Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6DT1

Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003909	molecular_function	DNA ligase activity
A	0003910	molecular_function	DNA ligase (ATP) activity
A	0005524	molecular_function	ATP binding
A	0006260	biological_process	DNA replication
A	0006281	biological_process	DNA repair
A	0006310	biological_process	DNA recombination
A	0016491	molecular_function	oxidoreductase activity
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding
E	0003909	molecular_function	DNA ligase activity
E	0003910	molecular_function	DNA ligase (ATP) activity
E	0005524	molecular_function	ATP binding
E	0006260	biological_process	DNA replication
E	0006281	biological_process	DNA repair
E	0006310	biological_process	DNA recombination
E	0016491	molecular_function	oxidoreductase activity
E	0016874	molecular_function	ligase activity
E	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue GOL A 501

Chain	Residue
A	LYS26
A	ASP27
A	GLU29
A	LYS32
A	VAL125
A	TRP126

site_id	AC2
Number of Residues	3
Details	binding site for residue GOL A 502

Chain	Residue
A	TYR141
A	TYR335
A	LYS367

site_id	AC3
Number of Residues	3
Details	binding site for residue GOL A 503

Chain	Residue
A	TYR380
A	ASN404
D	DG32

site_id	AC4
Number of Residues	2
Details	binding site for residue GOL A 504

Chain	Residue
A	ARG170
A	GLU210

site_id	AC5
Number of Residues	8
Details	binding site for residue GOL A 505

Chain	Residue
A	ARG182
A	ARG359
A	LYS365
A	DTT512
A	HOH703
C	DG12
C	DT13
C	AMP100

site_id	AC6
Number of Residues	16
Details	binding site for residue 1PE A 506

Chain	Residue
A	TYR45
A	TYR46
A	ILE47
A	ARG79
A	THR82
A	GLY83
A	ALA86
A	ASN262
A	LYS266
B	DG7
B	DC8
B	DG9
D	DG35
D	DC36
D	DA37
D	DT38

site_id	AC7
Number of Residues	3
Details	binding site for residue GOL A 507

Chain	Residue
A	GLU89
A	TYR93
A	ASP96

site_id	AC8
Number of Residues	9
Details	binding site for residue GOL A 508

Chain	Residue
A	SER407
A	GLY408
A	LEU409
A	ARG422
A	HOH607
C	DC14
C	DG15
D	DG29
D	DA30

site_id	AC9
Number of Residues	4
Details	binding site for residue GOL A 509

Chain	Residue
A	ARG297
A	LEU354
A	GLU356
A	ASN362

site_id	AD1
Number of Residues	3
Details	binding site for residue GOL A 510

Chain	Residue
A	GLY189
A	GLY267
A	ILE269

site_id	AD2
Number of Residues	6
Details	binding site for residue GOL A 511

Chain	Residue
A	GLU195
A	GLY414
A	VAL415
A	ARG424
A	GLU427
A	ASN428

site_id	AD3
Number of Residues	6
Details	binding site for residue DTT A 512

Chain	Residue
A	ARG41
A	ARG182
A	GOL505
A	HOH697
A	HOH703
B	DOC11

site_id	AD4
Number of Residues	2
Details	binding site for residue DTT A 513

Chain	Residue
A	GLU195
A	TYR432

site_id	AD5
Number of Residues	6
Details	binding site for residue GOL A 514

Chain	Residue
A	GLN44
A	LYS48
A	ARG111
A	CL516
B	DC8
B	HOH502

site_id	AD6
Number of Residues	3
Details	binding site for residue GOL A 515

Chain	Residue
A	SER118
D	DC28
D	DG29

site_id	AD7
Number of Residues	1
Details	binding site for residue CL A 516

Chain	Residue
A	GOL514

site_id	AD8
Number of Residues	7
Details	binding site for residue MG A 517

Chain	Residue
A	GLU217
A	HOH616
A	HOH639
B	DOC11
C	DG12
C	AMP100
C	HOH204

site_id	AD9
Number of Residues	1
Details	binding site for residue CL E 502

Chain	Residue
E	LYS367

site_id	AE1
Number of Residues	7
Details	binding site for residue DTT B 401

Chain	Residue
B	DC8
B	DG9
B	DT10
B	HOH503
B	HOH516
B	HOH519
D	DTT402

site_id	AE2
Number of Residues	17
Details	binding site for residue AMP C 100

Chain	Residue
A	ALA160
A	ARG164
A	ARG182
A	GLU217
A	TRP282
A	ILE347
A	LYS349
A	LYS365
A	LYS367
A	GOL505
A	MG517
A	HOH628
C	DG12
C	HOH204
A	GLN157
A	LEU158
A	LYS159

site_id	AE3
Number of Residues	6
Details	binding site for residue DTT D 401

Chain	Residue
A	THR15
C	DC18
C	DT19
D	DG25
D	DT26
D	DC27

site_id	AE4
Number of Residues	5
Details	binding site for residue DTT D 402

Chain	Residue
A	ARG383
B	DTT401
D	DG32
D	DA33
D	HOH502

site_id	AE5
Number of Residues	24
Details	binding site for Di-nucleotide AMP E 501 and DG G 12

Chain	Residue
E	ILE9
E	ALA10
E	SER11
E	GLY13
E	SER14
E	GLN17
E	LYS18
E	GLN157
E	LEU158
E	LYS159
E	ALA160
E	ARG164
E	ARG182
E	GLU217
E	TRP282
E	ILE347
E	LYS349
E	LYS365
E	LYS367
E	LEU458
F	DOC11
G	DT13
H	DC31
H	DG32

site_id	AE6
Number of Residues	11
Details	binding site for Di-nucleotide DT F 10 and DOC F 11

Chain	Residue
E	GLY162
E	ARG164
E	SER181
E	ALA183
E	ASN185
E	ASN258
E	PHE457
F	DG9
G	DG12
H	DG32
H	DA33

Functional Information from PROSITE/UniProt

site_id	PS00333
Number of Residues	24
Details	DNA_LIGASE_A2 ATP-dependent DNA ligase signature 2. EGIILKnidgl...WEnars..Knly..KFK

Chain	Residue	Details
A	GLU344-LYS367

site_id	PS00697
Number of Residues	9
Details	DNA_LIGASE_A1 ATP-dependent DNA ligase AMP-binding site. QLKADGARC

Chain	Residue	Details
A	GLN157-CYS165

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: N6-AMP-lysine intermediate => ECO:0000255\|PROSITE-ProRule:PRU10135

Chain	Residue	Details
A	LYS159
E	LYS159

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	ARG164
E	GLU344
E	ARG359
E	LYS365
A	ARG182
A	GLU217
A	GLU344
A	ARG359
A	LYS365
E	ARG164
E	ARG182
E	GLU217

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)