6DT1

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
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	0006974	biological_process	DNA damage response
A	0016491	molecular_function	oxidoreductase activity
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide 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	0006974	biological_process	DNA damage response
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	Active site: {"description":"N6-AMP-lysine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10135","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---