Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3KGD

Crystal structure of E. coli RNA 3' cyclase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003824	molecular_function	catalytic activity
A	0003963	molecular_function	RNA-3'-phosphate cyclase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0006396	biological_process	RNA processing
A	0016874	molecular_function	ligase activity
B	0000166	molecular_function	nucleotide binding
B	0003824	molecular_function	catalytic activity
B	0003963	molecular_function	RNA-3'-phosphate cyclase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0006396	biological_process	RNA processing
B	0016874	molecular_function	ligase activity
C	0000166	molecular_function	nucleotide binding
C	0003824	molecular_function	catalytic activity
C	0003963	molecular_function	RNA-3'-phosphate cyclase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0006396	biological_process	RNA processing
C	0016874	molecular_function	ligase activity
D	0000166	molecular_function	nucleotide binding
D	0003824	molecular_function	catalytic activity
D	0003963	molecular_function	RNA-3'-phosphate cyclase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0006396	biological_process	RNA processing
D	0016874	molecular_function	ligase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	19
Details	BINDING SITE FOR RESIDUE AMP A 501

Chain	Residue
A	GLN18
A	GLN288
A	HIS309
A	HOH367
A	HOH374
A	HOH386
A	HOH397
A	HOH439
A	HOH710
A	HOH1423
A	HOH1432
A	ARG21
A	GLN104
A	SER129
A	ALA130
A	PRO131
A	PHE251
A	TYR284
A	ASP287

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 340

Chain	Residue
A	GLY16
A	GLY17
A	ARG21
A	GLN51
A	ALA55
A	ILE93
A	VAL102
A	HOH457
A	HOH677

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 341

Chain	Residue
A	ASP88
A	PRO116
A	SER117
A	GLU171
A	HOH396
C	ARG4

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA A 342

Chain	Residue
A	GLY17
A	SO4344
A	HOH471

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 343

Chain	Residue
A	GLU14
A	ARG43
A	HOH429
A	HOH471
A	HOH542
A	HOH918

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 344

Chain	Residue
A	GLN51
A	HIS52
A	NA342
A	HOH399
A	HOH429
A	HOH677
A	HOH832

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 345

Chain	Residue
A	SER218
A	HIS220
A	HOH972
A	HOH1412
B	PRO228
B	ARG229
B	HOH1074

site_id	AC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE AMP B 501

Chain	Residue
B	GLN18
B	ARG21
B	GLN104
B	SER129
B	ALA130
B	PRO131
B	PHE251
B	TYR284
B	ASP287
B	GLN288
B	HIS309
B	HOH367
B	HOH409
B	HOH422
B	HOH446
B	HOH949
B	HOH1327

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 340

Chain	Residue
B	PHE112
B	LEU295
B	HOH1311
B	HOH1438
B	HOH1491

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL B 341

Chain	Residue
B	HIS-12
B	ARG85
B	HOH1266

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA B 342

Chain	Residue
B	ARG40
B	SO4343
B	HOH473

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 343

Chain	Residue
B	GLU14
B	ARG40
B	ARG43
B	NA342
B	HOH475
B	HOH835
B	HOH871
B	HOH1256

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 344

Chain	Residue
B	ARG208
B	SER259
B	ALA260
B	HOH1140

site_id	BC5
Number of Residues	19
Details	BINDING SITE FOR RESIDUE AMP C 501

Chain	Residue
C	GLN104
C	SER129
C	ALA130
C	PRO131
C	PHE251
C	TYR284
C	ASP287
C	GLN288
C	HIS309
C	HOH384
C	HOH394
C	HOH401
C	HOH402
C	HOH481
C	HOH621
C	HOH920
C	HOH1428
C	GLN18
C	ARG21

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 340

Chain	Residue
A	ASP114
C	GLU318
C	ARG324
C	PHE325
D	GLY200

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 341

Chain	Residue
B	HOH990
C	MET5
C	LEU78
C	ARG80
C	HOH1273

site_id	BC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GOL C 342

Chain	Residue
C	GLY16
C	ARG21
C	GLN51
C	HIS52
C	ALA55
C	ILE93
C	LEU101
C	VAL102
C	SO4346
C	HOH784
C	HOH1171
C	HOH1507

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA C 343

Chain	Residue
C	LEU275
C	ALA276
C	SER277
C	HOH442

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA C 344

Chain	Residue
C	ARG40
C	SO4345
C	HOH367
C	HOH1026

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 345

Chain	Residue
C	GLU14
C	ARG40
C	ARG43
C	NA344
C	HOH370
C	HOH715
C	HOH1178
C	HOH1211

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 346

Chain	Residue
C	GLN51
C	HIS52
C	GOL342
C	HOH819
C	HOH1178
C	HOH1268
C	HOH1405
C	HOH1507

site_id	CC4
Number of Residues	14
Details	BINDING SITE FOR RESIDUE AMP D 501

Chain	Residue
D	ARG21
D	GLN104
D	SER129
D	ALA130
D	PRO131
D	PHE251
D	TYR284
D	ASP287
D	GLN288
D	HIS309
D	HOH363
D	HOH413
D	HOH431
D	HOH528

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 340

Chain	Residue
D	LYS3
D	ARG4
D	MET5

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 341

Chain	Residue
D	HIS204
D	VAL205
D	ARG208
D	GLU261

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 342

Chain	Residue
D	GLY64
D	ALA65
D	THR66
D	ARG80
D	PRO81

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA D 343

Chain	Residue
D	ARG40
D	SO4344
D	HOH1378

site_id	CC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 D 344

Chain	Residue
D	GLU14
D	ARG40
D	ARG43
D	NA343
D	HOH358
D	HOH981
D	HOH1126

Functional Information from PROSITE/UniProt

site_id	PS01287
Number of Residues	11
Details	RTC RNA 3'-terminal phosphate cyclase signature. HGfyPaGGGvV

Chain	Residue	Details
A	HIS158-VAL168

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Tele-AMP-histidine intermediate","evidences":[{"source":"PubMed","id":"20399182","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1QMH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20399182","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3KGD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	2
Details	M-CSA 882

Chain	Residue	Details
A	GLU14	modifies pKa
A	HIS309	covalent catalysis

site_id	MCSA2
Number of Residues	2
Details	M-CSA 882

Chain	Residue	Details
B	GLU14	modifies pKa
B	HIS309	covalent catalysis

site_id	MCSA3
Number of Residues	2
Details	M-CSA 882

Chain	Residue	Details
C	GLU14	modifies pKa
C	HIS309	covalent catalysis

site_id	MCSA4
Number of Residues	2
Details	M-CSA 882

Chain	Residue	Details
D	GLU14	modifies pKa
D	HIS309	covalent catalysis

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