9DWM

DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000785	cellular_component	chromatin
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0003682	molecular_function	chromatin binding
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0006325	biological_process	chromatin organization
A	0006334	biological_process	nucleosome assembly
A	0010467	biological_process	gene expression
A	0030527	molecular_function	structural constituent of chromatin
A	0046982	molecular_function	protein heterodimerization activity
A	0070062	cellular_component	extracellular exosome
B	0000781	cellular_component	chromosome, telomeric region
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005694	cellular_component	chromosome
B	0006325	biological_process	chromatin organization
B	0006334	biological_process	nucleosome assembly
B	0016020	cellular_component	membrane
B	0030527	molecular_function	structural constituent of chromatin
B	0032200	biological_process	telomere organization
B	0032991	cellular_component	protein-containing complex
B	0043505	cellular_component	CENP-A containing nucleosome
B	0045653	biological_process	negative regulation of megakaryocyte differentiation
B	0046982	molecular_function	protein heterodimerization activity
B	0061644	biological_process	protein localization to CENP-A containing chromatin
B	0070062	cellular_component	extracellular exosome
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0019899	molecular_function	enzyme binding
C	0030527	molecular_function	structural constituent of chromatin
C	0031507	biological_process	heterochromatin formation
C	0046982	molecular_function	protein heterodimerization activity
C	0070062	cellular_component	extracellular exosome
D	0000786	cellular_component	nucleosome
D	0002227	biological_process	innate immune response in mucosa
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005615	cellular_component	extracellular space
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005694	cellular_component	chromosome
D	0005829	cellular_component	cytosol
D	0006334	biological_process	nucleosome assembly
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0042742	biological_process	defense response to bacterium
D	0042802	molecular_function	identical protein binding
D	0046982	molecular_function	protein heterodimerization activity
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
D	0070062	cellular_component	extracellular exosome
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000785	cellular_component	chromatin
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0003682	molecular_function	chromatin binding
E	0005515	molecular_function	protein binding
E	0005576	cellular_component	extracellular region
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0006325	biological_process	chromatin organization
E	0006334	biological_process	nucleosome assembly
E	0010467	biological_process	gene expression
E	0030527	molecular_function	structural constituent of chromatin
E	0046982	molecular_function	protein heterodimerization activity
E	0070062	cellular_component	extracellular exosome
F	0000781	cellular_component	chromosome, telomeric region
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0003723	molecular_function	RNA binding
F	0005515	molecular_function	protein binding
F	0005576	cellular_component	extracellular region
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005694	cellular_component	chromosome
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
F	0016020	cellular_component	membrane
F	0030527	molecular_function	structural constituent of chromatin
F	0032200	biological_process	telomere organization
F	0032991	cellular_component	protein-containing complex
F	0043505	cellular_component	CENP-A containing nucleosome
F	0045653	biological_process	negative regulation of megakaryocyte differentiation
F	0046982	molecular_function	protein heterodimerization activity
F	0061644	biological_process	protein localization to CENP-A containing chromatin
F	0070062	cellular_component	extracellular exosome
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0019899	molecular_function	enzyme binding
G	0030527	molecular_function	structural constituent of chromatin
G	0031507	biological_process	heterochromatin formation
G	0046982	molecular_function	protein heterodimerization activity
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
H	0002227	biological_process	innate immune response in mucosa
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005615	cellular_component	extracellular space
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005694	cellular_component	chromosome
H	0005829	cellular_component	cytosol
H	0006334	biological_process	nucleosome assembly
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0042742	biological_process	defense response to bacterium
H	0042802	molecular_function	identical protein binding
H	0046982	molecular_function	protein heterodimerization activity
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
H	0070062	cellular_component	extracellular exosome
L	0001701	biological_process	in utero embryonic development
L	0003677	molecular_function	DNA binding
L	0003684	molecular_function	damaged DNA binding
L	0003887	molecular_function	DNA-directed DNA polymerase activity
L	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005737	cellular_component	cytoplasm
L	0005874	cellular_component	microtubule
L	0005876	cellular_component	spindle microtubule
L	0006260	biological_process	DNA replication
L	0006261	biological_process	DNA-templated DNA replication
L	0006281	biological_process	DNA repair
L	0006284	biological_process	base-excision repair
L	0006287	biological_process	base-excision repair, gap-filling
L	0006290	biological_process	pyrimidine dimer repair
L	0006297	biological_process	nucleotide-excision repair, DNA gap filling
L	0006303	biological_process	double-strand break repair via nonhomologous end joining
L	0006915	biological_process	apoptotic process
L	0006954	biological_process	inflammatory response
L	0006974	biological_process	DNA damage response
L	0007435	biological_process	salivary gland morphogenesis
L	0008017	molecular_function	microtubule binding
L	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
L	0010332	biological_process	response to gamma radiation
L	0016445	biological_process	somatic diversification of immunoglobulins
L	0016446	biological_process	somatic hypermutation of immunoglobulin genes
L	0016740	molecular_function	transferase activity
L	0016779	molecular_function	nucleotidyltransferase activity
L	0016829	molecular_function	lyase activity
L	0019899	molecular_function	enzyme binding
L	0032991	cellular_component	protein-containing complex
L	0034061	molecular_function	DNA polymerase activity
L	0045471	biological_process	response to ethanol
L	0046872	molecular_function	metal ion binding
L	0048535	biological_process	lymph node development
L	0048536	biological_process	spleen development
L	0048872	biological_process	homeostasis of number of cells
L	0051402	biological_process	neuron apoptotic process
L	0051575	molecular_function	5'-deoxyribose-5-phosphate lyase activity
L	0055093	biological_process	response to hyperoxia
L	0071707	biological_process	immunoglobulin heavy chain V-D-J recombination
L	0071897	biological_process	DNA biosynthetic process
L	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA21-VAL27

