3RID - JenaLib

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Title :   X-RAY STRUCTURE OF THE C-TERMINAL SWAPPED DIMER OF P114A VARIANT OF RIBONUCLEASE A

Authors :   A. Merlino, A. Balsamo, L. Mazzarella, F. Sica

Date :   13 Apr 11 (Deposition) - 15 Feb 12 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.18

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

Keywords :   Ribonuclease Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Merlino, D. Picone, C. Ercole, A. Balsamo, F. Sica
Chain Termini Cross-Talk In The Swapping Process Of Bovine Pancreatic Ribonuclease.
Biochimie V. 94 1108 2012
PubMed-ID: 22273774 | Reference-DOI: 10.1016/J.BIOCHI.2012.01.010

Molecule 1 - RIBONUCLEASE PANCREATIC
	Chains	:	A, B, C, D
	EC Number	:	3.1.27.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RNASE1, RNS1
	Mutation	:	YES
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	RNASE 1, RNASE A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CGP	4	Ligand/Ion	2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CGP	2	Ligand/Ion	2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CGP	2	Ligand/Ion	2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:12 , VAL A:43 , ASN A:44 , THR A:45 , ARG A:85 , GLU A:86 , HOH A:1603 , HOH A:1621 , HOH A:1730 , HOH A:1785 , HOH A:1797 , HOH A:1870 , PHE B:120 , ASP B:121 , PO4 B:801 , HOH B:1360	BINDING SITE FOR RESIDUE CGP A 751
2	AC2	SOFTWARE	GLN A:11 , HIS A:12 , LYS A:41 , CGP A:751 , HOH A:1327 , HIS B:119 , PHE B:120	BINDING SITE FOR RESIDUE PO4 B 801
3	AC3	SOFTWARE	HIS A:119 , PHE A:120 , GLN B:11 , HIS B:12 , LYS B:41 , CGP B:753 , HOH B:1397 , HOH B:1447 , HOH B:1618	BINDING SITE FOR RESIDUE PO4 B 802
4	AC4	SOFTWARE	PHE A:120 , ASP A:121 , HIS B:12 , VAL B:43 , ASN B:44 , THR B:45 , LYS B:66 , ARG B:85 , GLU B:86 , PO4 B:802 , HOH B:1401 , HOH B:1422 , HOH B:1423 , HOH B:1424 , HOH B:1559 , HOH B:1747	BINDING SITE FOR RESIDUE CGP B 753
5	AC5	SOFTWARE	GLN C:11 , HIS C:12 , LYS C:41 , CGP C:755 , HOH C:1535 , HIS D:119 , PHE D:120	BINDING SITE FOR RESIDUE PO4 C 803
6	AC6	SOFTWARE	HIS C:12 , VAL C:43 , ASN C:44 , THR C:45 , ARG C:85 , GLU C:86 , PO4 C:803 , HOH C:1507 , HOH C:1767 , HOH C:1780 , HOH C:1912 , PHE D:120 , ASP D:121	BINDING SITE FOR RESIDUE CGP C 755
7	AC7	SOFTWARE	HIS C:119 , PHE C:120 , GLN D:11 , HIS D:12 , LYS D:41 , CGP D:757 , HOH D:1472 , HOH D:1776	BINDING SITE FOR RESIDUE PO4 D 804
8	AC8	SOFTWARE	PHE C:120 , ASP C:121 , ALA C:122 , HOH C:1503 , HIS D:12 , VAL D:43 , ASN D:44 , THR D:45 , LYS D:66 , ARG D:85 , GLU D:86 , PO4 D:804 , HOH D:1500 , HOH D:1502 , HOH D:1517 , HOH D:1524 , HOH D:1571 , HOH D:1722 , HOH D:1916	BINDING SITE FOR RESIDUE CGP D 757

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	Tyr B:92	-	Pro B:93
3	Tyr C:92	-	Pro C:93
4	Tyr D:92	-	Pro D:93

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_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.	RNAS1_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.	RNAS1_BOVIN	66-72	2	- - 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
1.1	ENSBTAT00000011586	1	ENSBTAE00000400684	chr10:25757929-25757973	45	RNAS1_BOVIN	-	0	0	-	-
1.2	ENSBTAT00000011586	2	ENSBTAE00000093931	chr10:25758709-25759510	802	RNAS1_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 RNAS1_BOVIN | P61823 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
          RNAS1_BOVIN    27 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 150
               SCOP domains d3rida_ A: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeee.eeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-124 UniProt: 1-159 [INCOMPLETE]                                                                           Transcript 1
                 3rid A   1 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNAYVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with RNAS1_BOVIN | P61823 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
          RNAS1_BOVIN    27 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 150
               SCOP domains d3ridb_ B: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: B:1-124 UniProt: 1-159 [INCOMPLETE]                                                                           Transcript 1
                 3rid B   1 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNAYVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:124
 aligned with RNAS1_BOVIN | P61823 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
          RNAS1_BOVIN    27 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 150
               SCOP domains d3ridc_ C: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeee.eeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: C:1-124 UniProt: 1-159 [INCOMPLETE]                                                                           Transcript 1
                 3rid C   1 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNAYVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:124
 aligned with RNAS1_BOVIN | P61823 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
          RNAS1_BOVIN    27 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 150
               SCOP domains d3ridd_ D: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: D:1-124 UniProt: 1-159 [INCOMPLETE]                                                                           Transcript 1
                 3rid D   1 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNAYVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

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	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: Ribonuclease A (also ribonuclease B, S) (173)

Cow (Bos taurus) [TaxId: 9913] (164)

1a	d3rida_	A:
1b	d3ridb_	B:
1c	d3ridc_	C:
1d	d3ridd_	D:

(no "CATH Domain" information available for 3RID)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RNAS1_BOVIN | P61823)

molecular function
	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: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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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
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	Cis Peptide Bonds
		Tyr A:92 - Pro A:93	[ RasMol ]
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		Tyr D:92 - Pro D:93	[ RasMol ]

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	3rid
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Description

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