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1MKD
Biol. Unit 2
Info
Asym.Unit (651 KB)
Biol.Unit 1 (326 KB)
Biol.Unit 2 (324 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PDE4D CATALYTIC DOMAIN AND ZARDAVERINE COMPLEX
Authors
:
M. E. Lee, J. Markowitz, J. -O. Lee, H. Lee
Date
:
29 Aug 02 (Deposition) - 01 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,E,H,I,J (1x)
Biol. Unit 2: C,D,F,G,K,L (1x)
Keywords
:
Pde, Zardaverine, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. E. Lee, J. Markowitz, J. -O. Lee, H. Lee
Crystal Structure Of Phosphodiesterase 4D And Inhibitor Complex
Febs Lett. V. 530 53 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
2a: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARa)
2b: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARb)
2c: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARc)
2d: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARd)
2e: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARe)
2f: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARf)
2g: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARg)
2h: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARh)
2i: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARi)
2j: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARj)
2k: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARk)
2l: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHE... (ZARl)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
3i: ZINC ION (ZNi)
3j: ZINC ION (ZNj)
3k: ZINC ION (ZNk)
3l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
ZAR
6
Ligand/Ion
6-(4-DIFLUOROMETHOXY-3-METHOXY-PHENYL)-2H-PYRIDAZIN-3-ONE
3
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(18, 18)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
13: CC9 (SOFTWARE)
14: DC1 (SOFTWARE)
15: DC3 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC8 (SOFTWARE)
18: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
HIS C:261 , HIS C:297 , ASP C:298 , ASP C:415
BINDING SITE FOR RESIDUE ZN C 2005
02
AC6
SOFTWARE
ASP C:298 , GLU C:327
BINDING SITE FOR RESIDUE MG C 2006
03
AC7
SOFTWARE
HIS D:261 , HIS D:297 , ASP D:298 , ASP D:415
BINDING SITE FOR RESIDUE ZN D 2007
04
AC8
SOFTWARE
ASP D:298
BINDING SITE FOR RESIDUE MG D 2008
05
BC2
SOFTWARE
HIS F:261 , HIS F:297 , ASP F:298 , ASP F:415
BINDING SITE FOR RESIDUE ZN F 2011
06
BC3
SOFTWARE
ASP F:298 , GLU F:327
BINDING SITE FOR RESIDUE MG F 2012
07
BC4
SOFTWARE
HIS G:261 , HIS G:297 , ASP G:298 , ASP G:415
BINDING SITE FOR RESIDUE ZN G 2013
08
BC5
SOFTWARE
ASP G:298 , GLU G:327
BINDING SITE FOR RESIDUE MG G 2014
09
CC3
SOFTWARE
HIS K:261 , HIS K:297 , ASP K:298 , ASP K:415
BINDING SITE FOR RESIDUE ZN K 2021
10
CC4
SOFTWARE
HIS K:297 , ASP K:298 , THR K:368
BINDING SITE FOR RESIDUE MG K 2022
11
CC5
SOFTWARE
HIS L:261 , HIS L:297 , ASP L:298 , ASP L:415
BINDING SITE FOR RESIDUE ZN L 2023
12
CC6
SOFTWARE
ASP L:298 , GLU L:327
BINDING SITE FOR RESIDUE MG L 2024
13
CC9
SOFTWARE
MET C:370 , ASN C:418 , PRO C:419 , TYR C:426 , TRP C:429 , THR C:430 , ILE C:433 , MET C:454 , GLN C:466 , PHE C:469
BINDING SITE FOR RESIDUE ZAR C 3003
14
DC1
SOFTWARE
MET D:370 , ASN D:418 , PRO D:419 , TYR D:426 , TRP D:429 , THR D:430 , ILE D:433 , MET D:454 , GLN D:466 , PHE D:469
BINDING SITE FOR RESIDUE ZAR D 3004
15
DC3
SOFTWARE
MET F:370 , ASN F:418 , PRO F:419 , TYR F:426 , TRP F:429 , THR F:430 , ILE F:433 , MET F:454 , GLN F:466 , PHE F:469
BINDING SITE FOR RESIDUE ZAR F 3006
16
DC4
SOFTWARE
MET G:370 , ASN G:418 , PRO G:419 , TYR G:426 , TRP G:429 , THR G:430 , ILE G:433 , MET G:454 , GLN G:466 , PHE G:469 , HOH G:1007
BINDING SITE FOR RESIDUE ZAR G 3007
17
DC8
SOFTWARE
MET K:370 , ASN K:418 , TYR K:426 , TRP K:429 , THR K:430 , ILE K:433 , MET K:454 , GLN K:466 , PHE K:469
BINDING SITE FOR RESIDUE ZAR K 3011
18
DC9
SOFTWARE
MET L:370 , ASN L:418 , PRO L:419 , TYR L:426 , TRP L:429 , THR L:430 , ILE L:433 , MET L:454 , GLN L:466 , PHE L:469
BINDING SITE FOR RESIDUE ZAR L 3012
[
close Site info
]
SAPs(SNPs)/Variants
(4, 24)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_068245 (T382P, chain C/D/F/G/K/L, )
2: VAR_069453 (E385A, chain C/D/F/G/K/L, )
3: VAR_069454 (G468D, chain C/D/F/G/K/L, )
4: VAR_069455 (I473T, chain C/D/F/G/K/L, )
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)
---
C/D/F/G/K/L
T
382
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
C/D/F/G/K/L
E
385
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
C/D/F/G/K/L
G
468
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
C/D/F/G/K/L
I
473
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (C:297-308,D:297-308,F:297-308,G:29...)
