1AFL - JenaLib

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Title :   RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOADENOSINE 2'-PHOSPHATE AT 1.7 ANGSTROM RESOLUTION

Authors :   D. D. Leonidas, K. R. Acharya

Date :   08 Mar 97 (Deposition) - 18 Mar 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

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

Reference :   D. D. Leonidas, R. Shapiro, L. I. Irons, N. Russo, K. R. Acharya
Crystal Structures Of Ribonuclease A Complexes With 5'-Diphosphoadenosine 3'-Phosphate And 5'-Diphosphoadenosine 2'-Phosphate At 1. 7 A Resolution.
Biochemistry V. 36 5578 1997
PubMed-ID: 9154942 | Reference-DOI: 10.1021/BI9700330
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE A
	Chains	:	A, B
	EC Number	:	3.1.27.5
	Organ	:	PANCREAS
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ATR	2	Ligand/Ion	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2	CIT	2	Ligand/Ion	CITRIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ATR	1	Ligand/Ion	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2	CIT	1	Ligand/Ion	CITRIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ATR	1	Ligand/Ion	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
2	CIT	1	Ligand/Ion	CITRIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:4 , LYS A:7 , GLN A:11 , HIS A:12 , LYS A:41 , CYS A:65 , ASN A:67 , GLN A:69 , ASN A:71 , ALA A:109 , GLU A:111 , VAL A:118 , HIS A:119 , PHE A:120 , HOH A:1014 , HOH A:1024 , HOH A:1028 , HOH A:1038 , HOH A:1051 , HOH A:1060	BINDING SITE FOR RESIDUE ATR A 125
2	AC2	SOFTWARE	THR A:70 , ALA B:4 , LYS B:7 , GLN B:11 , HIS B:12 , CYS B:65 , ASN B:67 , GLN B:69 , ASN B:71 , ALA B:109 , GLU B:111 , VAL B:118 , HIS B:119 , PHE B:120 , HOH B:1003 , HOH B:1004 , HOH B:1038 , HOH B:1045	BINDING SITE FOR RESIDUE ATR B 125
3	AC3	SOFTWARE	THR B:87 , GLY B:88 , SER B:89 , ALA B:96	BINDING SITE FOR RESIDUE CIT B 998
4	AC4	SOFTWARE	GLU A:2 , ARG A:10 , SER A:18 , SER A:32 , ARG A:33 , ASN A:34 , HOH A:1049	BINDING SITE FOR RESIDUE CIT A 999

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

Asymmetric Unit

No.	Residues
1	Tyr A:92	-	Pro A:93
2	Asn A:113	-	Pro A:114
3	Tyr B:92	-	Pro B:93
4	Asn B:113	-	Pro B:114

(no "SAP(SNP)/Variant" information available for 1AFL)

Asymmetric Unit (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 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_BOVIN	66-72	1	A:40-46 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_BOVIN	66-72	1	- B:40-46

Asymmetric Unit (1, 2)

	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	2	A:1-124 B:1-124	124 124

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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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 d1afla_ A: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains 1aflA00 A:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh............hhhhhhhh..........eeeee...hhhhhhhhh.eee........eee....eeeeeeee..........eeeeeeeeeeeee.........eeeeee 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
                 1afl A   1 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 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 d1aflb_ B: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains 1aflB00 B:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh............hhhhhhhh..........eeeee...hhhhhhhhh.eee........eee....eeeeeeee..........eeeeeeeeeeeee.........eeeeee 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
                 1afl B   1 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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	d1afla_	A:
1b	d1aflb_	B:

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	1aflA00	A:1-124
1b	1aflB00	B:1-124

(no "Pfam Domain" information available for 1AFL)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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
		Asn A:113 - Pro A:114	[ RasMol ]
		Asn B:113 - Pro B:114	[ RasMol ]
		Tyr A:92 - Pro A:93	[ RasMol ]
		Tyr B:92 - Pro B:93	[ RasMol ]

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	1afl
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(no "Related Entries Specified in the PDB File" available for 1AFL)

Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

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