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1H48

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product

Functional Information from GO Data
ChainGOidnamespacecontents
A0005515molecular_functionprotein binding
A0006744biological_processubiquinone biosynthetic process
A0008270molecular_functionzinc ion binding
A0008299biological_processisoprenoid biosynthetic process
A0008685molecular_function2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
A0016114biological_processterpenoid biosynthetic process
A0016829molecular_functionlyase activity
A0019288biological_processisopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
A0030145molecular_functionmanganese ion binding
A0042802molecular_functionidentical protein binding
A0046872molecular_functionmetal ion binding
B0005515molecular_functionprotein binding
B0006744biological_processubiquinone biosynthetic process
B0008270molecular_functionzinc ion binding
B0008299biological_processisoprenoid biosynthetic process
B0008685molecular_function2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
B0016114biological_processterpenoid biosynthetic process
B0016829molecular_functionlyase activity
B0019288biological_processisopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
B0030145molecular_functionmanganese ion binding
B0042802molecular_functionidentical protein binding
B0046872molecular_functionmetal ion binding
C0005515molecular_functionprotein binding
C0006744biological_processubiquinone biosynthetic process
C0008270molecular_functionzinc ion binding
C0008299biological_processisoprenoid biosynthetic process
C0008685molecular_function2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
C0016114biological_processterpenoid biosynthetic process
C0016829molecular_functionlyase activity
C0019288biological_processisopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
C0030145molecular_functionmanganese ion binding
C0042802molecular_functionidentical protein binding
C0046872molecular_functionmetal ion binding
D0005515molecular_functionprotein binding
D0006744biological_processubiquinone biosynthetic process
D0008270molecular_functionzinc ion binding
D0008299biological_processisoprenoid biosynthetic process
D0008685molecular_function2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
D0016114biological_processterpenoid biosynthetic process
D0016829molecular_functionlyase activity
D0019288biological_processisopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
D0030145molecular_functionmanganese ion binding
D0042802molecular_functionidentical protein binding
D0046872molecular_functionmetal ion binding
E0005515molecular_functionprotein binding
E0006744biological_processubiquinone biosynthetic process
E0008270molecular_functionzinc ion binding
E0008299biological_processisoprenoid biosynthetic process
E0008685molecular_function2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
E0016114biological_processterpenoid biosynthetic process
E0016829molecular_functionlyase activity
E0019288biological_processisopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
E0030145molecular_functionmanganese ion binding
E0042802molecular_functionidentical protein binding
E0046872molecular_functionmetal ion binding
F0005515molecular_functionprotein binding
F0006744biological_processubiquinone biosynthetic process
F0008270molecular_functionzinc ion binding
F0008299biological_processisoprenoid biosynthetic process
F0008685molecular_function2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
F0016114biological_processterpenoid biosynthetic process
F0016829molecular_functionlyase activity
F0019288biological_processisopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
F0030145molecular_functionmanganese ion binding
F0042802molecular_functionidentical protein binding
F0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 900
ChainResidue
AASP8
AHIS10
AHIS42
ACDI201

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 900
ChainResidue
BASP8
BHIS10
BHIS42
BCDI902

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN C 900
ChainResidue
CHIS10
CHIS42
CCDI902
CASP8

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN C 902
ChainResidue
AHIS5
AGLU149
BGLU149
CHIS5
CGLU149
CHOH1001

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 900
ChainResidue
DASP8
DHIS10
DHIS42
DCDI201

site_idAC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MN D 902
ChainResidue
DHIS5
DGLU149
DHOH301
EHIS5
EGLU149
FHIS5
FGLU149

site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN E 900
ChainResidue
EASP8
EHIS10
EHIS42
ECDI902

site_idAC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN F 900
ChainResidue
FASP8
FHIS10
FHIS42
FCDI902

site_idAC9
Number of Residues12
DetailsBINDING SITE FOR RESIDUE CDI A 421
ChainResidue
AASP8
AHIS10
AALA33
AHIS34
ASER35
AHIS42
AILE57
APHE61
AASP63
AZN202
BC5P901
BGLU135

site_idBC1
Number of Residues13
DetailsBINDING SITE FOR RESIDUE C5P A 901
ChainResidue
AASP56
AGLY58
ACDI201
AHOH308
BALA100
BPRO103
BLYS104
BMET105
BLEU106
BALA131
BTHR132
BTHR133
BGLU135