;
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
6
-
-
C:297-308
D:297-308
-
F:297-308
G:297-308
-
-
-
K:297-308
L:297-308
[
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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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1mkda_ (A:)
1b: SCOP_d1mkdb_ (B:)
1c: SCOP_d1mkdc_ (C:)
1d: SCOP_d1mkdd_ (D:)
1e: SCOP_d1mkde_ (E:)
1f: SCOP_d1mkdf_ (F:)
1g: SCOP_d1mkdg_ (G:)
1h: SCOP_d1mkdh_ (H:)
1i: SCOP_d1mkdi_ (I:)
1j: SCOP_d1mkdj_ (J:)
1k: SCOP_d1mkdk_ (K:)
1l: SCOP_d1mkdl_ (L:)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d1mkda_
A:
1b
d1mkdb_
B:
1c
d1mkdc_
C:
1d
d1mkdd_
D:
1e
d1mkde_
E:
1f
d1mkdf_
F:
1g
d1mkdg_
G:
1h
d1mkdh_
H:
1i
d1mkdi_
I:
1j
d1mkdj_
J:
1k
d1mkdk_
K:
1l
d1mkdl_
L:
[
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]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1mkdA00 (A:183-510)
1b: CATH_1mkdB00 (B:183-510)
1c: CATH_1mkdC00 (C:183-510)
1d: CATH_1mkdD00 (D:183-510)
1e: CATH_1mkdE00 (E:183-510)
1f: CATH_1mkdF00 (F:183-510)
1g: CATH_1mkdG00 (G:183-510)
1h: CATH_1mkdH00 (H:183-510)
1i: CATH_1mkdI00 (I:183-510)
1j: CATH_1mkdJ00 (J:183-510)
1k: CATH_1mkdK00 (K:183-510)
1l: CATH_1mkdL00 (L:183-510)
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(
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(
)
(
)
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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
1mkdA00
A:183-510
1b
1mkdB00
B:183-510
1c
1mkdC00
C:183-510
1d
1mkdD00
D:183-510
1e
1mkdE00
E:183-510
1f
1mkdF00
F:183-510
1g
1mkdG00
G:183-510
1h
1mkdH00
H:183-510
1i
1mkdI00
I:183-510
1j
1mkdJ00
J:183-510
1k
1mkdK00
K:183-510
1l
1mkdL00
L:183-510
[
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]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_PDEase_I_1mkdL01 (L:256-500)
1b: PFAM_PDEase_I_1mkdL02 (L:256-500)
1c: PFAM_PDEase_I_1mkdL03 (L:256-500)
1d: PFAM_PDEase_I_1mkdL04 (L:256-500)
1e: PFAM_PDEase_I_1mkdL05 (L:256-500)
1f: PFAM_PDEase_I_1mkdL06 (L:256-500)
1g: PFAM_PDEase_I_1mkdL07 (L:256-500)
1h: PFAM_PDEase_I_1mkdL08 (L:256-500)
1i: PFAM_PDEase_I_1mkdL09 (L:256-500)
1j: PFAM_PDEase_I_1mkdL10 (L:256-500)
1k: PFAM_PDEase_I_1mkdL11 (L:256-500)
1l: PFAM_PDEase_I_1mkdL12 (L:256-500)
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(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1mkdL01
L:256-500
1b
PDEase_I-1mkdL02
L:256-500
1c
PDEase_I-1mkdL03
L:256-500
1d
PDEase_I-1mkdL04
L:256-500
1e
PDEase_I-1mkdL05
L:256-500
1f
PDEase_I-1mkdL06
L:256-500
1g
PDEase_I-1mkdL07
L:256-500
1h
PDEase_I-1mkdL08
L:256-500
1i
PDEase_I-1mkdL09
L:256-500
1j
PDEase_I-1mkdL10
L:256-500
1k
PDEase_I-1mkdL11
L:256-500
1l
PDEase_I-1mkdL12
L:256-500
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