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3SL4
Asym. Unit
Info
Asym.Unit (244 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (63 KB)
Biol.Unit 4 (64 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 WITH COMPOUND 10D
Authors
:
S. F. Feil
Date
:
24 Jun 11 (Deposition) - 26 Oct 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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 Mechanism, Camp Hydrolysis, 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
(7, 82)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
1f: DIMETHYL SULFOXIDE (DMSf)
1g: DIMETHYL SULFOXIDE (DMSg)
1h: DIMETHYL SULFOXIDE (DMSh)
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)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
2aj: 1,2-ETHANEDIOL (EDOaj)
2ak: 1,2-ETHANEDIOL (EDOak)
2al: 1,2-ETHANEDIOL (EDOal)
2am: 1,2-ETHANEDIOL (EDOam)
2an: 1,2-ETHANEDIOL (EDOan)
2ao: 1,2-ETHANEDIOL (EDOao)
2ap: 1,2-ETHANEDIOL (EDOap)
2aq: 1,2-ETHANEDIOL (EDOaq)
2ar: 1,2-ETHANEDIOL (EDOar)
2as: 1,2-ETHANEDIOL (EDOas)
2at: 1,2-ETHANEDIOL (EDOat)
2au: 1,2-ETHANEDIOL (EDOau)
2av: 1,2-ETHANEDIOL (EDOav)
2aw: 1,2-ETHANEDIOL (EDOaw)
2ax: 1,2-ETHANEDIOL (EDOax)
2ay: 1,2-ETHANEDIOL (EDOay)
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)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
4a: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4a)
4b: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4b)
4c: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4c)
4d: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4d)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
5e: DI(HYDROXYETHYL)ETHER (PEGe)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
6c: PHOSPHATE ION (PO4c)
6d: PHOSPHATE ION (PO4d)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
7c: ZINC ION (ZNc)
7d: ZINC ION (ZNd)
7e: ZINC ION (ZNe)
7f: ZINC ION (ZNf)
7g: ZINC ION (ZNg)
7h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
8
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
51
Ligand/Ion
1,2-ETHANEDIOL
3
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
JN4
4
Ligand/Ion
ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(PHENYLACETYL)AMINO]-4,5,6,7-TETRAHYDROTHIENO[2,3-C]PYRIDINE-3-CARBOXYLATE
5
PEG
5
Ligand/Ion
DI(HYDROXYETHYL)ETHER
6
PO4
4
Ligand/Ion
PHOSPHATE ION
7
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(82, 82)
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)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
63: GC9 (SOFTWARE)
64: HC1 (SOFTWARE)
65: HC2 (SOFTWARE)
66: HC3 (SOFTWARE)
67: HC4 (SOFTWARE)
68: HC5 (SOFTWARE)
69: HC6 (SOFTWARE)
70: HC7 (SOFTWARE)
71: HC8 (SOFTWARE)
72: HC9 (SOFTWARE)
73: IC1 (SOFTWARE)
74: IC2 (SOFTWARE)
75: IC3 (SOFTWARE)
76: IC4 (SOFTWARE)
77: IC5 (SOFTWARE)
78: IC6 (SOFTWARE)
79: IC7 (SOFTWARE)
80: IC8 (SOFTWARE)
81: IC9 (SOFTWARE)
