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2VNP

Monoclinic form of IDI-1

Replaces:  2VEH
Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0003824molecular_functioncatalytic activity
A0004452molecular_functionisopentenyl-diphosphate delta-isomerase activity
A0005737cellular_componentcytoplasm
A0006974biological_processDNA damage response
A0008270molecular_functionzinc ion binding
A0008299biological_processisoprenoid biosynthetic process
A0016853molecular_functionisomerase activity
A0046872molecular_functionmetal ion binding
A0050992biological_processdimethylallyl diphosphate biosynthetic process
B0000287molecular_functionmagnesium ion binding
B0003824molecular_functioncatalytic activity
B0004452molecular_functionisopentenyl-diphosphate delta-isomerase activity
B0005737cellular_componentcytoplasm
B0006974biological_processDNA damage response
B0008270molecular_functionzinc ion binding
B0008299biological_processisoprenoid biosynthetic process
B0016853molecular_functionisomerase activity
B0046872molecular_functionmetal ion binding
B0050992biological_processdimethylallyl diphosphate biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN A1180
ChainResidue
AHIS25
AHIS32
AHIS69
AGLU114
AGLU116

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A1181
ChainResidue
AHOH2017
ACYS67
AGLU87
ADED1182
AHOH2008

site_idAC3
Number of Residues15
DetailsBINDING SITE FOR RESIDUE DED A1182
ChainResidue
ALYS21
AALA34
AARG51
ALYS55
ACYS67
AGLY68
AHIS69
AARG83
AGLU87
ATYR104
AGLU114
AGLU116
AMG1181
AHOH2028
AHOH2029

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN B1184
ChainResidue
BHIS25
BHIS32
BHIS69
BGLU114
BGLU116

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B1185
ChainResidue
BCYS67
BGLU87
BDED1186
BHOH2015
BHOH2025

site_idAC6
Number of Residues16
DetailsBINDING SITE FOR RESIDUE DED B1186
ChainResidue
BLYS21
BALA34
BSER36
BARG51
BLYS55
BCYS67
BGLY68
BHIS69
BARG83
BGLU87
BTYR104
BGLU114
BGLU116
BMG1185
BHOH2031
BHOH2032

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE:
ChainResidueDetails
ACYS67
AGLU116
BCYS67
BGLU116

site_idSWS_FT_FI2
Number of Residues14
DetailsBINDING:
ChainResidueDetails
ALYS21
BLYS55
BCYS67
BHIS69
BARG83
BGLU87
AARG51
ALYS55
ACYS67
AHIS69
AARG83
AGLU87
BLYS21
BARG51

site_idSWS_FT_FI3
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:12630859, ECO:0000269|PubMed:15643873
ChainResidueDetails
AHIS25
AHIS32
AGLU114
AGLU116
BHIS25
BHIS32
BGLU114
BGLU116

site_idSWS_FT_FI4
Number of Residues2
DetailsSITE: Essential for catalytic activity
ChainResidueDetails
ATYR104
BTYR104

Catalytic Information from CSA
site_idCSA1
Number of Residues4
DetailsAnnotated By Reference To The Literature 1i9a
ChainResidueDetails
ATRP161
AGLU87
AGLU116
ACYS67

site_idCSA2
Number of Residues4
DetailsAnnotated By Reference To The Literature 1i9a
ChainResidueDetails
BTRP161
BGLU87
BGLU116
BCYS67

site_idMCSA1
Number of Residues9
DetailsM-CSA 190
ChainResidueDetails
AHIS25metal ligand
AHIS32metal ligand
ACYS67hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
AHIS69metal ligand
AGLU87metal ligand
ATYR104hydrogen bond acceptor, hydrogen bond donor, proton donor
AGLU114metal ligand
AGLU116electrostatic stabiliser, hydrogen bond acceptor, metal ligand, proton acceptor, proton donor
ATRP161electrostatic stabiliser, polar/non-polar interaction

site_idMCSA2
Number of Residues9
DetailsM-CSA 190
ChainResidueDetails
BHIS25metal ligand
BHIS32metal ligand
BCYS67hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
BHIS69metal ligand
BGLU87metal ligand
BTYR104hydrogen bond acceptor, hydrogen bond donor, proton donor
BGLU114metal ligand
BGLU116electrostatic stabiliser, hydrogen bond acceptor, metal ligand, proton acceptor, proton donor
BTRP161electrostatic stabiliser, polar/non-polar interaction

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PDB entries from 2024-10-30

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