG A:116 , GLU A:150 , ASP A:151 , TYR A:153 , ASN A:162 , HOH A:453
BINDING SITE FOR RESIDUE EDO A 6
07
AC7
SOFTWARE
ASP A:156 , VAL A:157 , ALA A:158 , ARG A:346 , HOH A:462
BINDING SITE FOR RESIDUE EDO A 7
08
AC8
SOFTWARE
ASN A:278 , LEU A:279
BINDING SITE FOR RESIDUE EDO A 8
09
AC9
SOFTWARE
HOH A:26 , HOH A:64 , PHE A:238 , PHE A:249 , ARG A:257 , ARG A:261
BINDING SITE FOR RESIDUE EDO A 9
10
BC1
SOFTWARE
TYR A:159 , MET A:273 , LEU A:319 , ASN A:321 , PRO A:322 , TYR A:329 , ILE A:336 , MET A:337 , PHE A:340 , MET A:357 , SER A:368 , GLN A:369 , PHE A:372 , ILE A:376 , HOH A:451
BINDING SITE FOR RESIDUE JN8 A 440
11
BC2
SOFTWARE
LYS A:262 , ASP A:266 , HOH A:446 , HOH B:452
BINDING SITE FOR RESIDUE EDO A 441
12
BC3
SOFTWARE
HIS A:152 , GLU A:243 , ARG C:350
BINDING SITE FOR RESIDUE EDO A 442
13
BC4
SOFTWARE
ZN B:8 , HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318
BINDING SITE FOR RESIDUE ZN B 7
14
BC5
SOFTWARE
ZN B:7 , ASP B:201 , HOH B:470 , HOH B:471 , HOH B:472
BINDING SITE FOR RESIDUE ZN B 8
15
BC6
SOFTWARE
ASN B:115 , ARG B:116 , GLU B:150 , ASP B:151 , TYR B:153
BINDING SITE FOR RESIDUE EDO B 4
16
BC7
SOFTWARE
LEU B:176 , SER B:177 , THR B:178 , GLU B:182
BINDING SITE FOR RESIDUE EDO B 5
17
BC8
SOFTWARE
ASP B:374 , HIS B:378 , PRO B:379 , GLU B:382
BINDING SITE FOR RESIDUE EDO B 6
18
BC9
SOFTWARE
TYR B:159 , MET B:273 , LEU B:319 , ASN B:321 , THR B:333 , ILE B:336 , PHE B:340 , MET B:357 , CYS B:358 , SER B:368 , GLN B:369 , PHE B:372 , HOH B:443
BINDING SITE FOR RESIDUE JN8 B 440
19
CC1
SOFTWARE
GLU B:95 , ASP B:98 , GLY B:103 , HIS B:105
BINDING SITE FOR RESIDUE DMS B 14
20
CC2
SOFTWARE
ARG A:350 , HIS C:152 , GLU C:243
BINDING SITE FOR RESIDUE EDO C 3
21
CC3
SOFTWARE
ZN C:11 , ASP C:201 , HOH C:462 , HOH C:464
BINDING SITE FOR RESIDUE ZN C 10
22
CC4
SOFTWARE
ZN C:10 , HIS C:164 , HIS C:200 , ASP C:201 , ASP C:318 , HOH C:467
BINDING SITE FOR RESIDUE ZN C 11
23
CC5
SOFTWARE
HIS C:105 , PHE C:107 , ARG C:108 , GLU C:111 , GLN C:327 , LEU C:328 , GLN C:331
BINDING SITE FOR RESIDUE EPE C 2
24
CC6
SOFTWARE
LEU C:175 , THR C:178 , TRP C:384 , ASP C:391 , ALA C:392
BINDING SITE FOR RESIDUE EDO C 440
25
CC7
SOFTWARE
HIS B:389 , PRO B:390 , THR C:134 , PHE C:135 , LYS C:136 , ASN C:251 , GLN C:256
BINDING SITE FOR RESIDUE EDO C 4
26
CC8
SOFTWARE
GLU C:150 , ASP C:151 , TYR C:153 , ALA C:155
BINDING SITE FOR RESIDUE EDO C 5
27
CC9
SOFTWARE
LYS B:290 , GLY B:296 , THR C:253 , LYS C:254 , LYS C:255
BINDING SITE FOR RESIDUE EDO C 7
28
DC1
SOFTWARE
LEU C:234 , PHE C:238 , ARG C:261 , LEU D:221 , ASN D:224
BINDING SITE FOR RESIDUE EDO C 8
29
DC2
SOFTWARE
LYS C:262 , ASP C:266 , ASN D:224 , ASP D:225