82: JC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PO4 A:20 , HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:486
BINDING SITE FOR RESIDUE ZN A 1
02
AC2
SOFTWARE
PO4 A:20 , HOH A:54 , ASP A:201 , HOH A:486 , HOH A:490 , HOH A:529
BINDING SITE FOR RESIDUE ZN A 2
03
AC3
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH B:500 , HOH B:535
BINDING SITE FOR RESIDUE EDO A 4
04
AC4
SOFTWARE
GLU A:218 , LYS C:239
BINDING SITE FOR RESIDUE EDO A 5
05
AC5
SOFTWARE
PRO A:138 , ASP A:140 , THR A:141
BINDING SITE FOR RESIDUE DMS A 6
06
AC6
SOFTWARE
ARG A:350 , EDO C:8 , THR C:148 , ASP C:151
BINDING SITE FOR RESIDUE EDO A 7
07
AC7
SOFTWARE
ASP A:156 , ALA A:158 , PRO A:205 , GLU A:339 , ARG A:342 , ARG A:346 , HOH A:482
BINDING SITE FOR RESIDUE EDO A 9
08
AC8
SOFTWARE
LEU A:175 , THR A:178 , TRP A:384 , VAL A:388 , ILE A:395
BINDING SITE FOR RESIDUE EDO A 10
09
AC9
SOFTWARE
LEU A:132 , LYS A:136 , ILE A:137 , VAL A:139 , HOH A:471 , HOH A:478
BINDING SITE FOR RESIDUE EDO A 11
10
BC1
SOFTWARE
ASN A:115 , ARG A:116 , GLU A:150 , ASP A:151 , TYR A:153 , ASN A:162 , HOH A:542
BINDING SITE FOR RESIDUE PEG A 440
11
BC2
SOFTWARE
EDO A:18 , LEU A:188 , LYS A:255 , GLN A:256 , SER A:259 , DMS D:8 , GLU D:182
BINDING SITE FOR RESIDUE EDO A 13
12
BC3
SOFTWARE
PHE A:238 , PHE A:249 , ARG A:257 , ARG A:261 , HOH A:536 , HOH A:539
BINDING SITE FOR RESIDUE EDO A 14
13
BC4
SOFTWARE
ASP A:266 , GLN A:311
BINDING SITE FOR RESIDUE EDO A 15
14
BC5
SOFTWARE
GLU A:218 , HIS C:152 , LYS C:239 , HOH C:479
BINDING SITE FOR RESIDUE EDO A 16
15
BC6
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:162 , ILE A:163
BINDING SITE FOR RESIDUE EDO A 17
16
BC7
SOFTWARE
EDO A:13 , THR A:186 , LEU A:188 , SER A:259 , MET A:263
BINDING SITE FOR RESIDUE EDO A 18
17
BC8
SOFTWARE
ARG A:330 , GLU A:366 , THR A:409 , HOH A:463 , PRO B:411 , GLN B:412
BINDING SITE FOR RESIDUE EDO A 19
18
BC9
SOFTWARE
ZN A:1 , ZN A:2 , JN4 A:23 , HIS A:160 , HIS A:164 , ASP A:201 , ASP A:318 , HOH A:452 , HOH A:485 , HOH A:486
BINDING SITE FOR RESIDUE PO4 A 20
19
CC1
SOFTWARE
LYS A:239 , GLN A:242 , HOH A:547 , ASN C:216 , LYS D:239 , GLN D:242
BINDING SITE FOR RESIDUE EDO A 21
20
CC2
SOFTWARE
PO4 A:20 , TYR A:159 , LEU A:319 , ASN A:321 , PRO A:322 , TYR A:329 , THR A:333 , ILE A:336 , MET A:337 , MET A:357 , GLN A:369 , PHE A:372 , HOH A:444 , HOH A:485
BINDING SITE FOR RESIDUE JN4 A 23
21
CC3
SOFTWARE
GLN A:258 , EDO B:9 , GLN B:210 , ASN B:214
BINDING SITE FOR RESIDUE EDO A 441
22
CC4
SOFTWARE
HIS A:105 , VAL A:106 , PHE A:107 , ARG A:108 , GLN A:331
BINDING SITE FOR RESIDUE DMS A 442
23
CC5
SOFTWARE
THR A:148 , HIS A:152 , GLU A:243 , HOH A:462 , HOH C:73 , PHE C:211 , THR C:215 , ARG C:350
BINDING SITE FOR RESIDUE EDO A 443
24
CC6
SOFTWARE
PO4 B:20 , HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , HOH B:489
BINDING SITE FOR RESIDUE ZN B 1
25
CC7
SOFTWARE
PO4 B:20 , HOH B:47 , HOH B:57 , ASP B:201 , HOH B:484 , HOH B:489
