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5D4B

Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination

Functional Information from GO Data
ChainGOidnamespacecontents
A0003677molecular_functionDNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0006281biological_processDNA repair
A0016779molecular_functionnucleotidyltransferase activity
A0034061molecular_functionDNA polymerase activity
B0003677molecular_functionDNA binding
B0003887molecular_functionDNA-directed DNA polymerase activity
B0006281biological_processDNA repair
B0016779molecular_functionnucleotidyltransferase activity
B0034061molecular_functionDNA polymerase activity
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue MG A 601
ChainResidue
AASP343
AASP345
CDC6
CSO4401

site_idAC2
Number of Residues4
Detailsbinding site for residue NA A 602
ChainResidue
ATHR253
AVAL255
AVAL258
CDA4

site_idAC3
Number of Residues3
Detailsbinding site for residue SO4 A 603
ChainResidue
AMET339
ATHR340
ALYS338

site_idAC4
Number of Residues6
Detailsbinding site for residue SO4 A 604
ChainResidue
ALYS469
AARG480
BSER207
BLYS209
BGLU467
BARG468

site_idAC5
Number of Residues5
Detailsbinding site for residue MG B 601
ChainResidue
BASP343
BASP345
BSO4603
BHOH702
DDC6

site_idAC6
Number of Residues4
Detailsbinding site for residue NA B 602
ChainResidue
BTHR253
BVAL255
BVAL258
DDA4

site_idAC7
Number of Residues8
Detailsbinding site for residue SO4 B 603
ChainResidue
BGLY332
BGLY333
BARG336
BASP345
BMG601
BHOH702
BHOH707
DDC6

site_idAC8
Number of Residues3
Detailsbinding site for residue SO4 B 604
ChainResidue
BLYS338
BMET339
BTHR340

site_idAC9
Number of Residues2
Detailsbinding site for residue SO4 B 605
ChainResidue
ALYS426
BLYS426

site_idAD1
Number of Residues5
Detailsbinding site for residue SO4 B 606
ChainResidue
BASN184
BGLU185
BGLY186
BSER187
EDA1

site_idAD2
Number of Residues8
Detailsbinding site for residue SO4 C 401
ChainResidue
AGLY332
AGLY333
AARG336
ALYS338
AASP345
AMG601
CDC6
CHOH503

site_idAD3
Number of Residues4
Detailsbinding site for residue SO4 C 402
ChainResidue
CDA5
CDC6
CHOH501
CHOH502

Functional Information from PROSITE/UniProt
site_idPS00522
Number of Residues20
DetailsDNA_POLYMERASE_X DNA polymerase family X signature. GGFrRGkmtGhDVDFLItsP
ChainResidueDetails
AGLY332-PRO351

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsBINDING: BINDING => ECO:0000305, ECO:0007744|PDB:4I2B, ECO:0007744|PDB:4I2C, ECO:0007744|PDB:4I2D, ECO:0007744|PDB:4I2E
ChainResidueDetails
AGLY333
AHIS342
AGLY449
BGLY333
BHIS342
BGLY449

site_idSWS_FT_FI2
Number of Residues6
DetailsBINDING: BINDING => ECO:0000305, ECO:0007744|PDB:1JMS, ECO:0007744|PDB:4I2B
ChainResidueDetails
AASP343
AASP345
AASP434
BASP343
BASP345
BASP434

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:21183079
ChainResidueDetails
ASER134
BSER134

Catalytic Information from CSA
site_idMCSA1
Number of Residues3
DetailsM-CSA 632
ChainResidueDetails
AASP343metal ligand
AASP345metal ligand
AASP434metal ligand, proton acceptor, proton donor

site_idMCSA2
Number of Residues3
DetailsM-CSA 632
ChainResidueDetails
BASP343metal ligand
BASP345metal ligand
BASP434metal ligand, proton acceptor, proton donor

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PDB entries from 2024-07-17

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