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1DJW
Biol. Unit 2
Info
Asym.Unit (201 KB)
Biol.Unit 1 (92 KB)
Biol.Unit 2 (103 KB)
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Title
:
PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-2-METHYLENE-1,2-CYCLIC-MONOPHOSPHONATE
Authors
:
L. -O. Essen, O. Perisic, R. L. Williams
Date
:
24 Aug 96 (Deposition) - 23 Jul 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphoric Diester Hydrolase, Hydrolase, Lipid Degradation, Transducer, Calcium-Binding, Phospholipase C, Phosphoinositide-Specific
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. O. Essen, O. Perisic, M. Katan, Y. Wu, M. F. Roberts, R. L. Williams
Structural Mapping Of The Catalytic Mechanism For A Mammalian Phosphoinositide-Specific Phospholipase C.
Biochemistry V. 36 1704 1997
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
3a: INOSITOL-2-METHYLENE-1,2-CYCLIC-MO... (CIPa)
3b: INOSITOL-2-METHYLENE-1,2-CYCLIC-MO... (CIPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CIP
1
Ligand/Ion
INOSITOL-2-METHYLENE-1,2-CYCLIC-MONOPHOSPHATE
[
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Sites
(5, 5)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
CIP B:1 , ASN B:312 , GLU B:341 , ASP B:343 , GLU B:390
BINDING SITE FOR RESIDUE CA B 2
2
AC6
SOFTWARE
LYS B:646 , ASN B:649 , ILE B:651 , ASP B:653 , ASN B:677
BINDING SITE FOR RESIDUE CA B 3
3
AC7
SOFTWARE
ASP B:706 , TYR B:707 , ASP B:708 , HOH B:998
BINDING SITE FOR RESIDUE CA B 4
4
AC8
SOFTWARE
GLY B:583 , PRO B:584 , ASP B:587 , ARG B:701 , PHE B:715 , HOH B:884
BINDING SITE FOR RESIDUE ACT B 5
5
BC1
SOFTWARE
CA B:2 , HIS B:311 , ASN B:312 , TYR B:314 , GLU B:341 , ASP B:343 , HIS B:356 , GLU B:390 , ARG B:549 , TYR B:551 , HOH B:1016 , HOH B:1161
BINDING SITE FOR RESIDUE CIP B 1
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SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_PLCD1_RAT_001 (I412M, chain B, )
2: VAR_PLCD1_RAT_002 (T423S, chain B, )
3: VAR_PLCD1_RAT_004 (G668A, chain B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PLCD1_RAT_001
*
I
412
M
PLCD1_RAT
---
---
B
I
412
M
2
UniProt
VAR_PLCD1_RAT_002
*
T
423
S
PLCD1_RAT
---
---
B
T
423
S
3
UniProt
VAR_PLCD1_RAT_004
*
G
668
A
PLCD1_RAT
---
---
B
G
668
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 ()
2: EF_HAND_1 ()
3: PIPLC_X_DOMAIN (B:296-440)
4: PIPLC_Y_DOMAIN (B:492-609)
5: C2 (B:630-720)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
PLCD1_RAT
140-175
176-211
1
-
B:176-211
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
PLCD1_RAT
153-165
189-201
1
-
B:189-201
3
PIPLC_X_DOMAIN
PS50007
Phosphatidylinositol-specific phospholipase X-box domain profile.
PLCD1_RAT
296-440
1
-
B:296-440
4
PIPLC_Y_DOMAIN
PS50008
Phosphatidylinositol-specific phospholipase Y-box domain profile.
PLCD1_RAT
492-609
1
-
B:492-609
5
C2
PS50004
C2 domain profile.
PLCD1_RAT
630-720
1
-
B:630-720
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Exons
(0, 0)
Info
All Exons
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1djwa1 (A:200-298)
1b: SCOP_d1djwb1 (B:158-298)
2a: SCOP_d1djwa2 (A:626-756)
2b: SCOP_d1djwb2 (B:626-756)
3a: SCOP_d1djwa3 (A:299-625)
3b: SCOP_d1djwb3 (B:299-625)
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)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
EF-hand modules in multidomain proteins
(29)
Protein domain
:
Phosphoinositide-specific phospholipase C, isozyme D1 (PLC-D!)
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(10)
1a
d1djwa1
A:200-298
1b
d1djwb1
B:158-298
Class
:
All beta proteins
(24004)
Fold
:
C2 domain-like
(198)
Superfamily
:
C2 domain (Calcium/lipid-binding domain, CaLB)
(148)
Family
:
PLC-like (P variant)
(81)
Protein domain
:
PI-specific phospholipase C isozyme D1 (PLC-D1), C-terminal domain
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(10)
2a
d1djwa2
A:626-756
2b
d1djwb2
B:626-756
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLC-like phosphodiesterases
(46)
Family
:
Mammalian PLC
(12)
Protein domain
:
Phospholipase C isozyme D1 (PLC-D1)
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(10)
3a
d1djwa3
A:299-625
3b
d1djwb3
B:299-625
[
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]
CATH Domains
(3, 7)
Info
all CATH domains
1a: CATH_1djwA02 (A:293-625)
1b: CATH_1djwB03 (B:293-625)
2a: CATH_1djwA01 (A:210-292)
2b: CATH_1djwB02 (B:210-292)
2c: CATH_1djwB01 (B:158-209)
3a: CATH_1djwA03 (A:626-756)
3b: CATH_1djwB04 (B:626-754)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphatidylinositol (PI) phosphodiesterase
(37)
Norway rat (Rattus norvegicus)
(10)
1a
1djwA02
A:293-625
1b
1djwB03
B:293-625
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Norway rat (Rattus norvegicus)
(37)
2a
1djwA01
A:210-292
2b
1djwB02
B:210-292
2c
1djwB01
B:158-209
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
C2- domain Calcium/lipid binding domain
(78)
Norway rat (Rattus norvegicus)
(20)
3a
1djwA03
A:626-756
3b
1djwB04
B:626-754
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain B
Asymmetric Unit 1
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