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(-) Description

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 :  1.90
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)

(-) Compounds

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
    Mutation: YES
    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

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
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)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1X1Y)

(-) Sites  (0, 0)

(no "Site" information available for 1X1Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X1Y)

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1X1Y)

(-) 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:108
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    59        69        79        89        99       109       119       129       139       149        
           RNBR_BACAM    50 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1x1ya_ A: Barnase                                                                                           SCOP domains
               CATH domains 1x1yA00 A:3-110  [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
                 1x1y A   3 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    12        22        32        42        52        62        72        82        92       102        


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 d1x1yb_ B: Barnase                                                                                             SCOP domains
               CATH domains 1x1yB00 B:1-110  [code=3.10.450.30, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1x1y B   1 AAVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    10        20        30        40        50        60        70        80        90       100       110


Chain C from PDB  Type:PROTEIN  Length:108
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    59        69        79        89        99       109       119       129       139       149        
           RNBR_BACAM    50 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1x1yc_ C: Barnase                                                                                           SCOP domains
               CATH domains 1x1yC00 C:3-110  [code=3.10.450.30, no name defined]                                                         CATH domains
           Pfam domains (1) -----------------Ribonuclease-1x1yC01 C:20-109                                                             - Pfam domains (1)
           Pfam domains (2) -----------------Ribonuclease-1x1yC02 C:20-109                                                             - Pfam domains (2)
           Pfam domains (3) -----------------Ribonuclease-1x1yC03 C:20-109                                                             - Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhh.....eehhhhhhhh..hhhhhhhhhhh...eeeeeee..............eeeee...........eeeee....eeee.......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1x1y C   3 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    12        22        32        42        52        62        72        82        92       102        


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

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
           BARS_BACAM     1 MKKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS  90
               SCOP domains -d1x1yd1 D:1-89 Barstar (barnase inhibitor)                                                SCOP domains
               CATH domains 1x1yD00 D:0-89 Barnase, subunit D                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.hhh.hhhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeehhhhhhhh..hhhhhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1x1y D   0 MKKAVINGEQIRSISDLHQTLKKELALPEYYGENLAALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGADITIILS  89
                                     9        19        29        39        49        59        69        79        89


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 d1x1ye_ E: automated matches                                                              SCOP domains
               CATH domains 1x1yE00 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
                 1x1y E   1 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLAALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGADITIILS  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 d1x1yf_ F: automated matches                                                              SCOP domains
               CATH domains 1x1yF00 F:1-89 Barnase, subunit D                                                         CATH domains
           Pfam domains (1) --Barstar-1x1yF01 F:3-86                                                              --- Pfam domains (1)
           Pfam domains (2) --Barstar-1x1yF02 F:3-86                                                              --- Pfam domains (2)
           Pfam domains (3) --Barstar-1x1yF03 F:3-86                                                              --- Pfam domains (3)
         Sec.struct. author .eeeee.hhh.hhhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1x1y F   1 KKAVINGEQIRSISDLHQTLKKELALPEYYGENLAALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGADITIILS  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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: Barstar] (6)
(-)
Clan: no clan defined [family: Ribonuclease] (57)

(-) Gene Ontology  (11, 11)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BARS_BACAM | P11540: 1a19 1ab7 1ay7 1b27 1b2s 1b2u 1b3s 1bgs 1brs 1bta 1btb 1l1k 1x1u 1x1w 1x1x 2hxx 2za4 3da7
        RNBR_BACAM | P00648: 1a2p 1b20 1b21 1b27 1b2s 1b2u 1b2x 1b2z 1b3s 1ban 1bao 1bgs 1bne 1bnf 1bng 1bni 1bnj 1bnr 1bns 1brg 1brh 1bri 1brj 1brk 1brn 1brs 1bsa 1bsb 1bsc 1bsd 1bse 1fw7 1rnb 1x1u 1x1w 1x1x 1yvs 2c4b 2f4y 2f56 2f5m 2f5w 2kf3 2kf4 2kf5 2kf6 2za4 3da7 3kch 3q3f

(-) Related Entries Specified in the PDB File

1x1u RNASE-INHIBITOR COMPLEX: BARNASE(WT)-BARSTAR(PWT)
1x1w RNASE-INHIBITOR COMPLEX: BARNASE(WT)-BARSTAR(E80A)
1x1x RNASE-INHIBITOR COMPLEX: BARNASE(WT)-BARSTAR(E76A)