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3Q8H
Asym. Unit
Info
Asym.Unit (162 KB)
Biol.Unit 1 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI IN COMPLEX WITH CYTIDINE DERIVATIVE EBSI01028
Authors
:
Seattle Structural Genomics Center For Infectious Disease (S
Date
:
06 Jan 11 (Deposition) - 19 Jan 11 (Release) - 11 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Ispf, Mep Pathway, Lyase, Metal-Binding, Isoprene Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Zhang, S. Jakkaraju, J. Blain, K. Gogol, L. Zhao, R. C. Hartley, C. A. Karlsson, B. L. Staker, T. E. Edwards, L. J. Stewart, P. J. Myler, M. Clare, D. W. Begley, J. R. Horn, T. J. Hagen
Cytidine Derivatives As Ispf Inhibitors Of Burkolderia Pseudomallei.
Bioorg. Med. Chem. Lett. V. 23 6860 2013
(for further references see the
PDB file header
)
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: 5'-DEOXY-5'-[(IMIDAZO[2,1-B][1,3]T... (AO9a)
1b: 5'-DEOXY-5'-[(IMIDAZO[2,1-B][1,3]T... (AO9b)
1c: 5'-DEOXY-5'-[(IMIDAZO[2,1-B][1,3]T... (AO9c)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: POTASSIUM ION (Ka)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AO9
3
Ligand/Ion
5'-DEOXY-5'-[(IMIDAZO[2,1-B][1,3]THIAZOL-5-YLCARBONYL)AMINO]CYTIDINE
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
K
1
Ligand/Ion
POTASSIUM ION
4
ZN
3
Ligand/Ion
ZINC ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:10 , HIS A:12 , HIS A:44 , HOH B:166
BINDING SITE FOR RESIDUE ZN A 163
2
AC2
SOFTWARE
HIS A:36 , ASP A:58 , ILE A:59 , GLY A:60 , PHE A:63 , HOH A:169 , HOH A:171 , HOH A:180 , HOH A:209 , ALA B:102 , PRO B:105 , LYS B:106 , LEU B:107 , ALA B:108 , ALA B:133 , LYS B:134 , HOH B:166
BINDING SITE FOR RESIDUE AO9 A 165
3
AC3
SOFTWARE
HOH A:285 , HOH B:286 , HOH C:287
BINDING SITE FOR RESIDUE K A 170
4
AC4
SOFTWARE
ALA A:120 , ASP A:121 , HOH A:224
BINDING SITE FOR RESIDUE EDO A 172
5
AC5
SOFTWARE
ALA A:92 , ILE A:93 , LEU A:122 , ASP A:123 , HOH A:259
BINDING SITE FOR RESIDUE EDO A 173
6
AC6
SOFTWARE
ALA A:102 , PRO A:105 , LYS A:106 , LEU A:107 , ALA A:108 , ALA A:133 , LYS A:134 , THR A:135 , HOH A:195 , HOH A:266 , HOH A:293 , HIS C:36 , ASP C:58 , ILE C:59 , GLY C:60 , ARG C:61 , PHE C:63
BINDING SITE FOR RESIDUE AO9 A 164
7
AC7
SOFTWARE
ASP B:10 , HIS B:12 , HIS B:44 , HOH B:291
BINDING SITE FOR RESIDUE ZN B 163
8
AC8
SOFTWARE
HIS B:36 , ASP B:58 , ILE B:59 , GLY B:60 , ARG B:61 , PHE B:63 , LEU B:78 , HOH B:175 , HOH B:178 , HOH B:290 , HOH B:291 , ALA C:102 , PRO C:105 , LYS C:106 , LEU C:107 , ALA C:108 , ALA C:133 , LYS C:134
BINDING SITE FOR RESIDUE AO9 B 165
9
AC9
SOFTWARE
HOH A:195 , ASP C:10 , HIS C:12 , HIS C:44
BINDING SITE FOR RESIDUE ZN C 163
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: ISPF (A:37-52,B:37-52,C:37-52)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISPF
PS01350
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.
ISPF_BURPS
37-52
3
A:37-52
B:37-52
C:37-52
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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.
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3q8ha_ (A:)
1b: SCOP_d3q8hb_ (B:)
1c: SCOP_d3q8hc_ (C:)
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Protein Domains
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Organisms
(
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(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Bacillus chorismate mutase-like
(324)
Superfamily
:
IpsF-like
(56)
Family
:
automated matches
(21)
Protein domain
:
automated matches
(21)
Burkholderia pseudomallei [TaxId: 28450]
(11)
1a
d3q8ha_
A:
1b
d3q8hb_
B:
1c
d3q8hc_
C:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_YgbB_3q8hC01 (C:3-158)
1b: PFAM_YgbB_3q8hC02 (C:3-158)
1c: PFAM_YgbB_3q8hC03 (C:3-158)
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Clan
:
no clan defined [family: YgbB]
(24)
Family
:
YgbB
(24)
Burkholderia pseudomallei (Pseudomonas pseudomallei)
(1)
1a
YgbB-3q8hC01
C:3-158
1b
YgbB-3q8hC02
C:3-158
1c
YgbB-3q8hC03
C:3-158
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Asymmetric Unit 1
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Asym.Unit (162 KB)
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