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1V9P

Crystal Structure Of Nad+-Dependent DNA Ligase

Replaces:  1DGT
Functional Information from GO Data
ChainGOidnamespacecontents
A0003677molecular_functionDNA binding
A0003911molecular_functionDNA ligase (NAD+) activity
A0006260biological_processDNA replication
A0006281biological_processDNA repair
B0003677molecular_functionDNA binding
B0003911molecular_functionDNA ligase (NAD+) activity
B0006260biological_processDNA replication
B0006281biological_processDNA repair
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 701
ChainResidue
ACYS409
ACYS412
ACYS425
ACYS430

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 2701
ChainResidue
BCYS2409
BCYS2412
BCYS2425
BCYS2430

site_idAC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE AMP A 700
ChainResidue
AGLU116
AHIS117
ALYS118
AVAL119
AGLU174
ATYR226
AHIS256
ALYS291
ALYS315
ALEU85

site_idAC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE AMP B 2700
ChainResidue
BHOH1100
BLEU2085
BASN2087
BGLU2116
BHIS2117
BLYS2118
BVAL2119
BGLU2174
BTYR2226
BLYS2315

Functional Information from PROSITE/UniProt
site_idPS01055
Number of Residues30
DetailsDNA_LIGASE_N1 NAD-dependent DNA ligase signature 1. KVDGLSvnlyYeeGvLvfgaTRGDGevGEE
ChainResidueDetails
ALYS118-GLU147

site_idPS01056
Number of Residues16
DetailsDNA_LIGASE_N2 NAD-dependent DNA ligase signature 2. VGRTGrVTpVgvLePV
ChainResidueDetails
AVAL332-VAL347

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsActive site: {"description":"N6-AMP-lysine intermediate","evidences":[{"source":"HAMAP-Rule","id":"MF_01588","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10698952","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15268945","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues18
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01588","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"10698952","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01588","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10698952","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01588","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10698952","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1b04
ChainResidueDetails
ALYS118

site_idCSA2
Number of Residues1
DetailsAnnotated By Reference To The Literature 1b04
ChainResidueDetails
BLYS2118

site_idCSA3
Number of Residues4
DetailsAnnotated By Reference To The Literature 1b04
ChainResidueDetails
ALYS118
AARG201
AASP120
ALYS315

site_idCSA4
Number of Residues4
DetailsAnnotated By Reference To The Literature 1b04
ChainResidueDetails
BARG2201
BLYS2118
BLYS2315
BASP2120

site_idMCSA1
Number of Residues9
DetailsM-CSA 450
ChainResidueDetails
AGLU116electrostatic stabiliser
ALYS118covalent catalysis
AASP120electrostatic stabiliser
ATYR226electrostatic stabiliser
ALYS315electrostatic stabiliser
ACYS409metal ligand
ACYS412metal ligand
ACYS425metal ligand
ACYS430metal ligand

site_idMCSA2
Number of Residues9
DetailsM-CSA 450
ChainResidueDetails
BGLU2116electrostatic stabiliser
BLYS2118covalent catalysis
BASP2120electrostatic stabiliser
BTYR2226electrostatic stabiliser
BLYS2315electrostatic stabiliser
BCYS2409metal ligand
BCYS2412metal ligand
BCYS2425metal ligand
BCYS2430metal ligand

239803

PDB entries from 2025-08-06

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