Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5TB8

Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)3TC-TP and Mn2+.

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	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	0016740	molecular_function	transferase activity
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

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	binding site for residue 1RZ A 401

Chain	Residue
A	GLY179
A	ASP276
A	ASN279
A	MN405
A	MN406
A	HOH513
A	HOH514
A	HOH530
A	HOH537
A	HOH557
A	HOH600
A	SER180
P	DC10
T	DG6
A	ARG183
A	SER188
A	GLY189
A	ASP190
A	ASP192
A	TYR271
A	PHE272

site_id	AC2
Number of Residues	4
Details	binding site for residue MN A 402

Chain	Residue
A	HIS337
A	HIS339
A	HOH511
A	HOH647

site_id	AC3
Number of Residues	5
Details	binding site for residue MN A 403

Chain	Residue
A	GLU117
A	ASP321
A	ACT417
A	HOH535
A	HOH624

site_id	AC4
Number of Residues	4
Details	binding site for residue MN A 404

Chain	Residue
A	LYS48
A	HIS336
A	HIS338
A	HOH592

site_id	AC5
Number of Residues	5
Details	binding site for residue MN A 405

Chain	Residue
A	ASP190
A	ASP192
A	1RZ401
A	MN406
A	HOH530

site_id	AC6
Number of Residues	8
Details	binding site for residue MN A 406

Chain	Residue
A	ASP190
A	ASP192
A	ASP256
A	1RZ401
A	MN405
A	HOH557
A	HOH603
P	DC10

site_id	AC7
Number of Residues	2
Details	binding site for residue MN A 407

Chain	Residue
A	HIS285
A	GLU288

site_id	AC8
Number of Residues	5
Details	binding site for residue NA A 408

Chain	Residue
A	ASP130
A	ASP314
A	HOH520
A	HOH564
A	HOH644

site_id	AC9
Number of Residues	3
Details	binding site for residue NA A 409

Chain	Residue
A	ASP145
A	HIS252
A	HOH590

site_id	AD1
Number of Residues	5
Details	binding site for residue NA A 410

Chain	Residue
A	LYS60
A	LEU62
A	VAL65
D	DC3
D	HOH112

site_id	AD2
Number of Residues	6
Details	binding site for residue NA A 411

Chain	Residue
A	THR101
A	VAL103
A	ILE106
A	HOH650
P	DG9
P	HOH106

site_id	AD3
Number of Residues	6
Details	binding site for residue NA A 412

Chain	Residue
A	ASP91
A	GLN157
A	ACT416
A	HOH542
A	HOH550
A	HOH613

site_id	AD4
Number of Residues	2
Details	binding site for residue CL A 413

Chain	Residue
A	ASN294
A	THR297

site_id	AD5
Number of Residues	3
Details	binding site for residue CL A 414

Chain	Residue
A	ALA32
A	ILE33
A	HIS34

site_id	AD6
Number of Residues	8
Details	binding site for residue ACT A 415

Chain	Residue
A	HIS34
A	ASN37
A	ALA38
A	LYS41
A	LYS280
A	HOH538
D	DG1
T	DC5

site_id	AD7
Number of Residues	6
Details	binding site for residue ACT A 416

Chain	Residue
A	VAL29
A	ASP91
A	GLN157
A	ASP160
A	NA412
A	HOH550

site_id	AD8
Number of Residues	4
Details	binding site for residue ACT A 417

Chain	Residue
A	GLU117
A	ASP321
A	TYR322
A	MN403

site_id	AD9
Number of Residues	2
Details	binding site for residue ACT A 418

Chain	Residue
A	TYR36
A	HOH504

site_id	AE1
Number of Residues	2
Details	binding site for residue ACT A 419

Chain	Residue
A	LYS127
A	HOH505

site_id	AE2
Number of Residues	6
Details	binding site for residue ACT A 420

Chain	Residue
A	ASP246
A	TRP325
A	LYS326
A	ARG328
A	HOH570
A	HOH653

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	9
Details	Region: {"description":"DNA-binding"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	1
Details	Active site: {"description":"Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity","evidences":[{"source":"PubMed","id":"9572863","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12517346","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8841120","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9287163","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BPX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1BPZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MQ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ZQO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ZQQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8841119","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8ICW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8ICX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8ICY","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8841119","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8ICX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9287163","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BPY","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q8K409","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Omega-N-methylarginine; by PRMT6","evidences":[{"source":"PubMed","id":"16600869","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"19713937","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21362556","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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