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5LNR

Crystal structure of Arabidopsis thaliana Pdx1-PLP complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0005515molecular_functionprotein binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0005886cellular_componentplasma membrane
A0006520biological_processamino acid metabolic process
A0006979biological_processresponse to oxidative stress
A0006982biological_processresponse to lipid hydroperoxide
A0009651biological_processresponse to salt stress
A0010224biological_processresponse to UV-B
A0010335biological_processresponse to non-ionic osmotic stress
A0012505cellular_componentendomembrane system
A0015994biological_processchlorophyll metabolic process
A0016829molecular_functionlyase activity
A0036381molecular_functionpyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
A0042538biological_processhyperosmotic salinity response
A0042803molecular_functionprotein homodimerization activity
A0042819biological_processvitamin B6 biosynthetic process
A0042823biological_processpyridoxal phosphate biosynthetic process
A0046982molecular_functionprotein heterodimerization activity
B0005515molecular_functionprotein binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0005886cellular_componentplasma membrane
B0006520biological_processamino acid metabolic process
B0006979biological_processresponse to oxidative stress
B0006982biological_processresponse to lipid hydroperoxide
B0009651biological_processresponse to salt stress
B0010224biological_processresponse to UV-B
B0010335biological_processresponse to non-ionic osmotic stress
B0012505cellular_componentendomembrane system
B0015994biological_processchlorophyll metabolic process
B0016829molecular_functionlyase activity
B0036381molecular_functionpyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
B0042538biological_processhyperosmotic salinity response
B0042803molecular_functionprotein homodimerization activity
B0042819biological_processvitamin B6 biosynthetic process
B0042823biological_processpyridoxal phosphate biosynthetic process
B0046982molecular_functionprotein heterodimerization activity
C0005515molecular_functionprotein binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0005886cellular_componentplasma membrane
C0006520biological_processamino acid metabolic process
C0006979biological_processresponse to oxidative stress
C0006982biological_processresponse to lipid hydroperoxide
C0009651biological_processresponse to salt stress
C0010224biological_processresponse to UV-B
C0010335biological_processresponse to non-ionic osmotic stress
C0012505cellular_componentendomembrane system
C0015994biological_processchlorophyll metabolic process
C0016829molecular_functionlyase activity
C0036381molecular_functionpyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
C0042538biological_processhyperosmotic salinity response
C0042803molecular_functionprotein homodimerization activity
C0042819biological_processvitamin B6 biosynthetic process
C0042823biological_processpyridoxal phosphate biosynthetic process
C0046982molecular_functionprotein heterodimerization activity
D0005515molecular_functionprotein binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0005886cellular_componentplasma membrane
D0006520biological_processamino acid metabolic process
D0006979biological_processresponse to oxidative stress
D0006982biological_processresponse to lipid hydroperoxide
D0009651biological_processresponse to salt stress
D0010224biological_processresponse to UV-B
D0010335biological_processresponse to non-ionic osmotic stress
D0012505cellular_componentendomembrane system
D0015994biological_processchlorophyll metabolic process
D0016829molecular_functionlyase activity
D0036381molecular_functionpyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
D0042538biological_processhyperosmotic salinity response
D0042803molecular_functionprotein homodimerization activity
D0042819biological_processvitamin B6 biosynthetic process
D0042823biological_processpyridoxal phosphate biosynthetic process
D0046982molecular_functionprotein heterodimerization activity
Functional Information from PDB Data
site_idAC1
Number of Residues14
Detailsbinding site for residue PLP A 401
ChainResidue
AHIS132
AHOH869
AHOH906
AHOH923
AHOH929
DLYS204
AARG147
AGLU151
AARG154
AARG155
ALYS166
AHOH809
AHOH818
AHOH824

site_idAC2
Number of Residues8
Detailsbinding site for residue GOL A 402
ChainResidue
AASP41
ALYS98
AVAL251
AGLY252
AHOH850
AHOH859
AHOH986
AHOH989

