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2F9R
Asym. Unit
Info
Asym.Unit (406 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (104 KB)
Biol.Unit 3 (102 KB)
Biol.Unit 4 (102 KB)
Biol.Unit 5 (401 KB)
Biol.Unit 6 (205 KB)
Biol.Unit 7 (199 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE INACTIVE STATE OF THE SMASE I, A SPHINGOMYELINASE D FROM LOXOSCELES LAETA VENOM
Authors
:
M. T. Murakami, A. Gabdoulkhakov, M. F. Fernandes-Pedrosa, C. Betzel, D. V. Tambourgi, R. K. Arni
Date
:
06 Dec 05 (Deposition) - 27 Jun 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
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)
Biol. Unit 5: A,B,C,D (1x)
Biol. Unit 6: A,B (1x)
Biol. Unit 7: C,D (1x)
Keywords
:
Sphingomyelinase D, Catalytic Activity, Magnesium-Binding Site, Inactive State, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
M. T. Murakami, A. Gabdoulkhakov, M. F. Fernandes-Pedrosa, D. V. Tambourgi, R. K. Arni
Structural Basis For Metal Ion Coordination And The Catalytic Mechanism Of Sphingomyelinases D.
J. Biol. Chem. V. 280 13658 2005
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
1c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
View:
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No.
Name
Count
Type
Full Name
1
EPE
3
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
MG
4
Ligand/Ion
MAGNESIUM ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:32 , ASP A:34 , ASP A:91 , TRP A:230 , HOH A:719
BINDING SITE FOR RESIDUE MG A 601
2
AC2
SOFTWARE
GLU B:32 , ASP B:34 , ASP B:91 , HOH B:733 , HOH B:734
BINDING SITE FOR RESIDUE MG B 602
3
AC3
SOFTWARE
GLU C:32 , ASP C:34 , ASP C:91
BINDING SITE FOR RESIDUE MG C 603
4
AC4
SOFTWARE
GLU D:32 , ASP D:34 , ASP D:91 , TRP D:230 , HOH D:767
BINDING SITE FOR RESIDUE MG D 604
5
AC5
SOFTWARE
ALA B:16 , ARG B:59 , TRP B:60 , GLU B:61 , TYR B:62 , VAL B:65 , HOH B:726 , HOH B:741 , HOH B:794
BINDING SITE FOR RESIDUE EPE B 701
6
AC6
SOFTWARE
ARG B:4 , ASN B:267 , ALA C:16 , ARG C:59 , TRP C:60 , GLU C:61 , VAL C:65 , HOH C:751
BINDING SITE FOR RESIDUE EPE C 703
7
AC7
SOFTWARE
ARG A:4 , ASN A:267 , ALA D:16 , ARG D:59 , TRP D:60 , GLU D:61 , HOH D:758
BINDING SITE FOR RESIDUE EPE D 704
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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SCOP Domains
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2f9rA00 (A:1-285)
1b: CATH_2f9rB00 (B:1-285)
1c: CATH_2f9rC00 (C:1-285)
1d: CATH_2f9rD00 (D:1-285)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphatidylinositol (PI) phosphodiesterase
(37)
Loxosceles laeta. Organism_taxid: 58217.
(2)
1a
2f9rA00
A:1-285
1b
2f9rB00
B:1-285
1c
2f9rC00
C:1-285
1d
2f9rD00
D:1-285
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Pfam Domains
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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Show PDB file:
Asym.Unit (406 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
Biol.Unit 2 (104 KB)
Header - Biol.Unit 2
Biol.Unit 3 (102 KB)
Header - Biol.Unit 3
Biol.Unit 4 (102 KB)
Header - Biol.Unit 4
Biol.Unit 5 (401 KB)
Header - Biol.Unit 5
Biol.Unit 6 (205 KB)
Header - Biol.Unit 6
Biol.Unit 7 (199 KB)
Header - Biol.Unit 7
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