1X1X - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   WATER-MEDIATE INTERACTION AT APROTEIN-PROTEIN INTERFACE

Authors :   T. Ikura, Y. Urakubo, N. Ito

Date :   15 Apr 05 (Deposition) - 26 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Rnase-Inhibitor Complex, Hydrolase/Hydrolase Inhibitor, Hydrolase/Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ikura, Y. Urakubo, N. Ito
Water-Mediated Interaction At A Protein-Protein Interface
Chem. Phys. V. 307 111 2004
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE
	Chains	:	A, B, C
	EC Number	:	3.1.27.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PML2BS
	Expression System Strain	:	BL21(DE3)[PLYSE]
	Expression System Taxid	:	562
	Expression System Vector	:	PTZ18U
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS AMYLOLIQUEFACIENS
	Organism Taxid	:	1390
	Synonym	:	BARNASE, RNASE BA

Molecule 2 - BARSTAR
	Chains	:	D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PML2BS
	Expression System Strain	:	BL21(DE3)[PLYSE]
	Expression System Taxid	:	562
	Expression System Vector	:	PTZ18U
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	BACILLUS AMYLOLIQUEFACIENS
	Organism Taxid	:	1390
	Synonym	:	RIBONUCLEASE INHIBITOR

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B			E
Biological Unit 3 (1x)	:			C			F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1X1X)

(no "Site" information available for 1X1X)

(no "SS Bond" information available for 1X1X)

Asymmetric Unit

No.	Residues
1	Tyr D:47	-	Pro D:48
2	Tyr E:47	-	Pro E:48
3	Tyr F:47	-	Pro F:48

(no "SAP(SNP)/Variant" information available for 1X1X)

(no "PROSITE Motif" information available for 1X1X)

(no "Exon" information available for 1X1X)

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:110
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:110
                                    57        67        77        87        97       107       117       127       137       147       157
           RNBR_BACAM    48 AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1x1xa_ A: Barnase                                                                                             SCOP domains
               CATH domains 1x1xA00 A:1-110  [code=3.10.450.30, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.....eehhhhhhhh..hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1x1x A   1 AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:110
                                    57        67        77        87        97       107       117       127       137       147       157
           RNBR_BACAM    48 AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1x1xb_ B: Barnase                                                                                             SCOP domains
               CATH domains 1x1xB00 B:1-110  [code=3.10.450.30, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.....eehhhhhhhh..hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1x1x B   1 AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:109
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:109
                                    58        68        78        88        98       108       118       128       138       148         
           RNBR_BACAM    49 QVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1x1xc_ C: Barnase                                                                                            SCOP domains
               CATH domains 1x1xC00 C:2-110  [code=3.10.450.30, no name defined]                                                          CATH domains
           Pfam domains (1) ------------------Ribonuclease-1x1xC01 C:20-109                                                             - Pfam domains (1)
           Pfam domains (2) ------------------Ribonuclease-1x1xC02 C:20-109                                                             - Pfam domains (2)
           Pfam domains (3) ------------------Ribonuclease-1x1xC03 C:20-109                                                             - Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhh.....eehhhhhhhh..hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1x1x C   2 QVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    11        21        31        41        51        61        71        81        91       101

Chain D from PDB  Type:PROTEIN  Length:89
 aligned with BARS_BACAM | P11540 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:89
                                    11        21        31        41        51        61        71        81         
           BARS_BACAM     2 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS  90
               SCOP domains d1x1xd1 D:1-89 Barstar (barnase inhibitor)                                                SCOP domains
               CATH domains 1x1xD00 D:1-89 Barnase, subunit D                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhh.hhhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhh..eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1x1x D   1 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFRAAKAEGADITIILS  89
                                    10        20        30        40        50        60        70        80

Chain E from PDB  Type:PROTEIN  Length:89
 aligned with BARS_BACAM | P11540 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:89
                                    11        21        31        41        51        61        71        81         
           BARS_BACAM     2 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS  90
               SCOP domains d1x1xe_ E: Barstar (barnase inhibitor)                                                    SCOP domains
               CATH domains 1x1xE00 E:1-89 Barnase, subunit D                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh....eeeeeehhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1x1x E   1 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFRAAKAEGADITIILS  89
                                    10        20        30        40        50        60        70        80

Chain F from PDB  Type:PROTEIN  Length:89
 aligned with BARS_BACAM | P11540 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:89
                                    11        21        31        41        51        61        71        81         
           BARS_BACAM     2 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS  90
               SCOP domains d1x1xf_ F: Barstar (barnase inhibitor)                                                    SCOP domains
               CATH domains 1x1xF00 F:1-89 Barnase, subunit D                                                         CATH domains
           Pfam domains (1) --Barstar-1x1xF01 F:3-86                                                              --- Pfam domains (1)
           Pfam domains (2) --Barstar-1x1xF02 F:3-86                                                              --- Pfam domains (2)
           Pfam domains (3) --Barstar-1x1xF03 F:3-86                                                              --- Pfam domains (3)
         Sec.struct. author .eeeee.hhh.hhhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeehhhhhhhh..hhhhhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1x1x F   1 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFRAAKAEGADITIILS  89
                                    10        20        30        40        50        60        70        80

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: Microbial ribonucleases (174)

Superfamily: Microbial ribonucleases (174)

Family: Bacterial ribonucleases (89)

Protein domain: Barnase (49)

Bacillus amyloliquefaciens [TaxId: 1390] (49)

1a	d1x1xa_	A:
1b	d1x1xb_	B:
1c	d1x1xc_	C:

Class: Alpha and beta proteins (a/b) (23833)

Fold: Barstar-like (79)

Superfamily: Barstar-related (21)

Family: Barstar-related (21)

Protein domain: Barstar (barnase inhibitor) (15)

Bacillus amyloliquefaciens [TaxId: 1390] (15)

2a	d1x1xd1	D:1-89
2b	d1x1xe_	E:
2c	d1x1xf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Barnase; Chain D (18)

Homologous Superfamily: Barnase, subunit D (18)

Bacillus amyloliquefaciens. Organism_taxid: 1390. (9)

1a	1x1xD00	D:1-89
1b	1x1xE00	E:1-89
1c	1x1xF00	F:1-89

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.30, no name defined] (159)

Bacillus amyloliquefaciens. Organism_taxid: 1390. (15)

2a	1x1xC00	C:2-110
2b	1x1xA00	A:1-110
2c	1x1xB00	B:1-110

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RNBR_BACAM | P00648)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	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.

Chain D,E,F (BARS_BACAM | P11540)

cellular component
	GO:0005737		cytoplasm		All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr D:47 - Pro D:48	[ RasMol ]
		Tyr E:47 - Pro E:48	[ RasMol ]
		Tyr F:47 - Pro F:48	[ RasMol ]

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	3.1.27.-
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1x1u	RNASE-INHIBITOR COMPLEX: BARNASE(WT)-BARSTAR(PWT)
1x1w	RNASE-INHIBITOR COMPLEX: BARNASE(WT)-BARSTAR(E80A)
1x1y	RNASE-INHIBITOR COMPLEX: BARNASE(Q2A)-BARSTAR(D35A)

Description

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Ligands, Modified Residues, Ions (0, 0)

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SCOP Domains (2, 6)

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