Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4F5R

Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001701	biological_process	in utero embryonic development
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
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	0005737	cellular_component	cytoplasm
A	0005874	cellular_component	microtubule
A	0005876	cellular_component	spindle microtubule
A	0006259	biological_process	DNA metabolic process
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated DNA replication
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006287	biological_process	base-excision repair, gap-filling
A	0006290	biological_process	pyrimidine dimer repair
A	0006297	biological_process	nucleotide-excision repair, DNA gap filling
A	0006303	biological_process	double-strand break repair via nonhomologous end joining
A	0006915	biological_process	apoptotic process
A	0006954	biological_process	inflammatory response
A	0006974	biological_process	DNA damage response
A	0007435	biological_process	salivary gland morphogenesis
A	0008017	molecular_function	microtubule binding
A	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
A	0010332	biological_process	response to gamma radiation
A	0016445	biological_process	somatic diversification of immunoglobulins
A	0016446	biological_process	somatic hypermutation of immunoglobulin genes
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016829	molecular_function	lyase activity
A	0019899	molecular_function	enzyme binding
A	0032991	cellular_component	protein-containing complex
A	0034061	molecular_function	DNA polymerase activity
A	0045471	biological_process	response to ethanol
A	0046872	molecular_function	metal ion binding
A	0048535	biological_process	lymph node development
A	0048536	biological_process	spleen development
A	0048872	biological_process	homeostasis of number of cells
A	0051402	biological_process	neuron apoptotic process
A	0051575	molecular_function	5'-deoxyribose-5-phosphate lyase activity
A	0055093	biological_process	response to hyperoxia
A	0071707	biological_process	immunoglobulin heavy chain V-D-J recombination
A	0071897	biological_process	DNA biosynthetic process
A	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0001701	biological_process	in utero embryonic development
B	0003677	molecular_function	DNA binding
B	0003684	molecular_function	damaged DNA binding
B	0003887	molecular_function	DNA-directed DNA polymerase activity
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	0005737	cellular_component	cytoplasm
B	0005874	cellular_component	microtubule
B	0005876	cellular_component	spindle microtubule
B	0006259	biological_process	DNA metabolic process
B	0006260	biological_process	DNA replication
B	0006261	biological_process	DNA-templated DNA replication
B	0006281	biological_process	DNA repair
B	0006284	biological_process	base-excision repair
B	0006287	biological_process	base-excision repair, gap-filling
B	0006290	biological_process	pyrimidine dimer repair
B	0006297	biological_process	nucleotide-excision repair, DNA gap filling
B	0006303	biological_process	double-strand break repair via nonhomologous end joining
B	0006915	biological_process	apoptotic process
B	0006954	biological_process	inflammatory response
B	0006974	biological_process	DNA damage response
B	0007435	biological_process	salivary gland morphogenesis
B	0008017	molecular_function	microtubule binding
B	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
B	0010332	biological_process	response to gamma radiation
B	0016445	biological_process	somatic diversification of immunoglobulins
B	0016446	biological_process	somatic hypermutation of immunoglobulin genes
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016829	molecular_function	lyase activity
B	0019899	molecular_function	enzyme binding
B	0032991	cellular_component	protein-containing complex
B	0034061	molecular_function	DNA polymerase activity
B	0045471	biological_process	response to ethanol
B	0046872	molecular_function	metal ion binding
B	0048535	biological_process	lymph node development
B	0048536	biological_process	spleen development
B	0048872	biological_process	homeostasis of number of cells
B	0051402	biological_process	neuron apoptotic process
B	0051575	molecular_function	5'-deoxyribose-5-phosphate lyase activity
B	0055093	biological_process	response to hyperoxia
B	0071707	biological_process	immunoglobulin heavy chain V-D-J recombination
B	0071897	biological_process	DNA biosynthetic process
B	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Functional Information from PDB Data