BINDING SITE FOR RESIDUE EDO C 9
30
DC3
SOFTWARE
TYR C:159 , LEU C:319 , ASN C:321 , THR C:333 , ILE C:336 , PHE C:340 , CYS C:358 , GLN C:369 , PHE C:372 , HOH C:463
BINDING SITE FOR RESIDUE JN8 C 441
31
DC4
SOFTWARE
THR B:215 , ARG B:350 , THR D:148 , HIS D:152 , GLU D:243
BINDING SITE FOR RESIDUE EDO D 3
32
DC5
SOFTWARE
ZN D:13 , ASP D:201 , HOH D:442 , HOH D:448 , HOH D:450
BINDING SITE FOR RESIDUE ZN D 12
33
DC6
SOFTWARE
ZN D:12 , HIS D:164 , HIS D:200 , ASP D:201 , ASP D:318
BINDING SITE FOR RESIDUE ZN D 13
34
DC7
SOFTWARE
LEU A:188 , LYS A:255 , GLN A:256 , SER A:259 , GLU D:182
BINDING SITE FOR RESIDUE EDO D 2
35
DC8
SOFTWARE
EDO D:8 , LEU D:175 , THR D:178 , TRP D:384 , ASP D:391 , ILE D:395 , HOH D:456
BINDING SITE FOR RESIDUE EDO D 440
36
DC9
SOFTWARE
THR D:186 , ASP D:187 , LEU D:188 , GLN D:256
BINDING SITE FOR RESIDUE EDO D 4
37
EC1
SOFTWARE
HIS D:123
BINDING SITE FOR RESIDUE EDO D 5
38
EC2
SOFTWARE
ASN C:224 , SER C:226 , EDO D:9 , LYS D:262 , ILE D:265 , ASP D:266
BINDING SITE FOR RESIDUE EDO D 6
39
EC3
SOFTWARE
EDO A:4 , THR A:134 , PHE A:135 , ASN A:251 , GLN A:256 , PRO D:179 , ASP D:391
BINDING SITE FOR RESIDUE EDO D 7
40
EC4
SOFTWARE
TRP D:102 , EDO D:440 , HOH D:481
BINDING SITE FOR RESIDUE EDO D 8
41
EC5
SOFTWARE
HOH C:14 , HOH C:42 , ASP C:225 , EDO D:6 , GLN D:258 , ARG D:261 , LYS D:262
BINDING SITE FOR RESIDUE EDO D 9
42
EC6
SOFTWARE
PRO D:325 , LEU D:326 , THR D:398 , ASN D:402
BINDING SITE FOR RESIDUE EDO D 10
43
EC7
SOFTWARE
ASP D:156 , VAL D:157 , ALA D:158 , GLU D:339
BINDING SITE FOR RESIDUE EDO D 11
44
EC8
SOFTWARE
TYR D:159 , MET D:273 , LEU D:319 , ASN D:321 , PRO D:322 , THR D:333 , ILE D:336 , PHE D:340 , MET D:357 , SER D:368 , GLN D:369 , PHE D:372 , HOH D:474
BINDING SITE FOR RESIDUE JN8 D 15
[
close Site info
]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_068245 (T285P, chain A/B/C/D, )
2: VAR_069453 (E288A, chain A/B/C/D, )
3: VAR_069454 (G371D, chain A/B/C/D, )
4: VAR_069455 (I376T, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_068245
T
587
P
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:200-211,B:200-211,C:200-211,D:20...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDEASE_I
PS00126
3'5'-cyclic nucleotide phosphodiesterases signature.
PDE4D_HUMAN
502-513
4
A:200-211
B:200-211
C:200-211
D:200-211
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.34 (A:84-94 | B:88-94 | C:86-94 | D:88...)
Exon 1.35 (A:95-127 | B:95-127 | C:95-127 | D...)
Exon 1.36 (A:128-182 | B:128-182 | C:128-182 ...)
Exon 1.37 (A:183-216 | B:183-216 | C:183-216 ...)
Exon 1.38 (A:216-267 | B:216-267 | C:216-267 ...)
Exon 1.39 (A:268-308 | B:268-308 | C:268-308 ...)
