Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5XH6

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003723	molecular_function	RNA binding
A	0004518	molecular_function	nuclease activity
A	0004519	molecular_function	endonuclease activity
A	0004530	molecular_function	deoxyribonuclease I activity
A	0006259	biological_process	DNA metabolic process
A	0016787	molecular_function	hydrolase activity
A	0016829	molecular_function	lyase activity
A	0051607	biological_process	defense response to virus

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue NA A 1401

Chain	Residue
A	LYS757
A	HOH1575
A	HOH1822
B	A-4
B	HOH246
B	HOH256

site_id	AC2
Number of Residues	4
Details	binding site for residue CL A 1402

Chain	Residue
A	LYS1072
A	TYR1069
A	THR1070
A	SER1071

site_id	AC3
Number of Residues	7
Details	binding site for residue EDO A 1403

Chain	Residue
A	HIS977
A	VAL980
A	ASP981
A	LEU1028
A	HOH1684
B	G-3
B	A-2

site_id	AC4
Number of Residues	4
Details	binding site for residue EDO A 1404

Chain	Residue
A	VAL13
A	SER14
A	LYS15
A	ASP1021

site_id	AC5
Number of Residues	6
Details	binding site for residue EDO A 1405

Chain	Residue
A	THR2
A	GLN3
A	PHE7
A	ARG891
A	HOH1631
A	HOH1818

site_id	AC6
Number of Residues	6
Details	binding site for residue EDO A 1406

Chain	Residue
A	PHE1079
A	VAL1080
A	MET1119
A	LEU1129
A	GLY1131
A	GLN1303

site_id	AC7
Number of Residues	6
Details	binding site for residue EDO A 1407

Chain	Residue
A	VAL558
A	LYS559
A	ASN560
A	GLY561
A	ASP591
A	EDO1411

site_id	AC8
Number of Residues	3
Details	binding site for residue EDO A 1408

Chain	Residue
A	LEU95
A	ILE96
A	GLN99

site_id	AC9
Number of Residues	3
Details	binding site for residue EDO A 1409

Chain	Residue
A	GLN24
A	TYR564
A	PHE590

site_id	AD1
Number of Residues	7
Details	binding site for residue EDO A 1410

Chain	Residue
A	LYS530
A	ARG790
A	PHE870
A	HIS872
A	HOH1777
B	U-15
B	U-16

site_id	AD2
Number of Residues	4
Details	binding site for residue EDO A 1411

Chain	Residue
A	ASP591
A	PHE723
A	PHE769
A	EDO1407

site_id	AD3
Number of Residues	5
Details	binding site for residue EDO A 1412

Chain	Residue
A	PRO23
A	ASP867
A	PHE869
A	HOH1693
A	HOH1746

site_id	AD4
Number of Residues	3
Details	binding site for residue EDO A 1413

Chain	Residue
A	TRP1258
A	HOH1638
A	HOH1759

site_id	AD5
Number of Residues	6
Details	binding site for residue NA B 101

Chain	Residue
B	U10
B	G11
B	HOH245
B	HOH284
B	HOH294
C	HOH218

site_id	AD6
Number of Residues	4
Details	binding site for residue NA B 102

Chain	Residue
B	A2
B	HOH219
B	HOH268
B	HOH291

site_id	AD7
Number of Residues	6
Details	binding site for residue NA B 103

Chain	Residue
B	U16
B	G17
B	HOH202
B	HOH276
B	HOH285
B	HOH295

site_id	AD8
Number of Residues	4
Details	binding site for residue EDO B 104

Chain	Residue
A	HIS755
B	C-9
B	U-8
B	U-5

site_id	AD9
Number of Residues	8
Details	binding site for residue EDO B 105

Chain	Residue
A	THR16
A	GLN784
A	GLU786
B	G0
B	G1
B	A2
B	EDO107
B	HOH231

site_id	AE1
Number of Residues	4
Details	binding site for residue EDO B 106

Chain	Residue
A	TYR823
B	C-11
B	U-10
B	A-19

site_id	AE2
Number of Residues	7
Details	binding site for residue EDO B 107

Chain	Residue
B	A2
B	A3
B	EDO105
C	EDO102
A	GLN784
A	GLU786
B	G1

site_id	AE3
Number of Residues	5
Details	binding site for residue NA C 101

Chain	Residue
B	HOH224
B	HOH292
C	DG-14
C	HOH246
C	HOH252

site_id	AE4
Number of Residues	6
Details	binding site for residue EDO C 102

Chain	Residue
A	GLY171
A	ASN175
B	A3
B	EDO107
C	DT-2
C	HOH243

site_id	AE5
Number of Residues	4
Details	binding site for residue EDO C 103

Chain	Residue
A	LYS607
C	DA4
C	DG5
C	HOH216

site_id	AE6
Number of Residues	5
Details	binding site for residue EDO C 104

Chain	Residue
A	ASN631
A	TYR687
A	LYS689
C	DT3
C	HOH203

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	DNA binding: {"description":"PAM-binding on target DNA","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	22
Details	DNA binding: {"description":"Target DNA","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	34
Details	Region: {"description":"WED-I (OBD-I)","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	284
Details	Region: {"description":"REC1 (helical-I)","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	205
Details	Region: {"description":"WED-II (helical-II)","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	71
Details	Region: {"description":"WED-II (OBD-I)","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	119
Details	Region: {"description":"PI (LHD)","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	55
Details	Region: {"description":"RuvC-I","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	16
Details	Region: {"description":"Bridge helix","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	44
Details	Region: {"description":"RuvC-III","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000303"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	32
Details	Coiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	3
Details	Active site: {"description":"For pre-crRNA processing","evidences":[{"source":"UniProtKB","id":"A0Q7Q2","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	3
Details	Active site: {"description":"For DNase activity of RuvC domain","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	1
Details	Active site: {"description":"For DNase activity of nuclease domain","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	17
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	3
Details	Site: {"description":"Binds crRNA","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Site: {"description":"Binds PAM on target DNA","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	1
Details	Site: {"description":"Binds crRNA-target DNA heteroduplex","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	1
Details	Site: {"description":"Binds sequence-specific recognition of both target and non-target strand bases in PAM","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27444870","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	1
Details	Site: {"description":"Binds target DNA","evidences":[{"source":"PubMed","id":"27114038","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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