Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6XEZ

Structure of SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003723	molecular_function	RNA binding
A	0003968	molecular_function	RNA-directed RNA polymerase activity
A	0005524	molecular_function	ATP binding
A	0006351	biological_process	DNA-templated transcription
A	0039694	biological_process	viral RNA genome replication
B	0004197	molecular_function	cysteine-type endopeptidase activity
B	0008242	molecular_function	omega peptidase activity
B	0016740	molecular_function	transferase activity
C	0004197	molecular_function	cysteine-type endopeptidase activity
C	0008242	molecular_function	omega peptidase activity
C	0016740	molecular_function	transferase activity
D	0004197	molecular_function	cysteine-type endopeptidase activity
D	0008242	molecular_function	omega peptidase activity
D	0016740	molecular_function	transferase activity
E	0004386	molecular_function	helicase activity
E	0005524	molecular_function	ATP binding
E	0008270	molecular_function	zinc ion binding
F	0004386	molecular_function	helicase activity
F	0005524	molecular_function	ATP binding
F	0008270	molecular_function	zinc ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 1001

Chain	Residue
A	HIS295
A	CYS301
A	CYS306
A	CYS310

site_id	AC2
Number of Residues	5
Details	binding site for residue ZN A 1002

Chain	Residue
A	CYS487
A	PHE571
A	HIS642
A	CYS645
A	CYS646

site_id	AC3
Number of Residues	3
Details	binding site for residue MG A 1003

Chain	Residue
A	ASN209
A	ASP218
A	ADP1004

site_id	AC4
Number of Residues	9
Details	binding site for residue ADP A 1004

Chain	Residue
A	ASN52
A	LYS73
A	HIS75
A	ASN79
A	ARG116
A	ASN209
A	TYR217
A	ASP218
A	MG1003

site_id	AC5
Number of Residues	2
Details	binding site for residue 1N7 A 1005

Chain	Residue
A	VAL204
A	ILE223

site_id	AC6
Number of Residues	2
Details	binding site for residue 1N7 A 1006

Chain	Residue
A	ARG197
A	LYS288

site_id	AC7
Number of Residues	5
Details	binding site for residue ZN E 701

Chain	Residue
E	CYS5
E	CYS8
E	CYS26
E	CYS29
E	GLY99

site_id	AC8
Number of Residues	5
Details	binding site for residue ZN E 702

Chain	Residue
E	CYS50
E	ALA52
E	CYS55
E	CYS72
E	HIS75

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN E 703

Chain	Residue
E	CYS16
E	CYS19
E	HIS33
E	HIS39

site_id	AD1
Number of Residues	9
Details	binding site for residue ADP E 704

Chain	Residue
E	PRO283
E	GLY285
E	THR286
E	GLY287
E	LYS288
E	HIS290
E	ARG443
E	GLU540
E	AF3705

site_id	AD2
Number of Residues	6
Details	binding site for residue AF3 E 705

Chain	Residue
E	GLY285
E	THR286
E	LYS288
E	GLU375
E	ADP704
E	MG706

site_id	AD3
Number of Residues	2
Details	binding site for residue MG E 706

Chain	Residue
E	SER289
E	AF3705

site_id	AD4
Number of Residues	4
Details	binding site for residue 1N7 E 707

Chain	Residue
A	VAL905
E	VAL45
E	TYR70
E	PHE90

site_id	AD5
Number of Residues	5
Details	binding site for residue ZN F 1000

Chain	Residue
F	CYS5
F	CYS8
F	CYS26
F	CYS29
F	GLY99

site_id	AD6
Number of Residues	5
Details	binding site for residue ZN F 1001

Chain	Residue
F	CYS50
F	ALA52
F	CYS55
F	CYS72
F	HIS75

site_id	AD7
Number of Residues	4
Details	binding site for residue ZN F 1002

Chain	Residue
F	CYS16
F	CYS19
F	HIS33
F	HIS39

site_id	AD8
Number of Residues	10
Details	binding site for residue ADP F 1003

Chain	Residue
F	GLY282
F	PRO283
F	PRO284
F	GLY285
F	THR286
F	GLY287
F	LYS288
F	LYS320
F	ARG442
F	AF31004

site_id	AD9
Number of Residues	7
Details	binding site for residue AF3 F 1004

Chain	Residue
F	GLY282
F	PRO284
F	THR286
F	LYS288
F	ASP374
F	ADP1003
F	MG1005

site_id	AE1
Number of Residues	4
Details	binding site for residue MG F 1005

Chain	Residue
F	LYS288
F	SER289
F	ASP374
F	AF31004

Functional Information from PROSITE/UniProt

site_id	PS00213
Number of Residues	12
Details	LIPOCALIN Lipocalin signature. GTS..KFYGGWHNM

Chain	Residue	Details
A	GLY590-MET601

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	254
Details	Domain: {"description":"NiRAN","evidences":[{"source":"PROSITE-ProRule","id":"PRU01292","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	25
Details	Repeat: {"description":"LRR 7","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	98
Details	Domain: {"description":"Nsp12 Interface","evidences":[{"source":"PROSITE-ProRule","id":"PRU01344","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	162
Details	Domain: {"description":"RdRp catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU00539","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	214
Details	Region: {"description":"RdRp Fingers N-ter","evidences":[{"source":"PROSITE-ProRule","id":"PRU01293","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	10
Details	Region: {"description":"Interaction with RMP Remdesivir","evidences":[{"source":"PubMed","id":"32358203","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	38
Details	Region: {"description":"RdRp Palm N-ter","evidences":[{"source":"PROSITE-ProRule","id":"PRU01293","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	58
Details	Region: {"description":"RdRp Fingers C-ter","evidences":[{"source":"PROSITE-ProRule","id":"PRU01293","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	135
Details	Region: {"description":"RdRp Palm C-ter","evidences":[{"source":"PROSITE-ProRule","id":"PRU01293","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	3
Details	Active site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01293","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"33232691","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7CYQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01344","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32358203","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32526208","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33232691","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7CYQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01293","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32358203","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32526208","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33232691","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7CYQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01293","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32358203","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32526208","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33232691","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	54
Details	Repeat: {"description":"LRR 6","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	224
Details	Domain: {"description":"CV ZBD","evidences":[{"source":"PROSITE-ProRule","id":"PRU00986","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	40
Details	Repeat: {"description":"LRR 8","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	362
Details	Domain: {"description":"(+)RNA virus helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00990","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00986","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"33232691","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7CYQ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	14
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00990","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)