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2WWD
Asym. Unit
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Asym.Unit (87 KB)
Biol.Unit 1 (80 KB)
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(1)
Title
:
3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH PNEUMMOCOCCAL PEPTIDOGLYCAN FRAGMENT
Authors
:
I. Perez-Dorado, R. Sanles, J. A. Hermoso, A. Gonzalez, A. Garcia, P. Ga J. L. Garcia
Date
:
22 Oct 09 (Deposition) - 21 Apr 10 (Release) - 03 Apr 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Glycosidase, Choline-Binding Proteins
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Perez-Dorado, A. Gonzalez, M. Morales, R. Sanles, W. Striker, W. Vollmer, S. Mobashery, J. L. Garcia, M. Martinez-Ripoll, P. Garcia J. A. Hermoso
Insights Into Pneumococcal Fratricide From The Crystal Structures Of The Modular Killing Factor Lytc.
Nat. Struct. Mol. Biol. V. 17 576 2010
(for further references see the
PDB file header
)
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: CHOLINE ION (CHTa)
1b: CHOLINE ION (CHTb)
1c: CHOLINE ION (CHTc)
1d: CHOLINE ION (CHTd)
1e: CHOLINE ION (CHTe)
1f: CHOLINE ION (CHTf)
1g: CHOLINE ION (CHTg)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
3a: N-ACETYLMURAMYL-L-ALANYL-D-ISOGLUT... (MU2a)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CHT
7
Ligand/Ion
CHOLINE ION
2
GOL
7
Ligand/Ion
GLYCEROL
3
MU2
1
Ligand/Ion
N-ACETYLMURAMYL-L-ALANYL-D-ISOGLUTAMINE
4
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:365 , TYR A:405 , TYR A:407 , ALA A:428 , TYR A:430 , MU2 A:470
BINDING SITE FOR RESIDUE NAG A 469
02
AC2
SOFTWARE
SER A:73 , ASP A:74 , TYR A:407 , ARG A:408 , SER A:409 , ALA A:429 , TYR A:430 , THR A:431 , NAG A:469
BINDING SITE FOR RESIDUE MU2 A 470
03
AC3
SOFTWARE
LYS A:89 , MET A:94 , GLU A:98
BINDING SITE FOR RESIDUE GOL A 601
04
AC4
SOFTWARE
TYR A:105 , LYS A:106 , LYS A:133
BINDING SITE FOR RESIDUE GOL A 602
05
AC5
SOFTWARE
TRP A:122 , GLN A:144 , GLY A:145 , SER A:146 , TYR A:147
BINDING SITE FOR RESIDUE GOL A 603
06
AC6
SOFTWARE
GLN A:142 , TRP A:143 , ASP A:163
BINDING SITE FOR RESIDUE GOL A 604
07
AC7
SOFTWARE
TYR A:178 , ASN A:180 , GLN A:181 , LYS A:195 , TRP A:196
BINDING SITE FOR RESIDUE GOL A 605
08
AC8
SOFTWARE
LYS A:173 , ASN A:180 , GLN A:181 , GLU A:182
BINDING SITE FOR RESIDUE GOL A 606
09
AC9
SOFTWARE
ARG A:253 , GLU A:266 , ALA A:268 , ASP A:294
BINDING SITE FOR RESIDUE GOL A 607
10
BC1
SOFTWARE
TRP A:42 , GLY A:44 , TYR A:65 , PHE A:69 , GLY A:91 , TYR A:93
BINDING SITE FOR RESIDUE CHT A 701
11
BC2
SOFTWARE
TRP A:59 , TRP A:68 , TYR A:86 , MET A:94 , ASP A:114
BINDING SITE FOR RESIDUE CHT A 702
12
BC3
SOFTWARE
TRP A:82 , GLY A:84 , PHE A:109 , TYR A:117 , TRP A:135 , ARG A:259
BINDING SITE FOR RESIDUE CHT A 703
13
BC4
SOFTWARE
TRP A:99 , TRP A:108 , TYR A:130 , MET A:138 , GLN A:152
BINDING SITE FOR RESIDUE CHT A 704
14
BC5
SOFTWARE
TRP A:122 , TRP A:129 , TYR A:147
BINDING SITE FOR RESIDUE CHT A 705
15
BC6
SOFTWARE
GLY A:145 , TYR A:166 , PHE A:170 , TYR A:178 , TRP A:196
BINDING SITE FOR RESIDUE CHT A 706
16
BC7
SOFTWARE
TRP A:160 , TYR A:169 , TYR A:191 , SER A:213
BINDING SITE FOR RESIDUE CHT A 707
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_CW_binding_1_2wwdA01 (A:181-199)
1b: PFAM_CW_binding_1_2wwdA02 (A:181-199)
1c: PFAM_CW_binding_1_2wwdA03 (A:181-199)
1d: PFAM_CW_binding_1_2wwdA04 (A:181-199)
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Clans
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Clan
:
no clan defined [family: CW_binding_1]
(12)
Family
:
CW_binding_1
(12)
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
(9)
1a
CW_binding_1-2wwdA01
A:181-199
1b
CW_binding_1-2wwdA02
A:181-199
1c
CW_binding_1-2wwdA03
A:181-199
1d
CW_binding_1-2wwdA04
A:181-199
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Chain A
Asymmetric Unit 1
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Asym.Unit (87 KB)
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