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1IV4
Asym. Unit
Info
Asym.Unit (161 KB)
Biol.Unit 1 (80 KB)
Biol.Unit 2 (79 KB)
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(1)
Title
:
STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (BOUND FORM SUBSTRATE)
Authors
:
H. Kishida, T. Wada, S. Unzai, T. Kuzuyama, T. Terada, M. Sirouzu, S. Yokoyama, J. R. H. Tame, S. -Y. Park, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
11 Mar 02 (Deposition) - 11 Sep 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Isoprenoid, Non-Mevalonate, Synthase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Kishida, T. Wada, S. Unzai, T. Kuzuyama, M. Takagi, T. Terada, M. Shirouzu, S. Yokoyama, J. R. Tame, S. Y. Park
Structure And Catalytic Mechanism Of 2-C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate (Mecdp) Synthase, An Enzyme In The Non-Mevalonate Pathway Of Isoprenoid Synthesis.
Acta Crystallogr. , Sect. D V. 59 23 2003
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: CYTIDINE-5'-MONOPHOSPHATE (C5Pa)
1b: CYTIDINE-5'-MONOPHOSPHATE (C5Pb)
1c: CYTIDINE-5'-MONOPHOSPHATE (C5Pc)
1d: CYTIDINE-5'-MONOPHOSPHATE (C5Pd)
1e: CYTIDINE-5'-MONOPHOSPHATE (C5Pe)
1f: CYTIDINE-5'-MONOPHOSPHATE (C5Pf)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C5P
6
Ligand/Ion
CYTIDINE-5'-MONOPHOSPHATE
2
MG
12
Ligand/Ion
MAGNESIUM ION
[
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Sites
(18, 18)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:8 , HIS A:10 , HIS A:42 , MG A:1571 , HOH A:1625
BINDING SITE FOR RESIDUE MG A 1561
02
AC2
SOFTWARE
MG A:1572 , ASP B:208 , HIS B:210 , HIS B:242 , HOH B:1630
BINDING SITE FOR RESIDUE MG B 1562
03
AC3
SOFTWARE
MG B:1573 , ASP C:408 , HIS C:410 , HIS C:442 , HOH C:1632
BINDING SITE FOR RESIDUE MG C 1563
04
AC4
SOFTWARE
HOH D:234 , ASP D:1008 , HIS D:1010 , HIS D:1042 , MG D:1574 , HOH F:154
BINDING SITE FOR RESIDUE MG D 1564
05
AC5
SOFTWARE
HOH D:157 , MG D:1575 , ASP E:1208 , HIS E:1210 , HIS E:1242
BINDING SITE FOR RESIDUE MG E 1565
06
AC6
SOFTWARE
HOH F:170 , ASP F:1408 , HIS F:1410 , HIS F:1442 , MG F:1576
BINDING SITE FOR RESIDUE MG F 1566
07
AC7
SOFTWARE
ASP A:8 , MG A:1561 , HOH A:1625 , HOH A:1642 , LYS C:532 , C5P C:1601 , HOH C:1623
BINDING SITE FOR RESIDUE MG A 1571
08
AC8
SOFTWARE
LYS A:132 , C5P A:1602 , HOH A:1643 , ASP B:208 , MG B:1562 , HOH B:1630 , HOH B:1647
BINDING SITE FOR RESIDUE MG A 1572
09
AC9
SOFTWARE
LYS B:332 , C5P B:1603 , HOH B:1640 , ASP C:408 , MG C:1563 , HOH C:1622 , HOH C:1632
BINDING SITE FOR RESIDUE MG B 1573
10
BC1
SOFTWARE
HOH D:234 , ASP D:1008 , MG D:1564 , HOH F:154 , HOH F:416 , LYS F:1532 , C5P F:1604
BINDING SITE FOR RESIDUE MG D 1574
11
BC2
SOFTWARE
HOH D:157 , HOH D:161 , LYS D:1132 , C5P D:1605 , HOH E:204 , ASP E:1208 , MG E:1565
BINDING SITE FOR RESIDUE MG D 1575
12
BC3
SOFTWARE
LYS E:1332 , HOH F:170 , HOH F:176 , HOH F:193 , ASP F:1408 , MG F:1566 , C5P F:1606
BINDING SITE FOR RESIDUE MG F 1576
13
BC4
SOFTWARE
ASP A:56 , GLY A:58 , MG A:1571 , HOH A:1625 , LEU C:500 , PRO C:503 , LYS C:504 , LEU C:505 , GLY C:506 , ARG C:509 , PHE C:531 , LYS C:532 , THR C:533 , GLU C:535 , HOH C:1614 , HOH C:1623 , HOH C:1667 , HOH C:1682
