Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5ITY

Crystal Structure of Human NEIL1(P2G) bound to duplex DNA containing Thymine Glycol

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0005737	cellular_component	cytoplasm
A	0005813	cellular_component	centrosome
A	0005829	cellular_component	cytosol
A	0005856	cellular_component	cytoskeleton
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006287	biological_process	base-excision repair, gap-filling
A	0006979	biological_process	response to oxidative stress
A	0008270	molecular_function	zinc ion binding
A	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
A	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
A	0016829	molecular_function	lyase activity
A	0019104	molecular_function	DNA N-glycosylase activity
A	0032074	biological_process	negative regulation of nuclease activity
A	0045008	biological_process	depyrimidination
A	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003684	molecular_function	damaged DNA binding
B	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005694	cellular_component	chromosome
B	0005737	cellular_component	cytoplasm
B	0005813	cellular_component	centrosome
B	0005829	cellular_component	cytosol
B	0005856	cellular_component	cytoskeleton
B	0006281	biological_process	DNA repair
B	0006284	biological_process	base-excision repair
B	0006287	biological_process	base-excision repair, gap-filling
B	0006979	biological_process	response to oxidative stress
B	0008270	molecular_function	zinc ion binding
B	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
B	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
B	0016829	molecular_function	lyase activity
B	0019104	molecular_function	DNA N-glycosylase activity
B	0032074	biological_process	negative regulation of nuclease activity
B	0045008	biological_process	depyrimidination
B	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003684	molecular_function	damaged DNA binding
C	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005694	cellular_component	chromosome
C	0005737	cellular_component	cytoplasm
C	0005813	cellular_component	centrosome
C	0005829	cellular_component	cytosol
C	0005856	cellular_component	cytoskeleton
C	0006281	biological_process	DNA repair
C	0006284	biological_process	base-excision repair
C	0006287	biological_process	base-excision repair, gap-filling
C	0006979	biological_process	response to oxidative stress
C	0008270	molecular_function	zinc ion binding
C	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
C	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
C	0016829	molecular_function	lyase activity
C	0019104	molecular_function	DNA N-glycosylase activity
C	0032074	biological_process	negative regulation of nuclease activity
C	0045008	biological_process	depyrimidination
C	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue GOL B 501

Chain	Residue
A	ALA51
B	LEU138
B	GLN139
B	GLU140
B	TYR141

site_id	AC2
Number of Residues	23
Details	binding site for Di-nucleotide DA D 296 and CTG D 297

Chain	Residue
A	ARG118
A	ASN176
A	TYR177
A	ARG242
A	PHE256
A	ARG257
A	TYR263
A	ARG277
A	THR278
A	HOH604
D	DC295
D	DG298
D	DT312
D	DG313
D	HOH402
D	HOH406
D	HOH407
D	HOH410
D	HOH417
A	GLY2
A	GLU3
A	GLU6
A	MET81

site_id	AC3
Number of Residues	24
Details	binding site for Di-nucleotide CTG D 297 and DG D 298

Chain	Residue
A	GLY2
A	GLU3
A	GLU6
A	LYS54
A	GLY80
A	MET81
A	PHE120
A	GLY175
A	ASN176
A	TYR177
A	ARG242
A	PHE256
A	ARG257
A	TYR263
A	ARG277
A	HOH548
A	HOH604
D	DA296
D	DT299
D	DA309
D	DC310
D	HOH402
D	HOH405
D	HOH406

site_id	AC4
Number of Residues	18
Details	binding site for Di-nucleotide DA E 296 and CTG E 297

Chain	Residue
B	GLY2
B	GLU3
B	GLU6
B	MET81
B	ARG118
B	ASN176
B	TYR177
B	ARG242
B	PHE256
B	TYR263
B	ARG277
B	THR278
B	HOH658
E	DC295
E	DG298
E	DT312
E	DG313
E	HOH405

site_id	AC5
Number of Residues	20
Details	binding site for Di-nucleotide CTG E 297 and DG E 298

Chain	Residue
B	GLY2
B	GLU3
B	GLU6
B	LYS54
B	MET81
B	PHE120
B	GLY175
B	ASN176
B	TYR177
B	ARG242
B	PHE256
B	TYR263
B	ARG277
B	HOH658
B	HOH669
E	DA296
E	DT299
E	DA309
E	DC310
E	HOH405

site_id	AC6
Number of Residues	14
Details	binding site for Di-nucleotide DA F 296 and CTG F 297

Chain	Residue
C	THR278
F	DC295
F	DG298
F	DT312
F	DG313
C	GLY2
C	GLU3
C	GLU6
C	MET81
C	ARG118
C	ASN176
C	TYR177
C	TYR263
C	ARG277

site_id	AC7
Number of Residues	16
Details	binding site for Di-nucleotide CTG F 297 and DG F 298

Chain	Residue
C	GLY2
C	GLU3
C	GLU6
C	LYS54
C	GLY80
C	MET81
C	PHE120
C	GLY175
C	ASN176
C	TYR177
C	TYR263
C	ARG277
F	DA296
F	DT299
F	DA309
F	DC310

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: Schiff-base intermediate with DNA => ECO:0000305

Chain	Residue	Details
A	GLY2
B	GLY2
C	GLY2

site_id	SWS_FT_FI2
Number of Residues	3
Details	ACT_SITE: Proton donor => ECO:0000305

Chain	Residue	Details
A	GLU3
B	GLU3
C	GLU3

site_id	SWS_FT_FI3
Number of Residues	3
Details	ACT_SITE: Proton donor; for beta-elimination activity => ECO:0000305

Chain	Residue	Details
A	LYS54
B	LYS54
C	LYS54

site_id	SWS_FT_FI4
Number of Residues	3
Details	ACT_SITE: Proton donor; for delta-elimination activity => ECO:0000305

Chain	Residue	Details
A	ARG339
B	ARG339
C	ARG339

site_id	SWS_FT_FI5
Number of Residues	6
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	ASN176
A	ARG339
B	ASN176
B	ARG339
C	ASN176
C	ARG339

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