site_idAC3
Number of Residues5
Detailsbinding site for residue GOL A 403
ChainResidue
AASP197
AHOH940
CGLN243
DPHE104
DASN137

site_idAC4
Number of Residues9
Detailsbinding site for residue GOL B 402
ChainResidue
BASP41
BLYS98
BVAL251
BGLY252
BHOH845
BHOH906
BHOH953
BHOH971
BHOH990

site_idAC5
Number of Residues8
Detailsbinding site for residue GOL B 403
ChainResidue
BASP197
BHOH837
BHOH966
CPHE104
CASN137
DGLN243
DHOH859
DHOH1020

site_idAC6
Number of Residues8
Detailsbinding site for residue GOL C 402
ChainResidue
AGLN243
BPHE104
BASN137
CASP197
CHOH820
CHOH940
CHOH1000
CHOH1009

site_idAC7
Number of Residues9
Detailsbinding site for residue GOL C 403
ChainResidue
CASP41
CLYS98
CVAL251
CGLY252
CHOH826
CHOH854
CHOH930
CHOH935
CHOH963

site_idAC8
Number of Residues7
Detailsbinding site for residue GOL D 402
ChainResidue
APHE104
AASN137
BGLN243
BHOH1023
DASP197
DHOH810
DHOH892

site_idAC9
Number of Residues7
Detailsbinding site for residue GOL D 403
ChainResidue
DASP41
DLYS98
DGLY252
DHOH855
DHOH907
DHOH948
DHOH949

site_idAD1
Number of Residues20
Detailsbinding site for Di-peptide PLP B 401 and LYS B 166
ChainResidue
BGLU122
BHIS132
BCYS146
BARG147
BGLU151
BARG154
BARG155
BTHR165
BGLY167
BGLU168
BALA229
BHOH808
BHOH813
BHOH817
BHOH824
BHOH896
BHOH900
BHOH905
BHOH921
CLYS204

site_idAD2
Number of Residues21
Detailsbinding site for Di-peptide PLP C 401 and LYS C 166
ChainResidue
CARG147
CGLU151
CARG154
CARG155
CTHR165
CGLY167
CGLU168
CHIS180
CALA229
CHOH808
CHOH827
CHOH828
CHOH833
CHOH876
CHOH877
CHOH906
CHOH909
BLYS204
CGLU122
CHIS132
CCYS146

site_idAD3
Number of Residues21
Detailsbinding site for Di-peptide PLP D 401 and LYS D 166
ChainResidue
ALYS204
DGLU122
DHIS132
DCYS146
DARG147
DGLU151
DARG154
DARG155
DTHR165
DGLY167
DGLU168
DALA229
DGLY230
DHOH805
DHOH838
DHOH841
DHOH886
DHOH890
DHOH895
DHOH905
DHOH920

Functional Information from PROSITE/UniProt
site_idPS01235
Number of Residues19
DetailsPDXS_SNZ_1 PdxS/SNZ family signature. LPVVQFAAGGVATPADAAL
ChainResidueDetails
ALEU222-LEU240

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Schiff-base intermediate with D-ribose 5-phosphate => ECO:0000250|UniProtKB:O59080
ChainResidueDetails
ALYS98
BLYS98
CLYS98
DLYS98

site_idSWS_FT_FI2
Number of Residues16
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:O59080
ChainResidueDetails
AASP41
CGLY170
CGLY231
CGLY252
DASP41
DGLY170
DGLY231
DGLY252
AGLY170
AGLY231
AGLY252
BASP41
BGLY170
BGLY231
BGLY252
CASP41

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:Q03148
ChainResidueDetails
AARG182
BARG182
CARG182
DARG182

site_idSWS_FT_FI4
Number of Residues4
DetailsMOD_RES: N-acetylmethionine => ECO:0007744|PubMed:22223895
ChainResidueDetails
AMET2
BMET2
CMET2
DMET2

226707

PDB entries from 2024-10-30

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