Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4QIW

Crystal structure of euryarchaeal RNA polymerase from Thermococcus kodakarensis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0005737	cellular_component	cytoplasm
A	0006351	biological_process	DNA-templated transcription
A	0008270	molecular_function	zinc ion binding
A	0016779	molecular_function	nucleotidyltransferase activity
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0046872	molecular_function	metal ion binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0005737	cellular_component	cytoplasm
B	0006351	biological_process	DNA-templated transcription
B	0008270	molecular_function	zinc ion binding
B	0016779	molecular_function	nucleotidyltransferase activity
B	0032549	molecular_function	ribonucleoside binding
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046872	molecular_function	metal ion binding
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
C	0005694	cellular_component	chromosome
C	0005737	cellular_component	cytoplasm
C	0006351	biological_process	DNA-templated transcription
C	0016779	molecular_function	nucleotidyltransferase activity
C	0034062	molecular_function	5'-3' RNA polymerase activity
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
D	0005737	cellular_component	cytoplasm
D	0006351	biological_process	DNA-templated transcription
D	0016779	molecular_function	nucleotidyltransferase activity
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0046983	molecular_function	protein dimerization activity
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0003676	molecular_function	nucleic acid binding
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
E	0005737	cellular_component	cytoplasm
E	0006351	biological_process	DNA-templated transcription
E	0006352	biological_process	DNA-templated transcription initiation
E	0016779	molecular_function	nucleotidyltransferase activity
F	0000166	molecular_function	nucleotide binding
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
F	0005737	cellular_component	cytoplasm
F	0006351	biological_process	DNA-templated transcription
F	0006352	biological_process	DNA-templated transcription initiation
F	0016779	molecular_function	nucleotidyltransferase activity
F	0030880	cellular_component	RNA polymerase complex
F	0044237	biological_process	cellular metabolic process
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
H	0005737	cellular_component	cytoplasm
H	0006351	biological_process	DNA-templated transcription
H	0016779	molecular_function	nucleotidyltransferase activity
H	0034062	molecular_function	5'-3' RNA polymerase activity
I	0000287	molecular_function	magnesium ion binding
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0003677	molecular_function	DNA binding
I	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
I	0005737	cellular_component	cytoplasm
I	0006351	biological_process	DNA-templated transcription
I	0008270	molecular_function	zinc ion binding
I	0016779	molecular_function	nucleotidyltransferase activity
I	0034062	molecular_function	5'-3' RNA polymerase activity
I	0046872	molecular_function	metal ion binding
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0005737	cellular_component	cytoplasm
J	0006351	biological_process	DNA-templated transcription
J	0008270	molecular_function	zinc ion binding
J	0016779	molecular_function	nucleotidyltransferase activity
J	0032549	molecular_function	ribonucleoside binding
J	0034062	molecular_function	5'-3' RNA polymerase activity
J	0046872	molecular_function	metal ion binding
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
K	0005694	cellular_component	chromosome
K	0005737	cellular_component	cytoplasm
K	0006351	biological_process	DNA-templated transcription
K	0016779	molecular_function	nucleotidyltransferase activity
K	0034062	molecular_function	5'-3' RNA polymerase activity
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
L	0005737	cellular_component	cytoplasm
L	0006351	biological_process	DNA-templated transcription
L	0016779	molecular_function	nucleotidyltransferase activity
L	0034062	molecular_function	5'-3' RNA polymerase activity
L	0046983	molecular_function	protein dimerization activity
M	0000428	cellular_component	DNA-directed RNA polymerase complex
M	0003677	molecular_function	DNA binding
M	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
M	0005694	cellular_component	chromosome
M	0005737	cellular_component	cytoplasm
M	0006351	biological_process	DNA-templated transcription
M	0016779	molecular_function	nucleotidyltransferase activity
M	0034062	molecular_function	5'-3' RNA polymerase activity
N	0000428	cellular_component	DNA-directed RNA polymerase complex
N	0003677	molecular_function	DNA binding
N	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
N	0005694	cellular_component	chromosome
N	0005737	cellular_component	cytoplasm
N	0006351	biological_process	DNA-templated transcription
N	0008270	molecular_function	zinc ion binding
N	0016779	molecular_function	nucleotidyltransferase activity
N	0034062	molecular_function	5'-3' RNA polymerase activity
N	0046872	molecular_function	metal ion binding
O	0000428	cellular_component	DNA-directed RNA polymerase complex
O	0003677	molecular_function	DNA binding
O	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
O	0005737	cellular_component	cytoplasm
O	0006351	biological_process	DNA-templated transcription
O	0016779	molecular_function	nucleotidyltransferase activity
O	0034062	molecular_function	5'-3' RNA polymerase activity
O	0046983	molecular_function	protein dimerization activity
P	0000428	cellular_component	DNA-directed RNA polymerase complex
P	0003677	molecular_function	DNA binding
P	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
P	0005694	cellular_component	chromosome
P	0005737	cellular_component	cytoplasm
P	0006351	biological_process	DNA-templated transcription
P	0008270	molecular_function	zinc ion binding
P	0016779	molecular_function	nucleotidyltransferase activity
P	0034062	molecular_function	5'-3' RNA polymerase activity
P	0046872	molecular_function	metal ion binding
Q	0000428	cellular_component	DNA-directed RNA polymerase complex
Q	0003676	molecular_function	nucleic acid binding
Q	0003677	molecular_function	DNA binding
Q	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
Q	0005737	cellular_component	cytoplasm
Q	0006351	biological_process	DNA-templated transcription
Q	0006352	biological_process	DNA-templated transcription initiation
Q	0016779	molecular_function	nucleotidyltransferase activity
R	0000166	molecular_function	nucleotide binding
R	0000428	cellular_component	DNA-directed RNA polymerase complex
R	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
R	0005737	cellular_component	cytoplasm
R	0006351	biological_process	DNA-templated transcription
R	0006352	biological_process	DNA-templated transcription initiation
R	0016779	molecular_function	nucleotidyltransferase activity
R	0030880	cellular_component	RNA polymerase complex
R	0044237	biological_process	cellular metabolic process
S	0000428	cellular_component	DNA-directed RNA polymerase complex
S	0003677	molecular_function	DNA binding
S	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
S	0005737	cellular_component	cytoplasm
S	0006351	biological_process	DNA-templated transcription
S	0016779	molecular_function	nucleotidyltransferase activity
S	0034062	molecular_function	5'-3' RNA polymerase activity
T	0000428	cellular_component	DNA-directed RNA polymerase complex
T	0003677	molecular_function	DNA binding
T	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
T	0005694	cellular_component	chromosome
T	0005737	cellular_component	cytoplasm
T	0006351	biological_process	DNA-templated transcription
T	0016779	molecular_function	nucleotidyltransferase activity
T	0034062	molecular_function	5'-3' RNA polymerase activity
U	0000428	cellular_component	DNA-directed RNA polymerase complex
U	0003677	molecular_function	DNA binding
U	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
U	0005737	cellular_component	cytoplasm
U	0006351	biological_process	DNA-templated transcription
U	0016779	molecular_function	nucleotidyltransferase activity
U	0034062	molecular_function	5'-3' RNA polymerase activity
U	0046983	molecular_function	protein dimerization activity
V	0000428	cellular_component	DNA-directed RNA polymerase complex
V	0003677	molecular_function	DNA binding
V	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
V	0005694	cellular_component	chromosome
V	0005737	cellular_component	cytoplasm
V	0006351	biological_process	DNA-templated transcription
V	0008270	molecular_function	zinc ion binding
V	0016779	molecular_function	nucleotidyltransferase activity
V	0034062	molecular_function	5'-3' RNA polymerase activity
V	0046872	molecular_function	metal ion binding
W	0000428	cellular_component	DNA-directed RNA polymerase complex
W	0003677	molecular_function	DNA binding
W	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
W	0005694	cellular_component	chromosome
W	0005737	cellular_component	cytoplasm
W	0006351	biological_process	DNA-templated transcription
W	0008270	molecular_function	zinc ion binding
W	0016779	molecular_function	nucleotidyltransferase activity
W	0034062	molecular_function	5'-3' RNA polymerase activity
W	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 1001

