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1TB7
Biol. Unit 2
Info
Asym.Unit (126 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (61 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH AMP
Authors
:
K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessing G. Bollag
Date
:
19 May 04 (Deposition) - 03 Aug 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.63
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Pde4D, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. Hsieh, J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessinger, G. Bollag
A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases
Mol. Cell V. 15 279 2004
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Hetero Components
(2, 14)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
2a: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pa)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
B3P
-1
Ligand/Ion
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3
EDO
13
Ligand/Ion
1,2-ETHANEDIOL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(19, 19)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC5 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC6 (SOFTWARE)
13: CC7 (SOFTWARE)
14: CC8 (SOFTWARE)
15: CC9 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC5 (SOFTWARE)
18: DC6 (SOFTWARE)
19: DC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , MG B:1002 , AMP B:1003 , HOH B:1175
BINDING SITE FOR RESIDUE ZN B 1001
02
AC4
SOFTWARE
ASP B:201 , ZN B:1001 , AMP B:1003 , HOH B:1172 , HOH B:1173 , HOH B:1174 , HOH B:1175
BINDING SITE FOR RESIDUE MG B 1002
03
AC5
SOFTWARE
HIS B:160 , HIS B:164 , ASP B:201 , ASP B:318 , LEU B:319 , ASN B:321 , GLN B:369 , PHE B:372 , EDO B:543 , ZN B:1001 , MG B:1002 , HOH B:1004 , HOH B:1027 , HOH B:1104 , HOH B:1174 , HOH B:1175
BINDING SITE FOR RESIDUE AMP B 1003
04
AC7
SOFTWARE
GLU B:366 , EDO B:503
BINDING SITE FOR RESIDUE EDO B 501
05
AC9
SOFTWARE
ARG B:330 , THR B:333 , ASP B:334 , TYR B:406 , EDO B:501 , HOH B:1165
BINDING SITE FOR RESIDUE EDO B 503
06
BC1
SOFTWARE
SER B:208 , PHE B:340 , PRO B:356 , HOH B:1059
BINDING SITE FOR RESIDUE EDO B 508
07
BC2
SOFTWARE
SER B:259 , HOH B:1056
BINDING SITE FOR RESIDUE EDO B 509
08
BC5
SOFTWARE
PHE B:238 , ARG B:257 , ARG B:261 , HOH B:1084 , HOH B:1093
BINDING SITE FOR RESIDUE EDO B 517
09
CC2
SOFTWARE
HOH A:1032 , GLU B:218
BINDING SITE FOR RESIDUE EDO B 524
10
CC3
SOFTWARE
ASN A:224 , LYS B:262 , ILE B:265 , ASP B:266 , HOH B:1011 , HOH B:1087
BINDING SITE FOR RESIDUE EDO B 525
11
CC4
SOFTWARE
GLN A:407 , GLU B:150 , ASP B:151 , TYR B:153 , ASN B:162 , EDO B:534 , HOH B:1075
BINDING SITE FOR RESIDUE EDO B 526
12
CC6
SOFTWARE
ASN B:115 , ALA B:155 , ASN B:162 , ILE B:163 , EDO B:526 , HOH B:1075 , HOH B:1164
BINDING SITE FOR RESIDUE EDO B 534
13
CC7
SOFTWARE
ASN B:209 , GLU B:230 , MET B:273 , EDO B:543 , HOH B:1027
BINDING SITE FOR RESIDUE EDO B 535
14
CC8
SOFTWARE
ARG A:330 , GLU A:366 , TRP A:405 , TYR A:406 , HOH A:1088 , PRO B:411
BINDING SITE FOR RESIDUE EDO A 536
15
CC9
SOFTWARE
PRO A:325 , GLN A:327 , HOH A:1055 , TRP B:405 , HOH B:1076
BINDING SITE FOR RESIDUE EDO A 537
16
DC4
SOFTWARE
ASP B:266 , ILE B:307 , GLN B:311 , EDO B:542 , HOH B:1106
BINDING SITE FOR RESIDUE EDO B 541
17
DC5
SOFTWARE
ASP B:266 , LEU B:269 , LYS B:275 , GLN B:311 , EDO B:541
BINDING SITE FOR RESIDUE EDO B 542
18
DC6
SOFTWARE
HIS B:160 , HIS B:204 , GLY B:206 , VAL B:207 , SER B:208 , GLU B:339 , EDO B:535 , AMP B:1003 , HOH B:1027 , HOH B:1059
BINDING SITE FOR RESIDUE EDO B 543
19
DC7
SOFTWARE
LYS A:94 , GLU A:95 , GLU A:97 , ASP A:98 , HIS A:105 , ARG A:108 , HOH A:1147 , ASP B:394 , ASP B:397 , ASP B:401 , HOH B:1123
BINDING SITE FOR RESIDUE B3P A 601
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_068245 (T285P, chain B, )
2: VAR_069453 (E288A, chain B, )
3: VAR_069454 (G371D, chain B, )
4: VAR_069455 (I376T, chain B, )
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)
---
B
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
B
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
B
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
B
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (B:200-211)
;
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
1
-
B:200-211
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1tb7a_ (A:)
1b: SCOP_d1tb7b_ (B:)
View:
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Classes
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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
d1tb7a_
A:
1b
d1tb7b_
B:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1tb7B00 (B:86-411)
1b: CATH_1tb7A00 (A:87-411)
View:
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Classes
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
(66)
Homologous Superfamily
:
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
(66)
Human (Homo sapiens)
(64)
1a
1tb7B00
B:86-411
1b
1tb7A00
A:87-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1tb7B01 (B:159-403)
1b: PFAM_PDEase_I_1tb7B02 (B:159-403)
View:
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Label:
Clans
(
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(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1tb7B01
B:159-403
1b
PDEase_I-1tb7B02
B:159-403
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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