BINDING SITE FOR RESIDUE ZN B 2
26
CC8
SOFTWARE
SER B:208 , PHE B:340 , PRO B:356 , CYS B:358 , HOH B:482
BINDING SITE FOR RESIDUE EDO B 4
27
CC9
SOFTWARE
EDO B:18 , ASP B:140 , LYS B:290 , VAL B:292 , THR C:253 , LYS C:254 , HOH C:485
BINDING SITE FOR RESIDUE EPE B 6
28
DC1
SOFTWARE
EDO B:13 , GLU B:150 , ASP B:151 , TYR B:153 , ASN B:162
BINDING SITE FOR RESIDUE DMS B 7
29
DC2
SOFTWARE
GLU B:218
BINDING SITE FOR RESIDUE EDO B 8
30
DC3
SOFTWARE
GLN A:258 , EDO A:441 , ASN B:214 , HOH B:515 , SER D:294 , SER D:295
BINDING SITE FOR RESIDUE EDO B 9
31
DC4
SOFTWARE
HOH B:71 , GLU B:218
BINDING SITE FOR RESIDUE EDO B 10
32
DC5
SOFTWARE
HOH B:58 , GLN B:210 , HOH B:454 , HOH B:509
BINDING SITE FOR RESIDUE EDO B 11
33
DC6
SOFTWARE
DMS B:7 , ASN B:115 , ALA B:155 , ASN B:162 , ILE B:163 , ARG B:335
BINDING SITE FOR RESIDUE EDO B 13
34
DC7
SOFTWARE
PHE B:211 , ASN B:214 , GLU B:347 , MET B:352 , GLU B:353 , SER B:355
BINDING SITE FOR RESIDUE EDO B 15
35
DC8
SOFTWARE
LEU B:176 , SER B:177 , THR B:178 , LEU B:181 , GLU B:182 , HOH B:459 , HOH B:486
BINDING SITE FOR RESIDUE EDO B 16
36
DC9
SOFTWARE
ALA B:183 , PHE B:185
BINDING SITE FOR RESIDUE EDO B 17
37
EC1
SOFTWARE
EPE B:6 , EDO B:19 , LYS B:290 , LEU B:387 , VAL B:388 , HIS B:389 , HOH B:527 , HOH C:485
BINDING SITE FOR RESIDUE EDO B 18
38
EC2
SOFTWARE
EDO B:18 , PRO B:179 , ALA B:180 , HIS B:389 , PRO B:390 , ASP B:391 , EDO C:6 , THR C:253 , LYS C:255
BINDING SITE FOR RESIDUE EDO B 19
39
EC3
SOFTWARE
ZN B:1 , ZN B:2 , JN4 B:21 , HIS B:160 , HIS B:164 , ASP B:201 , ASP B:318 , HOH B:451 , HOH B:489 , HOH B:510
BINDING SITE FOR RESIDUE PO4 B 20
40
EC4
SOFTWARE
PO4 B:20 , TYR B:159 , MET B:273 , LEU B:319 , ASN B:321 , TRP B:332 , THR B:333 , ILE B:336 , MET B:337 , MET B:357 , GLN B:369 , PHE B:372 , HOH B:510 , HOH B:526
BINDING SITE FOR RESIDUE JN4 B 21
41
EC5
SOFTWARE
EDO A:7 , HIS C:152 , GLU C:243
BINDING SITE FOR RESIDUE EDO C 8
42
EC6
SOFTWARE
PO4 C:17 , HIS C:164 , HIS C:200 , ASP C:201 , ASP C:318 , HOH C:487
BINDING SITE FOR RESIDUE ZN C 1
43
EC7
SOFTWARE
PO4 C:17 , ASP C:201 , HOH C:481 , HOH C:487 , HOH C:491 , HOH C:516
BINDING SITE FOR RESIDUE ZN C 2
44
EC8
SOFTWARE
ASN C:115 , ALA C:155 , ASN C:161 , ASN C:162 , ILE C:163
BINDING SITE FOR RESIDUE EDO C 4
45
EC9
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 5
46
FC1
SOFTWARE
EDO B:19 , LEU C:188 , LYS C:255 , SER C:259
BINDING SITE FOR RESIDUE EDO C 6
47
FC2
SOFTWARE
HIS C:105 , VAL C:106 , PHE C:107 , ARG C:108 , GLU C:111 , GLN C:327 , LEU C:328 , GLN C:331
BINDING SITE FOR RESIDUE EPE C 7
48
FC3
SOFTWARE
LEU C:175 , THR C:178 , TRP C:384 , ASP C:391
BINDING SITE FOR RESIDUE EDO C 440
49
FC4
SOFTWARE
ARG C:257 , ARG C:261 , HOH C:489
BINDING SITE FOR RESIDUE DMS C 10
50
FC5
SOFTWARE
LYS C:262 , ASP C:266 , ASN D:224 , ASP D:225
BINDING SITE FOR RESIDUE EDO C 11
51
FC6
SOFTWARE
ASP C:266 , ALA C:270 , LYS C:275 , GLN C:311
