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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  COMPLEX OF A CAMELID SINGLE-DOMAIN VHH ANTIBODY FRAGMENT WITH RNASE A AT 1.65A RESOLUTION: SE3-MONO-1 CRYSTAL FORM WITH THREE SE-MET SITES (M34, M51, M83) IN VHH SCAFFOLD
 
Authors :  V. Tereshko, S. Uysal, A. Koide, K. Margalef, S. Koide, A. A. Kossiakoff
Date :  11 Mar 07  (Deposition) - 11 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Semet Phasing, Camelid Single-Domain Antibody, Vhh, Cab-Rn05, Rnase A, Yeast Surface Display, Hydrolase, Hydrolase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Tereshko, S. Uysal, A. Koide, K. Margalef, S. Koide, A. A. Kossiakof
Toward Chaperone-Assisted Crystallography: Protein Engineering Enhancement Of Crystal Packing And X-Ray Phasin Capabilities Of A Camelid Single-Domain Antibody (Vhh) Scaffold
Protein Sci. V. 17 1175 2008
PubMed-ID: 18445622  |  Reference-DOI: 10.1110/PS.034892.108

(-) Compounds

Molecule 1 - RIBONUCLEASE PANCREATIC
    Chains: A
    EC Number: 3.1.27.5
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: RNASE 1, RNASE A
 
Molecule 2 - ANTIBODY CAB-RN05
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: ARABIAN CAMEL
    Organism Scientific: CAMELUS DROMEDARIUS
    Organism Taxid: 9838

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2P43)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:84
2A:40 -A:95
3A:58 -A:110
4A:65 -A:72
5B:22 -B:96

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:92 -Pro A:93
2Asn A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P43)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.RNAS1_BOVIN66-72  1A:40-46

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000115861ENSBTAE00000400684chr10:25757929-2575797345RNAS1_BOVIN-00--
1.2ENSBTAT000000115862ENSBTAE00000093931chr10:25758709-25759510802RNAS1_BOVIN1-1591591A:1-124124

(-) Sequences/Alignments

Asymmetric/Biological 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 d2p43a_ A: automated matches                                                                                                 SCOP domains
               CATH domains 2p43A00 A:1-124 P-30 Protein                                                                                                 CATH domains
               Pfam domains RnaseA-2p43A01 A:1-121                                                                                                   --- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee 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
                 2p43 A   1 KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d2p43b_ B: automated matches                                                                                                SCOP domains
               CATH domains 2p43B00 B:-1-121 Immunoglobulins                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.eeee....eeeeeeee.......eeeeeee......eeeeeee......ee.hhhh..eeee......eeeeee...hhhhheeeeeee.....hhhhh.ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p43 B  -1 GSQVQLVESGGGLVQAGGSLRLSCAASGYAYTYIYmGWFRQAPGKEREGVAAmDSGGGGTLYADSVKGRFTISRDKGKNTVYLQmDSLKPEDTATYYCAAGGYELRDRTYGQWGQGTQVTVSS 121
                                     8        18        28     |  38        48  |     58        68        78    |   88        98       108       118   
                                                              34-MSE           51-MSE                          83-MSE
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RnaseA] (125)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

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  2p43
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  RNAS1_BOVIN | P61823
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  3.1.27.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNAS1_BOVIN | P61823: 1a2w 1a5p 1a5q 1afk 1afl 1afu 1aqp 1b6v 1bel 1bzq 1c0b 1c0c 1c8w 1c9v 1c9x 1cjq 1cjr 1d5d 1d5e 1d5h 1dfj 1dy5 1eic 1eid 1eie 1eos 1eow 1f0v 1fev 1fs3 1gv7 1izp 1izq 1izr 1j7z 1j80 1j81 1j82 1jn4 1js0 1jvt 1jvu 1jvv 1kf2 1kf3 1kf4 1kf5 1kf7 1kf8 1kh8 1lsq 1o0f 1o0h 1o0m 1o0n 1o0o 1qhc 1rar 1ras 1rat 1rbb 1rbc 1rbd 1rbe 1rbf 1rbg 1rbh 1rbi 1rbj 1rbn 1rbw 1rbx 1rca 1rcn 1rha 1rhb 1rnc 1rnd 1rnm 1rnn 1rno 1rnq 1rnu 1rnv 1rnw 1rnx 1rny 1rnz 1rob 1rpf 1rpg 1rph 1rsm 1rta 1rtb 1ruv 1srn 1ssa 1ssb 1ssc 1u1b 1un5 1w4o 1w4p 1w4q 1wbu 1xps 1xpt 1ymn 1ymr 1ymw 1z3l 1z3m 1z3p 1z6d 1z6s 2aas 2apq 2apu 2blp 2blz 2e33 2e3w 2g4w 2g4x 2g8q 2g8r 2nui 2op2 2oqf 2p42 2p44 2p45 2p46 2p47 2p48 2p49 2p4a 2qca 2rat 2rln 2rns 2w5g 2w5i 2w5k 2w5l 2w5m 2xog 2xoi 3a1r 3d6o 3d6p 3d6q 3d7b 3d8y 3d8z 3dh5 3dh6 3di7 3di8 3di9 3dib 3dic 3dxg 3dxh 3eux 3euy 3euz 3ev0 3ev1 3ev2 3ev3 3ev4 3ev5 3ev6 3fkz 3fl0 3fl1 3fl3 3i67 3i6f 3i6h 3i6j 3i7w 3i7x 3i7y 3jw1 3lxo 3mwq 3mwr 3mx8 3mzq 3mzr 3oqy 3oqz 3or0 3ql1 3ql2 3qsk 3rat 3rh1 3rid 3rn3 3rsd 3rsk 3rsp 3srn 4ao1 4g8v 4g8y 4g90 4j5z 4j60 4j61 4j62 4j63 4j64 4j65 4j66 4j67 4j68 4j69 4j6a 4k7l 4k7m 4l55 4mxf 4o36 4o37 4okf 4ooh 4ot4 4peq 4pou 4qh3 4rat 4rsd 4rsk 4rte 4s0q 4s18 4srn 4wyn 4wyp 4wyz 4ygw 4zz4 5d6u 5d97 5e5e 5e5f 5et4 5jlg 5jmg 5jml 5rat 5rsa 6rat 6rsa 7rat 7rsa 8rat 8rsa 9rat 9rsa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2P43)