BINDING SITE FOR RESIDUE C5P C 1601
14
BC5
SOFTWARE
LEU A:100 , PRO A:103 , LYS A:104 , LEU A:105 , GLY A:106 , ARG A:109 , PHE A:131 , LYS A:132 , THR A:133 , GLU A:135 , MG A:1572 , HOH A:1640 , HOH A:1643 , HOH A:1692 , ASP B:256 , GLY B:258 , HOH B:1630
BINDING SITE FOR RESIDUE C5P A 1602
15
BC6
SOFTWARE
LEU B:300 , PRO B:303 , LYS B:304 , LEU B:305 , GLY B:306 , PHE B:331 , LYS B:332 , THR B:333 , GLU B:335 , MG B:1573 , HOH B:1619 , HOH B:1640 , HOH B:1686 , ASP C:456 , GLY C:458 , HOH C:1632
BINDING SITE FOR RESIDUE C5P B 1603
16
BC7
SOFTWARE
ASP D:1056 , GLY D:1058 , MG D:1574 , HOH F:117 , HOH F:154 , HOH F:416 , LEU F:1500 , PRO F:1503 , LYS F:1504 , LEU F:1505 , GLY F:1506 , ARG F:1509 , PHE F:1531 , LYS F:1532 , THR F:1533 , GLU F:1535
BINDING SITE FOR RESIDUE C5P F 1604
17
BC8
SOFTWARE
HOH D:76 , HOH D:157 , HOH D:161 , HOH D:383 , HOH D:428 , LEU D:1100 , PRO D:1103 , LYS D:1104 , LEU D:1105 , GLY D:1106 , ARG D:1109 , PHE D:1131 , LYS D:1132 , THR D:1133 , MG D:1575 , ASP E:1256 , GLY E:1258
BINDING SITE FOR RESIDUE C5P D 1605
18
BC9
SOFTWARE
LEU E:1300 , PRO E:1303 , LYS E:1304 , LEU E:1305 , GLY E:1306 , ARG E:1309 , PHE E:1331 , LYS E:1332 , THR E:1333 , HOH F:142 , HOH F:170 , HOH F:193 , HOH F:397 , ASP F:1456 , ILE F:1457 , GLY F:1458 , MG F:1576
BINDING SITE FOR RESIDUE C5P F 1606
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: ISPF (A:35-50,B:235-250,C:435-450,D:1035...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISPF
PS01350
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.
ISPF_THET8
35-50
6
A:35-50
B:235-250
C:435-450
D:1035-1050
E:1235-1250
F:1435-1450
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Exons
(0, 0)
Info
All Exons
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1iv4a_ (A:)
1b: SCOP_d1iv4b_ (B:)
1c: SCOP_d1iv4c_ (C:)
1d: SCOP_d1iv4d_ (D:)
1e: SCOP_d1iv4e_ (E:)
1f: SCOP_d1iv4f_ (F:)
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)
(
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)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Bacillus chorismate mutase-like
(324)
Superfamily
:
IpsF-like
(56)
Family
:
IpsF-like
(35)
Protein domain
:
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF
(27)
Thermus thermophilus [TaxId: 274]
(4)
1a
d1iv4a_
A:
1b
d1iv4b_
B:
1c
d1iv4c_
C:
1d
d1iv4d_
D:
1e
d1iv4e_
E:
1f
d1iv4f_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1iv4A00 (A:2-151)
1b: CATH_1iv4B00 (B:202-351)
1c: CATH_1iv4C00 (C:402-551)
1d: CATH_1iv4D00 (D:1002-1151)
1e: CATH_1iv4E00 (E:1202-1351)
1f: CATH_1iv4F00 (F:1402-1551)
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(
)
Homologous Superfamilies
(
)
(
)
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)
Thermus thermophilus. Organism_taxid: 274.
(4)
1a
1iv4A00
A:2-151
1b
1iv4B00
B:202-351
1c
1iv4C00
C:402-551
1d
1iv4D00
D:1002-1151
1e
1iv4E00
E:1202-1351
1f
1iv4F00
F:1402-1551
[
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Pfam Domains
(0, 0)
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all PFAM domains
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