BINDING SITE FOR RESIDUE EDO C 12
52
FC7
SOFTWARE
ASP C:156 , VAL C:157 , ALA C:158 , GLU C:339 , ARG C:342 , HOH C:507
BINDING SITE FOR RESIDUE EDO C 13
53
FC8
SOFTWARE
ASP A:156 , GLU C:150 , ASP C:151 , TYR C:153
BINDING SITE FOR RESIDUE EDO C 14
54
FC9
SOFTWARE
HIS C:154 , ASP C:203 , PRO C:205 , LEU C:219
BINDING SITE FOR RESIDUE EDO C 15
55
GC1
SOFTWARE
ZN C:1 , ZN C:2 , JN4 C:18 , HIS C:160 , HIS C:164 , ASP C:201 , ASP C:318 , HOH C:484 , HOH C:487 , HOH C:503
BINDING SITE FOR RESIDUE PO4 C 17
56
GC2
SOFTWARE
PO4 C:17 , TYR C:159 , MET C:273 , LEU C:319 , ASN C:321 , PRO C:322 , THR C:333 , ILE C:336 , MET C:337 , MET C:357 , GLN C:369 , PHE C:372 , HOH C:482 , HOH C:484
BINDING SITE FOR RESIDUE JN4 C 18
57
GC3
SOFTWARE
THR B:215 , ARG B:350 , HOH B:528 , THR D:148 , HIS D:152 , GLU D:243 , HOH D:495
BINDING SITE FOR RESIDUE EDO D 5
58
GC4
SOFTWARE
EDO D:7 , ASN D:100 , LYS D:101 , TRP D:102 , VAL D:174 , HOH D:447 , HOH D:534
BINDING SITE FOR RESIDUE PEG D 12
59
GC5
SOFTWARE
PO4 D:24 , HIS D:164 , HIS D:200 , ASP D:201 , ASP D:318 , HOH D:482
BINDING SITE FOR RESIDUE ZN D 1
60
GC6
SOFTWARE
PO4 D:24 , HOH D:76 , ASP D:201 , HOH D:482 , HOH D:546 , HOH D:557
BINDING SITE FOR RESIDUE ZN D 2
61
GC7
SOFTWARE
THR A:134 , ASN A:251 , GLN A:256 , HOH A:460 , PRO D:179 , ASP D:391
BINDING SITE FOR RESIDUE EDO D 4
62
GC8
SOFTWARE
LEU D:181 , ALA D:183 , VAL D:184 , PHE D:185 , HOH D:449
BINDING SITE FOR RESIDUE EDO D 440
63
GC9
SOFTWARE
ASN D:115
BINDING SITE FOR RESIDUE EDO D 6
64
HC1
SOFTWARE
PEG D:12 , LEU D:175 , THR D:178 , ASP D:391 , HOH D:473
BINDING SITE FOR RESIDUE EDO D 7
65
HC2
SOFTWARE
EDO A:13 , HOH A:477 , SER D:177 , THR D:178 , PRO D:179 , GLU D:182
BINDING SITE FOR RESIDUE DMS D 8
66
HC3
SOFTWARE
GLU B:349 , ARG B:350 , ASP D:140 , THR D:144
BINDING SITE FOR RESIDUE DMS D 9
67
HC4
SOFTWARE
HIS D:123
BINDING SITE FOR RESIDUE EDO D 10
68
HC5
SOFTWARE
EDO D:14 , ASP D:266 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 11
69
HC6
SOFTWARE
ASP C:225 , HOH C:464 , GLN D:258 , LYS D:262 , ASP D:266
BINDING SITE FOR RESIDUE PEG D 441
70
HC7
SOFTWARE
EDO D:17 , ASN D:115 , GLU D:150 , ASP D:151 , TYR D:153 , ASN D:162
BINDING SITE FOR RESIDUE DMS D 13
71
HC8
SOFTWARE
EDO D:11 , ASP D:266 , LYS D:275 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 14
72
HC9
SOFTWARE
MET D:286 , THR D:289 , LYS D:291 , LEU D:299
BINDING SITE FOR RESIDUE EDO D 15
73
IC1
SOFTWARE
PRO D:325 , LEU D:326 , ASP D:401 , ASN D:402
BINDING SITE FOR RESIDUE PEG D 16
74
IC2
SOFTWARE
DMS D:13 , ASN D:115 , ALA D:155 , ASN D:161 , ASN D:162
BINDING SITE FOR RESIDUE EDO D 17
75
IC3
SOFTWARE
ASN D:100 , GLU D:128 , HIS D:173 , SER D:177 , HOH D:472
BINDING SITE FOR RESIDUE EDO D 18
76
IC4
SOFTWARE
ASP D:156 , VAL D:157 , ALA D:158 , PRO D:205 , GLU D:339 , ARG D:346 , HOH D:476
BINDING SITE FOR RESIDUE PEG D 19
77
IC5
SOFTWARE
