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1XX1
Biol. Unit 1
Info
Asym.Unit (214 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (106 KB)
Biol.Unit 3 (206 KB)
Biol.Unit 4 (208 KB)
Biol.Unit 5 (208 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR ION-COORDINATION AND THE CATALYTIC MECHANISM OF SPHINGOMYELINASES D
Authors
:
M. T. Murakami, D. V. Tambourgi, R. K. Arni
Date
:
03 Nov 04 (Deposition) - 18 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Biol. Unit 4: A,B,C,D (1x)
Biol. Unit 5: A,B,C,D (1x)
Keywords
:
Structure, Quick Cryo-Soaking, Activity, Smase D, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. T. Murakami, 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
(for further references see the
PDB file header
)
[
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]
Hetero Components
(2, 13)
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)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
SO4
12
Ligand/Ion
SULFATE ION
[
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]
Sites
(19, 19)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC6 (SOFTWARE)
16: CC7 (SOFTWARE)
17: DC1 (SOFTWARE)
18: DC2 (SOFTWARE)
19: DC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:12 , HIS A:47 , LEU A:198 , TRP A:230 , MG A:9001 , HOH A:9102 , HOH A:9251 , HOH A:9252 , PRO B:50
BINDING SITE FOR RESIDUE SO4 A 3001
02
AC2
SOFTWARE
PRO A:50 , HIS B:12 , HIS B:47 , LEU B:198 , TRP B:230 , MG B:9002 , HOH B:9104 , HOH B:9256 , HOH B:9259
BINDING SITE FOR RESIDUE SO4 B 3002
03
AC5
SOFTWARE
ARG A:4 , HOH A:9045 , HOH A:9172 , VAL D:65 , LYS D:68 , EPE D:2004
BINDING SITE FOR RESIDUE SO4 A 4001
04
AC6
SOFTWARE
ARG B:4 , HOH B:9094 , HOH B:9151 , VAL C:65 , LYS C:68 , EPE C:2003
BINDING SITE FOR RESIDUE SO4 B 4002
05
AC8
SOFTWARE
GLY A:39 , SER A:40 , GLN A:101 , HOH A:9015 , HOH A:9210 , HOH B:9146
BINDING SITE FOR RESIDUE SO4 A 5001
06
AC9
SOFTWARE
GLY B:39 , SER B:40 , GLN B:101 , HOH B:9111 , HOH B:9134 , HOH B:9181 , HOH B:9228
BINDING SITE FOR RESIDUE SO4 B 5002
07
BC3
SOFTWARE
GLN A:19 , ARG A:55 , ASP A:56 , HOH A:9009 , HOH A:9023 , HOH A:9180 , HOH A:9243 , LYS C:234 , VAL C:235 , HOH C:9045
BINDING SITE FOR RESIDUE SO4 A 6001
08
BC4
SOFTWARE
GLN B:19 , ARG B:55 , ASP B:56 , HOH B:9012 , HOH B:9087 , HOH B:9229 , LYS D:234 , VAL D:235 , HOH D:9088
BINDING SITE FOR RESIDUE SO4 B 6002
09
BC5
SOFTWARE
LYS A:234 , VAL A:235 , HOH A:9161 , GLN C:19 , ARG C:55 , ASP C:56 , HOH C:9009 , HOH C:9019 , HOH C:9057
BINDING SITE FOR RESIDUE SO4 C 6003
10
BC6
SOFTWARE
LYS B:234 , VAL B:235 , GLN D:19 , ARG D:55 , ASP D:56 , HOH D:9007 , HOH D:9009 , HOH D:9061 , HOH D:9127
BINDING SITE FOR RESIDUE SO4 D 6004
11
BC7
SOFTWARE
ARG A:103 , ARG A:143
BINDING SITE FOR RESIDUE SO4 A 7001
12
BC8
SOFTWARE
ARG B:103 , ARG B:143
BINDING SITE FOR RESIDUE SO4 B 7002
13
CC2
SOFTWARE
GLU A:159 , HIS A:191 , HOH A:9144 , HOH A:9146 , HOH A:9213
BINDING SITE FOR RESIDUE SO4 A 8001
14
CC3
SOFTWARE
GLU B:159 , HIS B:191 , HOH B:9052 , HOH B:9082 , HOH B:9119 , HOH B:9133 , HOH B:9176
BINDING SITE FOR RESIDUE SO4 B 8002
15
CC6
SOFTWARE
GLU A:32 , ASP A:34 , ASP A:91 , SO4 A:3001 , HOH A:9245 , HOH A:9251 , HOH A:9252
BINDING SITE FOR RESIDUE MG A 9001
16
CC7
SOFTWARE
GLU B:32 , ASP B:34 , ASP B:91 , SO4 B:3002 , HOH B:9256 , HOH B:9259 , HOH B:9274
BINDING SITE FOR RESIDUE MG B 9002
17
DC1
SOFTWARE
ALA A:16 , ARG A:59 , TRP A:60 , GLU A:61 , TYR A:62 , VAL A:65 , HOH A:9052 , HOH A:9197 , HOH A:9242 , HOH B:9154
BINDING SITE FOR RESIDUE EPE A 2001
18
DC2
SOFTWARE
ARG B:4 , ASN B:267 , ASP B:268 , SO4 B:4002 , HOH B:9197 , ALA C:16 , ARG C:59 , TRP C:60 , GLU C:61 , VAL C:65 , HOH C:9090 , HOH C:9184 , HOH C:9219
BINDING SITE FOR RESIDUE EPE C 2003
19
DC3
SOFTWARE
ARG A:4 , ASN A:267 , ASP A:268 , SO4 A:4001 , ALA D:16 , ARG D:59 , TRP D:60 , GLU D:61 , VAL D:65 , HOH D:9040 , HOH D:9154 , HOH D:9205
BINDING SITE FOR RESIDUE EPE D 2004
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
Info
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1xx1A00 (A:1-285)
1b: CATH_1xx1B00 (B:1-285)
1c: CATH_1xx1C00 (C:1-285)
1d: CATH_1xx1D00 (D:1-285)
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Classes
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(
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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)
Loxosceles laeta. Organism_taxid: 58217.
(2)
1a
1xx1A00
A:1-285
1b
1xx1B00
B:1-285
1c
1xx1C00
C:1-285
1d
1xx1D00
D:1-285
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GDPD_2_1xx1D01 (D:226-255)
1b: PFAM_GDPD_2_1xx1D02 (D:226-255)
1c: PFAM_GDPD_2_1xx1D03 (D:226-255)
1d: PFAM_GDPD_2_1xx1D04 (D:226-255)
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Clan
:
PLC
(20)
Family
:
GDPD_2
(2)
Loxosceles laeta (South American recluse spider) (Scytodes laeta)
(1)
1a
GDPD_2-1xx1D01
D:226-255
1b
GDPD_2-1xx1D02
D:226-255
1c
GDPD_2-1xx1D03
D:226-255
1d
GDPD_2-1xx1D04
D:226-255
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