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

Chain	Residue
A	THR101
A	VAL103
A	ILE106
A	HOH509
P	DG9
P	HOH110

site_id	AC2
Number of Residues	19
Details	BINDING SITE FOR RESIDUE 6CF A 402

Chain	Residue
A	ARG183
A	SER188
A	GLY189
A	TYR271
A	PHE272
A	GLY274
A	ASP276
A	ASN279
A	HOH545
A	HOH585
A	HOH621
A	HOH624
A	HOH679
A	HOH680
P	DC10
T	DG6
A	ARG149
A	GLY179
A	SER180

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MN B 401

Chain	Residue
B	ASP190
B	ASP192
B	ASP256
B	MN402
B	6CF404
B	HOH562
G	DC10

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN B 402

Chain	Residue
B	ASP190
B	ASP192
B	MN401
B	6CF404
B	HOH618

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 403

Chain	Residue
B	ASP314
B	ASP318
B	HOH582
B	HOH609
B	HOH616
B	HOH617

site_id	AC6
Number of Residues	21
Details	BINDING SITE FOR RESIDUE 6CF B 404

Chain	Residue
B	ARG149
B	GLY179
B	SER180
B	ARG183
B	SER188
B	GLY189
B	ASP190
B	ASP192
B	TYR271
B	PHE272
B	THR273
B	GLY274
B	ASP276
B	ASN279
B	MN401
B	MN402
B	HOH514
B	HOH562
B	HOH618
F	DG6
G	DC10

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN D 101

Chain	Residue
D	DG4
D	HOH202
D	HOH208
D	HOH214
D	HOH215
D	HOH216

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN T 101

Chain	Residue
T	DG3
T	HOH213
T	HOH225
T	HOH233
T	HOH234
T	HOH235

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA T 102

Chain	Residue
T	HOH229
T	HOH236
T	HOH237
T	HOH238

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA G 101

Chain	Residue
G	DG4
G	HOH210
G	HOH211
G	HOH212

Functional Information from PROSITE/UniProt

site_id	PS00522
Number of Residues	20
Details	DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP

Chain	Residue	Details
A	GLY179-PRO198

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269\|PubMed:9572863

Chain	Residue	Details
A	LYS72
B	LYS72

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:12517346, ECO:0000269\|PubMed:8841120, ECO:0000269\|PubMed:9287163, ECO:0007744\|PDB:1BPX, ECO:0007744\|PDB:1BPZ, ECO:0007744\|PDB:1MQ3, ECO:0007744\|PDB:1ZQO, ECO:0007744\|PDB:1ZQQ

Chain	Residue	Details
A	LYS60
B	THR101
B	VAL103
B	ILE106
A	LEU62
A	VAL65
A	THR101
A	VAL103
A	ILE106
B	LYS60
B	LEU62
B	VAL65

site_id	SWS_FT_FI3
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:8841119, ECO:0007744\|PDB:8ICW, ECO:0007744\|PDB:8ICX, ECO:0007744\|PDB:8ICY

Chain	Residue	Details
A	ARG149
A	SER180
A	GLY189
B	ARG149
B	SER180
B	GLY189

site_id	SWS_FT_FI4
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:8841119, ECO:0007744\|PDB:8ICX

Chain	Residue	Details
A	ARG183
B	ARG183

site_id	SWS_FT_FI5
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:9287163, ECO:0007744\|PDB:1BPY

Chain	Residue	Details
A	ASP190
A	ASP192
A	ASP256
B	ASP190
B	ASP192
B	ASP256

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q8K409

Chain	Residue	Details
A	LYS72
B	LYS72

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269\|PubMed:16600869

Chain	Residue	Details
A	ARG83
A	ARG152
B	ARG83
B	ARG152

site_id	SWS_FT_FI8
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:19713937, ECO:0000269\|PubMed:21362556

Chain	Residue	Details
A	LYS41
A	LYS61
A	LYS81
B	LYS41
B	LYS61
B	LYS81

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