Chain	Residue
A	ASP461
A	ASP463
A	ASP465

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1002

Chain	Residue
A	CYS60
A	CYS63
A	CYS70
A	HIS73

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 1003

Chain	Residue
A	CYS147
A	HIS149
A	CYS150
A	CYS100
A	CYS103

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG A 1004

Chain	Residue
A	ASP461
B	GLU737

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 1201

Chain	Residue
B	CYS1065
B	CYS1068
B	CYS1083
B	CYS1086

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN N 1401

Chain	Residue
N	CYS10
N	CYS44
N	CYS45

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN P 1501

Chain	Residue
P	CYS11
P	GLY12
P	GLU14
P	CYS30

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG I 1101

Chain	Residue
I	ASP461
I	ASP463
I	ASP465

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN I 1102

Chain	Residue
I	CYS60
I	CYS63
I	CYS70
I	HIS73

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN I 1103

Chain	Residue
I	CYS100
I	CYS103
I	CYS147
I	HIS149
I	CYS150

site_id	BC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG I 1104

Chain	Residue
I	ASP461

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN J 1301

Chain	Residue
J	CYS1065
J	CYS1068
J	CYS1083
J	CYS1086
J	GLU1090

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN V 1601

Chain	Residue
V	CYS7
V	THR9
V	CYS10
V	CYS44
V	CYS45

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN W 1701

Chain	Residue
W	CYS11
W	GLU14
W	CYS30

Functional Information from PROSITE/UniProt

site_id	PS00446
Number of Residues	41
Details	RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NALRRtilsevptfAvdeVefleNdSalfDEiIAhRLAMIP

Chain	Residue	Details
D	ASN27-PRO67

site_id	PS01110
Number of Residues	14
Details	RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HVLVPEHriLseEE

Chain	Residue	Details
H	HIS12-GLU25

site_id	PS01111
Number of Residues	15
Details	RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TrFEkARiIGaRAlQ

Chain	Residue	Details
K	THR5-GLN19

site_id	PS01112
Number of Residues	10
Details	RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFTCG

Chain	Residue	Details
N	ILE2-GLY11

site_id	PS01154
Number of Residues	32
Details	RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. LegEdHTFaNlLtetLhenehVtfagYtieHP

Chain	Residue	Details
L	LEU17-PRO48

site_id	PS01166
Number of Residues	13
Details	RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGV

Chain	Residue	Details
B	GLY879-VAL891

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00615

Chain	Residue	Details
P	CYS11
P	CYS27
P	CYS30
W	CYS11
W	CYS27
W	CYS30
V	CYS44
V	CYS45

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