English 日本語简体中文繁體中文 한국어

✖

Menu

RCSB PDB PDBe BMRB Adv. Search Search help

Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4LND

Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003824	molecular_function	catalytic activity
A	0004518	molecular_function	nuclease activity
A	0004519	molecular_function	endonuclease activity
A	0006281	biological_process	DNA repair
B	0003677	molecular_function	DNA binding
B	0003824	molecular_function	catalytic activity
B	0004518	molecular_function	nuclease activity
B	0004519	molecular_function	endonuclease activity
B	0006281	biological_process	DNA repair
C	0003677	molecular_function	DNA binding
C	0003824	molecular_function	catalytic activity
C	0004518	molecular_function	nuclease activity
C	0004519	molecular_function	endonuclease activity
C	0006281	biological_process	DNA repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 401

Chain	Residue
A	ASP70
A	GLU96
A	HOH501
A	HOH502
A	HOH503
A	HOH504

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 401

Chain	Residue
B	HOH502
B	HOH503
B	HOH504
B	ASP70
B	GLU96
B	HOH501

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 401

Chain	Residue
C	ASP70
C	GLU96
C	HOH501
C	HOH502
C	HOH503
C	HOH504

Functional Information from PROSITE/UniProt

site_id	PS00726
Number of Residues	10
Details	AP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK

Chain	Residue	Details
A	PRO89-LYS98

site_id	PS00727
Number of Residues	17
Details	AP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW

Chain	Residue	Details
A	ASP251-TRP267

site_id	PS00728
Number of Residues	12
Details	AP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS

Chain	Residue	Details
A	ASN277-SER288

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: ACT_SITE => ECO:0000269\|PubMed:15380100

Chain	Residue	Details
A	TYR171
B	TYR171
C	TYR171

site_id	SWS_FT_FI2
Number of Residues	3
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269\|PubMed:9351835, ECO:0007744\|PDB:1BIX

Chain	Residue	Details
A	ASP210
B	ASP210
C	ASP210

site_id	SWS_FT_FI3
Number of Residues	3
Details	ACT_SITE: Proton acceptor => ECO:0000255\|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	HIS309
B	HIS309
C	HIS309

site_id	SWS_FT_FI4
Number of Residues	18
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	ASN68
B	ASN212
B	ASP308
B	HIS309
C	ASN68
C	GLU96
C	ASP210
C	ASN212
C	ASP308
C	HIS309
A	GLU96
A	ASP210
A	ASN212
A	ASP308
A	HIS309
B	ASN68
B	GLU96
B	ASP210

site_id	SWS_FT_FI5
Number of Residues	3
Details	SITE: Transition state stabilizer => ECO:0000269\|PubMed:8932375

Chain	Residue	Details
A	ASN212
B	ASN212
C	ASN212

site_id	SWS_FT_FI6
Number of Residues	3
Details	SITE: Important for catalytic activity => ECO:0000269\|PubMed:21762700, ECO:0000269\|PubMed:9804799

Chain	Residue	Details
A	ASP283
B	ASP283
C	ASP283

site_id	SWS_FT_FI7
Number of Residues	3
Details	SITE: Interaction with DNA substrate

Chain	Residue	Details
A	HIS309
B	HIS309
C	HIS309

site_id	SWS_FT_FI8
Number of Residues	3
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER54
B	SER54
C	SER54

site_id	SWS_FT_FI9
Number of Residues	6
Details	MOD_RES: S-nitrosocysteine; alternate => ECO:0000269\|PubMed:17403694

Chain	Residue	Details
A	CYS65
A	CYS93
B	CYS65
B	CYS93
C	CYS65
C	CYS93

site_id	SWS_FT_FI10
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS197
B	LYS197
C	LYS197

site_id	SWS_FT_FI11
Number of Residues	3
Details	MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250\|UniProtKB:P28352

Chain	Residue	Details
A	THR233
B	THR233
C	THR233

site_id	SWS_FT_FI12
Number of Residues	3
Details	MOD_RES: S-nitrosocysteine => ECO:0000269\|PubMed:17403694

Chain	Residue	Details
A	CYS310
B	CYS310
C	CYS310

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
A	ASP70	metal ligand
A	GLU96	metal ligand
A	TYR171	electrostatic stabiliser, metal ligand
A	ASP210	increase nucleophilicity, metal ligand, proton acceptor
A	ASN212
A	ASP283	electrostatic stabiliser
A	ASP308	metal ligand
A	HIS309	electrostatic stabiliser, metal ligand

site_id	MCSA2
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
B	ASP70	metal ligand
B	GLU96	metal ligand
B	TYR171	electrostatic stabiliser, metal ligand
B	ASP210	increase nucleophilicity, metal ligand, proton acceptor
B	ASN212
B	ASP283	electrostatic stabiliser
B	ASP308	metal ligand
B	HIS309	electrostatic stabiliser, metal ligand

site_id	MCSA3
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
C	ASP70	metal ligand
C	GLU96	metal ligand
C	TYR171	electrostatic stabiliser, metal ligand
C	ASP210	increase nucleophilicity, metal ligand, proton acceptor
C	ASN212
C	ASP283	electrostatic stabiliser
C	ASP308	metal ligand
C	HIS309	electrostatic stabiliser, metal ligand

237423

PDB entries from 2025-06-11

PDB statistics

PDBj update info

Contact PDBj

numon