Exon 1.40 (A:309-369 | B:309-369 | C:309-369 ...)
Exon 1.41j (A:370-410 | B:370-412 | C:370-410 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.33b/1.34
2: Boundary 1.34/1.35
3: Boundary 1.35/1.36
4: Boundary 1.36/1.37
5: Boundary 1.37/1.38
6: Boundary 1.38/1.39
7: Boundary 1.39/1.40
8: Boundary 1.40/1.41j
9: Boundary 1.41j/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.13a
ENST00000340635
13a
ENSE00001559328
chr5:
59189625-59188995
631
PDE4D_HUMAN
1-152
152
0
-
-
1.21b
ENST00000340635
21b
ENSE00001136096
chr5:
58511794-58511603
192
PDE4D_HUMAN
152-216
65
0
-
-
1.22
ENST00000340635
22
ENSE00001682119
chr5:
58489362-58489326
37
PDE4D_HUMAN
216-228
13
0
-
-
1.23
ENST00000340635
23
ENSE00001754547
chr5:
58481088-58481015
74
PDE4D_HUMAN
229-253
25
0
-
-
1.24
ENST00000340635
24
ENSE00001719283
chr5:
58476470-58476421
50
PDE4D_HUMAN
253-270
18
0
-
-
1.31d
ENST00000340635
31d
ENSE00001750566
chr5:
58334798-58334686
113
PDE4D_HUMAN
270-307
38
0
-
-
1.33b
ENST00000340635
33b
ENSE00000914184
chr5:
58289292-58289199
94
PDE4D_HUMAN
308-339
32
0
-
-
1.34
ENST00000340635
34
ENSE00001136103
chr5:
58287831-58287659
173
PDE4D_HUMAN
339-396
58
4
A:84-94
B:88-94
C:86-94
D:88-94
11
7
9
7
1.35
ENST00000340635
35
ENSE00001001090
chr5:
58286729-58286631
99
PDE4D_HUMAN
397-429
33
4
A:95-127
B:95-127
C:95-127
D:95-127
33
33
33
33
1.36
ENST00000340635
36
ENSE00001001087
chr5:
58285746-58285582
165
PDE4D_HUMAN
430-484
55
4
A:128-182
B:128-182
C:128-182
D:128-182
55
55
55
55
1.37
ENST00000340635
37
ENSE00001001091
chr5:
58284419-58284320
100
PDE4D_HUMAN
485-518
34
4
A:183-216
B:183-216
C:183-216
D:183-216
34
34
34
34
1.38
ENST00000340635
38
ENSE00001175221
chr5:
58273172-58273018
155
PDE4D_HUMAN
518-569
52
4
A:216-267
B:216-267
C:216-267
D:216-267
52
52
52
52
1.39
ENST00000340635
39
ENSE00001001088
chr5:
58272299-58272177
123
PDE4D_HUMAN
570-610
41
4
A:268-308
B:268-308
C:268-308
D:268-308
41
41
41
41
1.40
ENST00000340635
40
ENSE00001698537
chr5:
58271666-58271484
183
PDE4D_HUMAN
611-671
61
4
A:309-369
B:309-369
C:309-369
D:309-369
61
61
61
61
1.41j
ENST00000340635
41j
ENSE00001989721
chr5:
58270907-58264865
6043
PDE4D_HUMAN
672-809
138
4
A:370-410
B:370-412
C:370-410
D:370-411
41
43
41
42
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3sl6a_ (A:)
1b: SCOP_d3sl6b_ (B:)
1c: SCOP_d3sl6c_ (C:)
1d: SCOP_d3sl6d_ (D:)
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Protein Domains
(
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(
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Organisms
(
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
HD-domain/PDEase-like
(204)
Superfamily
:
HD-domain/PDEase-like
(204)
Family
:
PDEase
(118)
Protein domain
:
Catalytic domain of cyclic nucleotide phosphodiesterase pde4d
(33)
Human (Homo sapiens) [TaxId: 9606]
(33)
1a
d3sl6a_
A:
1b
d3sl6b_
B:
1c
d3sl6c_
C:
1d
d3sl6d_
D:
[
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
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Atom Selection
(currently selected atoms:
all
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Protein
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Sidechain
Hetero
Ligand
Solvent
All Atoms
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Protein & NOT Site
Protein & NOT PROSITE
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Chain B
Chain C
Chain D
Asymmetric Unit 1
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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)
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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") .
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Asym.Unit (232 KB)
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