site_idBC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE CDI B 421
ChainResidue
BASP8
BHIS10
BHIS34
BSER35
BHIS42
BILE57
BPHE61
BZN903
CC5P901
CGLU135

site_idBC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE C5P B 901
ChainResidue
BASP56
BGLY58
BASP63
BCDI902
BHOH1001
CALA100
CPRO103
CLYS104
CMET105
CLEU106
CALA131
CTHR132
CTHR133

site_idBC4
Number of Residues15
DetailsBINDING SITE FOR RESIDUE CDI C 421
ChainResidue
AHOH301
AGLU135
CASP8
CHIS10
CALA33
CHIS34
CSER35
CHIS42
CILE57
CGLY58
CPHE61
CASP63
CZN903
AC5P203
CHOH1004

site_idBC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE C5P C 901
ChainResidue
AALA100
APRO103
ALYS104
AMET105
ALEU106
AALA131
ATHR132
ATHR133
AGLU135
CASP56
CGLY58
CLYS59
CASP63
CCDI902
CHOH1004
AHOH301

site_idBC6
Number of Residues11
DetailsBINDING SITE FOR RESIDUE CDI D 421
ChainResidue
DASP8
DHIS10
DHIS34
DSER35
DHIS42
DILE57
DGLY58
DPHE61
DASP63
DZN202
EC5P901

site_idBC7
Number of Residues12
DetailsBINDING SITE FOR RESIDUE C5P D 901
ChainResidue
DGLY58
DASP63
DCDI201
EALA100
EPRO103
ELYS104
EMET105
ELEU106
EALA131
ETHR132
ETHR133
EGLU135

site_idBC8
Number of Residues12
DetailsBINDING SITE FOR RESIDUE CDI E 421
ChainResidue
EASP8
EHIS10
EHIS34
ESER35
EHIS42
EILE57
EPHE61
EPRO62
EASP63
EZN903
FC5P901
FGLU135

site_idBC9
Number of Residues12
DetailsBINDING SITE FOR RESIDUE C5P E 901
ChainResidue
EASP56
EGLY58
ELYS59
ECDI902
FALA100
FPRO103
FLYS104
FMET105
FLEU106
FALA131
FTHR132
FTHR133

site_idCC1
Number of Residues13
DetailsBINDING SITE FOR RESIDUE CDI F 421
ChainResidue
DGLU135
FASP8
FHIS10
FALA33
FHIS34
FSER35
FHIS42
FILE57
FGLY58
FPHE61
FASP63
FZN903
DC5P204

site_idCC2
Number of Residues12
DetailsBINDING SITE FOR RESIDUE C5P F 901
ChainResidue
DALA100
DPRO103
DLYS104
DMET105
DLEU106
DALA131
DTHR132
DTHR133
DGLU135
FASP56
FGLY58
FCDI902

site_idCC3
Number of Residues18
DetailsBINDING SITE FOR RESIDUE GPP G 903
ChainResidue
APHE7
AGLY138
APHE139
ATHR140
AARG142
AGLU149
BPHE7
BGLY138
BPHE139
BTHR140
BARG142
CPHE7
CGLY138
CPHE139
CTHR140
CARG142
CGLU149
CHOH1001

site_idCC4
Number of Residues18
DetailsBINDING SITE FOR RESIDUE GPP H 903
ChainResidue
DPHE7
DTHR134
DGLY138
DPHE139
DTHR140
DARG142
DHOH301
EPHE7
EGLY138
EPHE139
ETHR140
EARG142
EGLU149
FGLY138
FPHE139
FTHR140
FARG142
FGLU149

Functional Information from PROSITE/UniProt
site_idPS01350
Number of Residues16
DetailsISPF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. SDGDVAlHAltDAllG
ChainResidueDetails
ASER35-GLY50

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1JY8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U40","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues18
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H47","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1JY8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U40","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ESJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FBA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KNJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U43","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1U43","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues24
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11829504","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1JY8","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U40","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues36
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KNJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ESJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FBA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues18
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11997478","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GX1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16511114","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YQN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"15608374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16392111","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19320487","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3ELC","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1H48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2GZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ERN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ESJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FBA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues12
DetailsSite: {"description":"Transition state stabilizer","evidences":[{"source":"HAMAP-Rule","id":"MF_00107","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11786530","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

239149

PDB entries from 2025-07-23

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