Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

4YDU

Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP

Replaces:  4WOS
Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0000408cellular_componentEKC/KEOPS complex
A0002949biological_processtRNA threonylcarbamoyladenosine modification
A0005506molecular_functioniron ion binding
A0005515molecular_functionprotein binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006400biological_processtRNA modification
A0008033biological_processtRNA processing
A0016746molecular_functionacyltransferase activity
A0016747molecular_functionacyltransferase activity, transferring groups other than amino-acyl groups
A0042802molecular_functionidentical protein binding
A0046872molecular_functionmetal ion binding
A0061711molecular_functionN(6)-L-threonylcarbamoyladenine synthase activity
A0070525biological_processtRNA threonylcarbamoyladenosine metabolic process
A0140032molecular_functionglycosylation-dependent protein binding
A1990145biological_processmaintenance of translational fidelity
B0000287molecular_functionmagnesium ion binding
B0000408cellular_componentEKC/KEOPS complex
B0002949biological_processtRNA threonylcarbamoyladenosine modification
B0005506molecular_functioniron ion binding
B0005515molecular_functionprotein binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006400biological_processtRNA modification
B0008033biological_processtRNA processing
B0016746molecular_functionacyltransferase activity
B0016747molecular_functionacyltransferase activity, transferring groups other than amino-acyl groups
B0042802molecular_functionidentical protein binding
B0046872molecular_functionmetal ion binding
B0061711molecular_functionN(6)-L-threonylcarbamoyladenine synthase activity
B0070525biological_processtRNA threonylcarbamoyladenosine metabolic process
B0140032molecular_functionglycosylation-dependent protein binding
B1990145biological_processmaintenance of translational fidelity
C0000408cellular_componentEKC/KEOPS complex
C0002949biological_processtRNA threonylcarbamoyladenosine modification
C0005515molecular_functionprotein binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0008033biological_processtRNA processing
C0008237molecular_functionmetallopeptidase activity
C0042802molecular_functionidentical protein binding
C1990145biological_processmaintenance of translational fidelity
D0000408cellular_componentEKC/KEOPS complex
D0002949biological_processtRNA threonylcarbamoyladenosine modification
D0005515molecular_functionprotein binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0008033biological_processtRNA processing
D0008237molecular_functionmetallopeptidase activity
D0042802molecular_functionidentical protein binding
D1990145biological_processmaintenance of translational fidelity
Functional Information from PDB Data
site_idAC1
Number of Residues20
Detailsbinding site for residue ADP A 401
ChainResidue
AHIS111
AASN272
ATHR299
AASP300
AFE403
AHOH522
AHOH531
AHOH565
AHOH569
AHOH580
AHOH592
AHIS115
AHOH604
ASER136
AGLY137
AGLY163
AASP167
APRO181
AGLY268
AVAL269

site_idAC2
Number of Residues5
Detailsbinding site for residue MG A 402
ChainResidue
AASP11
AGLU12
AHOH580
AHOH586
AHOH604

site_idAC3
Number of Residues4
Detailsbinding site for residue FE A 403
ChainResidue
AHIS111
AHIS115
AASP300
AADP401

site_idAC4
Number of Residues3
Detailsbinding site for residue ACT A 404
ChainResidue
AMET310
AVAL311
ALYS314

site_idAC5
Number of Residues2
Detailsbinding site for residue ACT A 405
ChainResidue
BTHR318
BALA319

site_idAC6
Number of Residues2
Detailsbinding site for residue ACT A 406
ChainResidue
AHOH514
BASP103

site_idAC7
Number of Residues3
Detailsbinding site for residue ACT A 407
ChainResidue
APHE100
AALA101
CLEU53

site_idAC8
Number of Residues20
Detailsbinding site for residue ADP B 401
ChainResidue
BHIS111
BHIS115
BSER136
BGLY137
BGLY163
BASP167
BGLY180
BGLY268
BVAL269
BASN272
BTHR299
BASP300
BFE403
BHOH525
BHOH559
BHOH566
BHOH573
BHOH606
BHOH607
BHOH608

site_idAC9
Number of Residues4
Detailsbinding site for residue MG B 402
ChainResidue
BASP11
BGLU12
BHOH605
BHOH606

site_idAD1
Number of Residues4
Detailsbinding site for residue FE B 403
ChainResidue
BHIS111
BHIS115
BASP300
BADP401

site_idAD2
Number of Residues4
Detailsbinding site for residue ACT B 404
ChainResidue
BPRO205
BARG253
BACT405
BHOH620

site_idAD3
Number of Residues3
Detailsbinding site for residue ACT B 405
ChainResidue
BTHR202
BPRO205
BACT404

site_idAD4
Number of Residues12
Detailsbinding site for residue ADP C 301
ChainResidue
AVAL85
CARG32
CGLU33
CHIS34
CTHR35
CSER67
CILE73
CARG118
CACT302
CHOH422
CHOH425
CHOH426

site_idAD5
Number of Residues2
Detailsbinding site for residue ACT C 302
ChainResidue
CARG32
CADP301

site_idAD6
Number of Residues5
Detailsbinding site for residue ACT C 303
ChainResidue
CALA108
CTHR109
CARG110
CGLU159
CVAL161

site_idAD7
Number of Residues15
Detailsbinding site for residue ADP D 301
ChainResidue
DSER67
DTHR69
DILE73
DARG118
DACT304
DHOH433
DHOH446
DHOH457
DHOH466
BVAL85
BHOH615
DARG32
DGLU33
DHIS34
DTHR35

site_idAD8
Number of Residues5
Detailsbinding site for residue ACT D 302
ChainResidue
DVAL143
DLEU218
DASN220
DASN221
DHOH493

site_idAD9
Number of Residues4
Detailsbinding site for residue ACT D 303
ChainResidue
DTHR109
DARG110
DGLU159
DVAL161

site_idAE1
Number of Residues2
Detailsbinding site for residue ACT D 304
ChainResidue
DARG32
DADP301

site_idAE2
Number of Residues7
Detailsbinding site for residue ACT D 305
ChainResidue
DGLY66
DPHE68
DALA117
DTYR123
DARG219
DHOH457
DHOH497

site_idAE3
Number of Residues8
Detailsbinding site for residue ACT D 306
ChainResidue
BVAL52
BARG53
BPRO57
BHOH586
DGLN79
DGLU211
DALA213
DHOH477

Functional Information from PROSITE/UniProt
site_idPS01016
Number of Residues21
DetailsGLYCOPROTEASE Glycoprotease family signature. RSlafaWDvPaIpvhHmeGHL
ChainResidueDetails
AARG96-LEU116

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues14
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01445
ChainResidueDetails
AHIS111
BLEU134
BASP167
BGLY180
BASN272
BASP300
AHIS115
ALEU134
AASP167
AGLY180
AASN272
AASP300
BHIS111
BHIS115

219140

PDB entries from 2024-05-01

PDB statisticsPDBj update infoContact PDBjnumon