3BCP - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SWAPPED NON COVALENT FORM OF P19A/L28Q/N67D BS-RNASE

Authors :   A. Merlino, C. Ercole, D. Picone, E. Pizzo, L. Mazzarella, F. Sica

Date :   13 Nov 07 (Deposition) - 12 Feb 08 (Release) - 16 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.57

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Domain Swapping, Bovine Seminal Ribonuclease, Non Covalent Dimer, Antitumor Activity, Allosteric Enzyme, Endonuclease, Hydrolase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Merlino, C. Ercole, D. Picone, E. Pizzo, L. Mazzarella, F. Sica
The Buried Diversity Of Bovine Seminal Ribonuclease: Shape And Cytotoxicity Of The Swapped Non-Covalent Form Of The Enzyme
J. Mol. Biol. V. 376 427 2008
PubMed-ID: 18164315 | Reference-DOI: 10.1016/J.JMB.2007.11.008
(for further references see the PDB file header)

Molecule 1 - SEMINAL RIBONUCLEASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.27.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SRN
	Mutation	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	SEMINAL RNASE, S-RNASE, RIBONUCLEASE BS-1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	YCM	8	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	YCM	4	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	YCM	4	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Biological Unit 3 (1, 8)

No.	Name	Count	Type	Full Name
1	YCM	8	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(no "Site" information available for 3BCP)

Asymmetric Unit

No.	Residues
1	A:26	-	A:84
2	A:40	-	A:95
3	A:58	-	A:110
4	A:65	-	A:72
5	B:26	-	B:84
6	B:40	-	B:95
7	B:58	-	B:110
8	B:65	-	B:72
9	C:26	-	C:84
10	C:40	-	C:95
11	C:58	-	C:110
12	C:65	-	C:72
13	D:26	-	D:84
14	D:40	-	D:95
15	D:58	-	D:110
16	D:65	-	D:72

Asymmetric Unit

No.	Residues
1	Tyr A:92	-	Pro A:93
2	Lys A:113	-	Pro A:114
3	Tyr B:92	-	Pro B:93
4	Lys B:113	-	Pro B:114
5	Tyr C:92	-	Pro C:93
6	Lys C:113	-	Pro C:114
7	Tyr D:92	-	Pro D:93
8	Lys D:113	-	Pro D:114

(no "SAP(SNP)/Variant" information available for 3BCP)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	4	A:40-46 B:40-46 C:40-46 D:40-46

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	2	A:40-46 B:40-46 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	2	- - C:40-46 D:40-46

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNS_BOVIN	66-72	4	A:40-46 B:40-46 C:40-46 D:40-46

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENSBTAT00000036229	2	ENSBTAE00000284222	chr10:25625986-25626024	39	RNS_BOVIN	-	0	0	-	-
1.3b	ENSBTAT00000036229	3b	ENSBTAE00000284221	chr10:25626721-25627530	810	RNS_BOVIN	1-159	159	4	A:1-124 B:1-124 C:1-124 D:1-124	124 124 124 124

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d3bcpa_ A: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 3bcpA00 A:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhh..ee..........ee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: A:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 3bcp A   1 KESAAAKFERQHMDSGNSASSSSNYCNQMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKDGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30||      40        50        60        70        80        90       100       110       120    
                                                         31-YCM                                                                                         
                                                          32-YCM

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d3bcpb_ B: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 3bcpB00 B:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: B:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 3bcp B   1 KESAAAKFERQHMDSGNSASSSSNYCNQMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKDGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30||      40        50        60        70        80        90       100       110       120    
                                                         31-YCM                                                                                         
                                                          32-YCM

Chain C from PDB  Type:PROTEIN  Length:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d3bcpc_ C: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 3bcpC00 C:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhh.........eeeee..hhhhhhhhh..eee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: C:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 3bcp C   1 KESAAAKFERQHMDSGNSASSSSNYCNQMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKDGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30||      40        50        60        70        80        90       100       110       120    
                                                         31-YCM                                                                                         
                                                          32-YCM

Chain D from PDB  Type:PROTEIN  Length:124
 aligned with RNS_BOVIN | P00669 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
            RNS_BOVIN    27 KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 150
               SCOP domains d3bcpd_ D: Seminal ribonucleasease                                                                                           SCOP domains
               CATH domains 3bcpD00 D:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhh.........eeeee..hhhhhhhhhhh...........eee....eeeeeeee..........eeeeeeee.eeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3b  PDB: D:1-124 UniProt: 1-159 [INCOMPLETE]                                                                          Transcript 1
                 3bcp D   1 KESAAAKFERQHMDSGNSASSSSNYCNQMMccRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKDGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV 124
                                    10        20        30||      40        50        60        70        80        90       100       110       120    
                                                         31-YCM                                                                                         
                                                          32-YCM

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: RNase A-like (356)

Superfamily: RNase A-like (356)

Family: Ribonuclease A-like (347)

Protein domain: Seminal ribonucleasease (17)

Cow (Bos taurus) [TaxId: 9913] (17)

1a	d3bcpa_	A:
1b	d3bcpb_	B:
1c	d3bcpc_	C:
1d	d3bcpd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: P-30 Protein (299)

Homologous Superfamily: P-30 Protein (299)

Cattle (Bos taurus) (152)

1a	3bcpA00	A:1-124
1b	3bcpB00	B:1-124
1c	3bcpC00	C:1-124
1d	3bcpD00	D:1-124

(no "Pfam Domain" information available for 3BCP)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RNS_BOVIN | P00669)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0004522	ribonuclease A activity	Catalysis of the endonucleolytic cleavage of RNA to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		YCM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3bcp)

	Cis Peptide Bonds
		Lys A:113 - Pro A:114	[ RasMol ]
		Lys B:113 - Pro B:114	[ RasMol ]
		Lys C:113 - Pro C:114	[ RasMol ]
		Lys D:113 - Pro D:114	[ RasMol ]
		Tyr A:92 - Pro A:93	[ RasMol ]
		Tyr B:92 - Pro B:93	[ RasMol ]
		Tyr C:92 - Pro C:93	[ RasMol ]
		Tyr D:92 - Pro D:93	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3bcp
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RNS_BOVIN \| P00669
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.27.5
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RNS_BOVIN \| P00669
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

3bcm	THE SAME PROTEIN, UNSWAPPED FORM
3bco	THE SAME PROTEIN, SWAPPED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (0, 0)

SS Bonds (16, 16)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (1, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File