---

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
B	GLY14-HIS18

---

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
A	LYS14-LEU20

---

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG92-GLY114

---

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

Chain	Residue	Details
L	GLY179-PRO198

---

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
A	PRO66-ILE74

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	ACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863

Chain	Residue	Details
L	LYS72
H	PRO1

---

site_id	SWS_FT_FI2
Number of Residues	6
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
L	LYS60
L	LEU62
L	VAL65
L	THR101
L	VAL103
L	ILE106

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY

Chain	Residue	Details
L	ARG149
H	LYS11
H	LYS15
H	LYS16
H	LYS20
H	LYS23
H	LYS43
H	LYS85
L	SER180
L	GLY189
D	LYS16
D	LYS20
D	LYS23
D	LYS43
D	LYS85
H	LYS5

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX

Chain	Residue	Details
L	ARG183
H	SER6
G	LYS9
G	LYS95

---

site_id	SWS_FT_FI5
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY

Chain	Residue	Details
L	ASP190
L	ASP192
L	ASP256
F	LYS8
F	LYS16
F	LYS44

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409

Chain	Residue	Details
L	LYS72
H	SER14
B	LYS77
B	LYS91
F	LYS12
F	LYS31
F	LYS77
F	LYS91

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869

Chain	Residue	Details
L	ARG83
L	ARG152

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556

Chain	Residue	Details
L	LYS41
D	LYS116
L	LYS61
L	LYS81
H	LYS116
H	LYS120

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475

Chain	Residue	Details
D	GLU35
H	GLU35
C	LYS125
G	LYS118
G	LYS119
G	LYS125

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q6ZWY9

Chain	Residue	Details
D	SER36
H	SER36
E	LYS14
E	LYS56

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16627869

Chain	Residue	Details
D	LYS46
D	LYS108
H	LYS46
H	LYS108

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537

Chain	Residue	Details
D	LYS57
H	LYS57
G	LYS119

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
D	ARG79
H	ARG79

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
D	ARG86
D	ARG92
H	ARG86
H	ARG92

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729

Chain	Residue	Details
D	THR115
H	THR115
F	LYS91

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000269|PubMed:22121020

Chain	Residue	Details
D	SER112
H	SER112
B	LYS79
F	LYS20
F	LYS59
F	LYS79

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876

Chain	Residue	Details
D	LYS5
H	LYS5

---

site_id	SWS_FT_FI18
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563, ECO:0000269|PubMed:22121020

Chain	Residue	Details
A	SER57
D	LYS120
H	LYS120

---

site_id	SWS_FT_FI19
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6

Chain	Residue	Details
D	LYS20
H	LYS20

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816

Chain	Residue	Details
D	LYS34
H	LYS34

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243

Chain	Residue	Details
A	SER86
E	SER86

---

site_id	SWS_FT_FI22
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332

Chain	Residue	Details
A	THR107
E	THR107

---

site_id	SWS_FT_FI23
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
A	LYS115
E	LYS115

---

site_id	SWS_FT_FI24
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229

Chain	Residue	Details
A	LYS122
E	LYS122

---

site_id	SWS_FT_FI25
Number of Residues	2
Details	LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806

Chain	Residue	Details
A	LYS18
E	LYS18

---

site_id	SWS_FT_FI26
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000269|PubMed:21076176

Chain	Residue	Details
A	ALA110
E	ALA110

---