ASN C:231 , LEU C:234 , PHE C:238 , ARG C:261 , LEU D:221 , ASN D:224 , HOH D:488
BINDING SITE FOR RESIDUE EDO D 20
78
IC6
SOFTWARE
ASN C:231 , EDO D:22 , MET D:222 , TYR D:223 , ASN D:224 , SER D:226 , ASN D:231 , HOH D:452 , HOH D:468
BINDING SITE FOR RESIDUE EDO D 21
79
IC7
SOFTWARE
EDO D:21 , SER D:226 , ASN D:231 , HOH D:468
BINDING SITE FOR RESIDUE EDO D 22
80
IC8
SOFTWARE
HIS D:105 , VAL D:106 , PHE D:107 , ARG D:108 , GLN D:327 , LEU D:328 , GLN D:331
BINDING SITE FOR RESIDUE DMS D 23
81
IC9
SOFTWARE
ZN D:1 , ZN D:2 , HIS D:160 , HIS D:164 , ASP D:201 , ASP D:318 , JN4 D:442 , HOH D:482 , HOH D:483 , HOH D:518
BINDING SITE FOR RESIDUE PO4 D 24
82
JC1
SOFTWARE
PO4 D:24 , TYR D:159 , MET D:273 , LEU D:319 , ASN D:321 , PRO D:322 , TYR D:329 , THR D:333 , ILE D:336 , MET D:337 , MET D:357 , SER D:368 , GLN D:369 , PHE D:372 , HOH D:483 , HOH D:554 , HOH D:559
BINDING SITE FOR RESIDUE JN4 D 442
[
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)
[
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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
[
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Exons
(8, 32)
Info
All Exons
Exon 1.34 (A:83-94 | 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:370-411 | B:370-412 | C:370-410 ...)
View:
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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:83-94
B:88-94
C:86-94
D:88-94
12
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:370-411
B:370-412
C:370-410
D:370-411
42
43
41
42
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3sl4a_ (A:)
1b: SCOP_d3sl4b_ (B:)
1c: SCOP_d3sl4c_ (C:)
1d: SCOP_d3sl4d_ (D:)
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Protein Domains
(
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(
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Organisms
(
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(
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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
d3sl4a_
A:
1b
d3sl4b_
B:
1c
d3sl4c_
C:
1d
d3sl4d_
D:
[
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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
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Sorry, no Info available
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Atom Selection
(currently selected atoms:
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Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
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All Atoms
Protein & NOT Variant
Protein & NOT Site
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Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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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)
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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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