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3GDE

The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0003677molecular_functionDNA binding
A0003909molecular_functionDNA ligase activity
A0003910molecular_functionDNA ligase (ATP) activity
A0005524molecular_functionATP binding
A0006260biological_processDNA replication
A0006273biological_processlagging strand elongation
A0006281biological_processDNA repair
A0006310biological_processDNA recombination
A0006974biological_processDNA damage response
A0016874molecular_functionligase activity
A0046872molecular_functionmetal ion binding
A0051301biological_processcell division
A0071897biological_processDNA biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PO4 A 556
ChainResidue
AARG269
AARG411
ALYS417
APO4557
AHOH586
AHOH587
AHOH692
AHOH890
AHOH893

site_idAC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 A 557
ChainResidue
ALYS249
AGLU395
ALYS417
ALYS419
AGLU423
APO4556
APO4558
AHOH870
AHOH971
AHOH1012

site_idAC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PO4 A 558
ChainResidue
AARG528
ALYS531
APO4557
AHOH730
AHOH890
AHOH904
AHOH990
AHOH1012

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PO4 A 559
ChainResidue
AGLN311
AARG526
AHOH748
AHOH866

Functional Information from PROSITE/UniProt
site_idPS00333
Number of Residues25
DetailsDNA_LIGASE_A2 ATP-dependent DNA ligase signature 2. EGVMIKlpssp...YIpgkrg.Knwl..KVK
ChainResidueDetails
AGLU395-LYS419

site_idPS00697
Number of Residues9
DetailsDNA_LIGASE_A1 ATP-dependent DNA ligase AMP-binding site. EWKFDGSRV
ChainResidueDetails
AGLU247-VAL255

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"N6-AMP-lysine intermediate","evidences":[{"source":"HAMAP-Rule","id":"MF_00407","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues7
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00407","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1a0i
ChainResidueDetails
ALYS249

246704

PDB entries from 2025-12-24

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