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2UZH
Asym. Unit
Info
Asym.Unit (88 KB)
Biol.Unit 1 (81 KB)
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(1)
Title
:
MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (ISPF)
Authors
:
L. Buetow, A. C. Brown, T. Parish, W. N. Hunter
Date
:
27 Apr 07 (Deposition) - 06 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Ispf, Lyase, Mycobacteria, Complex With Cdp, Non-Mevalonate Pathway Of Isoprenoid Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Buetow, A. C. Brown, T. Parish, W. N. Hunter
The Structure Of Mycobacteria 2C-Methyl-D- Erythritol-2, 4-Cyclodiphosphate Synthase, An Essential Enzyme, Provides A Platform For Drug Discovery.
Bmc Struct. Biol. V. 7 68 2007
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Hetero Components
(7, 15)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: CYTIDINE-5'-DIPHOSPHATE (CDPa)
2b: CYTIDINE-5'-DIPHOSPHATE (CDPb)
2c: CYTIDINE-5'-DIPHOSPHATE (CDPc)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
5a: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEa)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
6b: DI(HYDROXYETHYL)ETHER (PEGb)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
7c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
CDP
3
Ligand/Ion
CYTIDINE-5'-DIPHOSPHATE
3
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
4
GOL
3
Ligand/Ion
GLYCEROL
5
IPE
1
Ligand/Ion
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
6
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
7
ZN
3
Ligand/Ion
ZINC ION
[
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Sites
(15, 15)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:11 , HIS A:13 , HIS A:45 , CDP C:1158
BINDING SITE FOR RESIDUE ZN A1157
02
AC2
SOFTWARE
GLY A:103 , ASN A:104 , PRO A:106 , LYS A:107 , VAL A:108 , GLY A:109 , ALA A:131 , THR A:132 , THR A:133 , HOH A:2072 , HOH A:2073 , HOH A:2074 , HOH A:2075 , HOH A:2076 , HOH A:2077 , HOH A:2078 , ASP B:11 , VAL B:12 , HIS B:13 , HIS B:45 , ASP B:59 , LEU B:60 , GLY B:61 , HOH B:2037 , ZN C:1157
BINDING SITE FOR RESIDUE CDP A1158
03
AC3
SOFTWARE
CDP B:1158 , ASP C:11 , HIS C:13 , HIS C:45
BINDING SITE FOR RESIDUE ZN B1157
04
AC4
SOFTWARE
ARG B:72 , GLY B:103 , ASN B:104 , PRO B:106 , LYS B:107 , VAL B:108 , GLY B:109 , ALA B:131 , THR B:132 , THR B:133 , ZN B:1157 , HOH B:2102 , HOH B:2103 , HOH B:2104 , HOH B:2105 , HOH B:2106 , ASP C:11 , VAL C:12 , HIS C:13 , ASP C:59 , LEU C:60 , GLY C:61 , HOH C:2028
BINDING SITE FOR RESIDUE CDP B1158
05
AC5
SOFTWARE
CDP A:1158 , ASP B:11 , HIS B:13 , HIS B:45
BINDING SITE FOR RESIDUE ZN C1157
06
AC6
SOFTWARE
ASP A:11 , VAL A:12 , HIS A:13 , ASP A:59 , GLY A:61 , ZN A:1157 , HOH A:2020 , GLY C:103 , ASN C:104 , PRO C:106 , LYS C:107 , VAL C:108 , GLY C:109 , ALA C:131 , THR C:132 , THR C:133 , ASP C:135 , HOH C:2075 , HOH C:2076 , HOH C:2078 , HOH C:2079 , HOH C:2080
BINDING SITE FOR RESIDUE CDP C1158
07
AC7
SOFTWARE
SER A:53 , GLY A:56 , LEU A:57 , GLY A:58 , ARG C:112 , GLN C:116 , SER C:128 , VAL C:129 , SER C:130 , HOH C:2071
BINDING SITE FOR RESIDUE EDO C1160
08
AC8
SOFTWARE
ARG A:112 , GLN A:116 , SER A:128 , VAL A:129 , SER A:130 , HOH A:2079 , LEU B:52 , SER B:53 , GLY B:56 , LEU B:57 , GLY B:58
BINDING SITE FOR RESIDUE EDO A1160
09
AC9
SOFTWARE
GLY A:138 , LEU A:139 , ARG A:142 , GLY B:138 , LEU B:139 , ARG B:142 , ALA B:147 , GLY C:138 , LEU C:139
BINDING SITE FOR RESIDUE IPE B1160
10
BC1
SOFTWARE
GLY A:85 , ASN A:89 , GLY C:124 , ACT C:1162 , HOH C:2068 , HOH C:2081
BINDING SITE FOR RESIDUE GOL C1161
11
BC2
SOFTWARE
GLN A:116 , VAL A:127 , SER A:128 , HOH A:2080 , ARG B:5 , HOH B:2004
BINDING SITE FOR RESIDUE GOL A1161
12
BC3
SOFTWARE
PRO B:14 , ILE B:15 , GLU B:16 , GLU B:121 , PEG B:1162 , HOH B:2107 , HOH B:2108
BINDING SITE FOR RESIDUE GOL B1161
13
BC4
SOFTWARE
HIS A:82 , GLY A:85 , ASN A:89 , ARG C:84 , GLU C:121 , GLY C:124 , GOL C:1161
BINDING SITE FOR RESIDUE ACT C1162
14
BC5
SOFTWARE
ILE B:15 , CYS B:25 , ALA B:77 , ARG B:81 , VAL B:118 , ARG B:142 , GLU B:144 , GOL B:1161 , HOH B:2038 , HOH B:2088
BINDING SITE FOR RESIDUE PEG B1162
15
BC6
SOFTWARE
ARG B:19 , ASP B:30 , ALA B:31 , ASP B:32 , ARG B:81 , HIS B:82 , HOH B:2109 , ARG C:142
BINDING SITE FOR RESIDUE PEG B1163
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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
(1, 3)
Info
all CATH domains
1a: CATH_2uzhA00 (A:3-157)
1b: CATH_2uzhB00 (B:3-157)
1c: CATH_2uzhC00 (C:3-157)
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
60s Ribosomal Protein L30; Chain: A;
(235)
Homologous Superfamily
:
[code=3.30.1330.50, no name defined]
(46)
Mycobacterium smegmatis. Organism_taxid: 1772. Strain: mc(2)155.
(1)
1a
2uzhA00
A:3-157
1b
2uzhB00
B:3-157
1c
2uzhC00
C:3-157
[
close CATH info
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_YgbB_2uzhC01 (C:4-157)
1b: PFAM_YgbB_2uzhC02 (C:4-157)
1c: PFAM_YgbB_2uzhC03 (C:4-157)
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Clans
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)
(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: YgbB]
(24)
Family
:
YgbB
(24)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
(1)
1a
YgbB-2uzhC01
C:4-157
1b
YgbB-2uzhC02
C:4-157
1c
YgbB-2uzhC03
C:4-157
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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