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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 40% DIMETHYLFORMAMIDE: ONE OF TWELVE IN MSCS SET
 
Authors :  B. M. Kearney, M. Dechene, P. D. Swartz, C. Mattos
Date :  11 Feb 13  (Deposition) - 22 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Endoribonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Kearney, D. Roberts, M. Dechene, P. D. Swartz, C. Mattos
Drop: A Program For Analysis Of Water Structure On Protein Surfaces
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEASE PANCREATIC
    Chains: A
    EC Number: 3.1.27.5
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Other Details: PANCREAS
    Synonym: RNASE 1, RNASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1DMF5Ligand/IonDIMETHYLFORMAMIDE
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:11 , HIS A:12 , LYS A:41 , HIS A:119 , PHE A:120 , HOH A:304 , HOH A:356BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWARETHR A:3 , ALA A:4 , ALA A:5 , SER A:23 , HOH A:328BINDING SITE FOR RESIDUE DMF A 202
3AC3SOFTWAREGLN A:55 , LYS A:61 , THR A:87 , GLY A:88 , SER A:89BINDING SITE FOR RESIDUE DMF A 207
4AC4SOFTWAREALA A:5 , SER A:23 , TYR A:97 , LYS A:98 , THR A:99 , HOH A:337BINDING SITE FOR RESIDUE DMF A 208
5AC5SOFTWAREGLU A:2 , ARG A:10 , ASN A:34 , SER A:77 , THR A:78 , HIS A:105BINDING SITE FOR RESIDUE DMF A 209
6AC6SOFTWARESER A:32 , GLU A:49 , ASP A:53 , THR A:78 , MET A:79 , HOH A:303 , HOH A:314 , HOH A:422BINDING SITE FOR RESIDUE DMF A 217

(-) SS Bonds  (4, 4)

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

(-) 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 4J65)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J65)

(-) Exons   (0, 0)

(no "Exon" information available for 4J65)

(-) 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
                                                                                                                                                            
               SCOP domains d4j65a_ A: Ribonuclease A (also ribonuclease B, S)                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j65 A   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)
    → 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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J65)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J65)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  4j65
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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 2p43 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 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

4j5z CRYSTAL STRUCTURE OF RIBONUCLEASE A IN AQUEOUS SOLUTION: ONE OF TWELVE IN MSCS SET
4j60 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 25% CYCLOPENTANOL: ONE OF TWELVE IN MSCS SET
4j61 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 40% CYCLOPENTANONE: ONE OF TWELVE IN MSCS SET
4j62 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 40% CYCLOHEXANOL: ONE OF TWELVE IN MSCS SET
4j63 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 40% CYCLOHEXANONE: ONE OF TWELVE IN MSCS SET
4j64 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 40% DIOXANE: ONE OF TWELVE IN MSCS SET
4j66 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 25% DIMETHYL SULFOXIDE: ONE OF TWELVE IN MSCS SET
4j67 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 50% 1,6- HEXANEDIOL: ONE OF TWELVE IN MSCS SET
4j68 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 40% ISOPROPANOL: ONE OF TWELVE IN MSCS SET
4j69 CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 50% S,R,S- BISFURANOL: ONE OF TWELVE IN MSCS SET
4j6a CRYSTAL STRUCTURE OF RIBONUCLEASE A SOAKED IN 40% 2,2,2- TRIFLUOROETHANOL: ONE OF TWELVE IN MSCS SET