4FBA - JenaLib

Title :   STRUCTURE OF MUTANT RIP FROM BARLEY SEEDS IN COMPLEX WITH ADENINE

Authors :   B. -G. Lee, M. K. Kim, S. W. Suh, H. K. Song

Date :   22 May 12 (Deposition) - 31 Oct 12 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Hydrolase, Ribosome Inactivating Protein, Rrna N-Glycosylase Activity, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. G. Lee, M. K. Kim, B. W. Kim, S. W. Suh, H. K. Song
Structures Of The Ribosome-Inactivating Protein From Barley Seeds Reveal A Unique Activation Mechanism.
Acta Crystallogr. , Sect. D V. 68 1488 2012
PubMed-ID: 23090398 | Reference-DOI: 10.1107/S0907444912037110

Compounds

Molecule 1 - PROTEIN SYNTHESIS INHIBITOR I
	Chains	:	A, B, C, D
	EC Number	:	3.2.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RIP30
	Mutation	:	YES
	Organism Common	:	BARLEY
	Organism Scientific	:	HORDEUM VULGARE
	Organism Taxid	:	4513
	Synonym	:	RIBOSOME-INACTIVATING PROTEIN I, RRNA N-GLYCOSIDASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 4)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ADE	4	Ligand/Ion	ADENINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ADE	1	Ligand/Ion	ADENINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ADE	1	Ligand/Ion	ADENINE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ADE	1	Ligand/Ion	ADENINE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	ADE	1	Ligand/Ion	ADENINE

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:86 , TYR A:87 , LEU A:88 , GLY A:116 , TYR A:118 , LEU A:170 , ARG A:178 , HOH A:419	BINDING SITE FOR RESIDUE ADE A 301
2	AC2	SOFTWARE	ILE B:86 , TYR B:87 , LEU B:88 , GLY B:116 , TYR B:118 , LEU B:170 , ARG B:178 , HOH B:429	BINDING SITE FOR RESIDUE ADE B 301
3	AC3	SOFTWARE	ILE C:86 , TYR C:87 , LEU C:88 , GLY C:116 , TYR C:118 , LEU C:170 , GLU C:175 , ARG C:178 , HOH C:402	BINDING SITE FOR RESIDUE ADE C 301
4	AC4	SOFTWARE	ILE D:86 , TYR D:87 , LEU D:88 , GLY D:116 , LEU D:170 , ARG D:178 , HOH D:614 , HOH D:714	BINDING SITE FOR RESIDUE ADE D 301

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhh..hhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba A   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273

Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhh..hhhhhh.eehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba B   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273

Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhh.hhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba C   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273

Chain D from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhhhhhhhhhh.eehhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fba D   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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Biological Units
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