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(-) Description

Title :  RIBONUCLEASE T1 (ASN9ALA/THR93ALA DOUBLEMUTANT) COMPLEXED WITH 2'GMP
 
Authors :  U. Langhorst, R. Loris, V. P. Denisov, J. Doumen, P. Roose, D. Maes, B. Halle, J. Steyaert
Date :  14 Sep 98  (Deposition) - 23 Sep 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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, Endoribonuclease, Ribonuclease, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Langhorst, R. Loris, V. P. Denisov, J. Doumen, P. Roose, D. Maes, B. Halle, J. Steyaert
Dissection Of The Structural And Functional Role Of A Conserved Hydration Site In Rnase T1.
Protein Sci. V. 8 722 1999
PubMed-ID: 10211818
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (RIBONUCLEASE T1)
    Chains: A, B, C, D
    EC Number: 3.1.27.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: WK6
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ASPERGILLUS ORYZAE
    Organism Taxid: 5062
    Other Details: COMPLEXED WITH GUANOSINE-2'-MONOPHOSPHATE
    Synonym: RNASE T1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
12GP5Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2CA2Ligand/IonCALCIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12GP1Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12GP1Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
12GP2Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
12GP1Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY C:47 , ASP C:49 , HOH C:331 , HOH C:335 , HOH C:339 , TYR D:45BINDING SITE FOR RESIDUE CA C 305
02AC2SOFTWARETYR C:45 , GLY D:47 , ASP D:49BINDING SITE FOR RESIDUE CA D 306
03AC3SOFTWAREASN A:36 , TYR A:38 , HIS A:40 , LYS A:41 , TYR A:42 , ASN A:43 , ASN A:44 , TYR A:45 , GLU A:46 , GLU A:58 , ASN A:98 , PHE A:100 , HOH A:318BINDING SITE FOR RESIDUE 2GP A 307
04AC4SOFTWARETYR B:38 , HIS B:40 , LYS B:41 , TYR B:42 , ASN B:43 , ASN B:44 , TYR B:45 , GLU B:46 , GLU B:58 , ASN B:98 , PHE B:100 , HOH B:331 , HOH D:360BINDING SITE FOR RESIDUE 2GP B 308
05AC5SOFTWARESER A:53 , HOH A:317 , HIS C:40 , LYS C:41 , TYR C:42 , ASN C:43 , ASN C:44 , TYR C:45 , GLU C:46 , PHE C:100 , HOH C:316BINDING SITE FOR RESIDUE 2GP C 309
06AC6SOFTWARESER A:53 , SER A:54 , PRO A:55 , ASN A:81 , GLU A:82 , ASN A:83 , HOH A:317 , ASN C:36 , TYR C:38 , HIS C:40 , GLU C:58 , SER C:72 , PRO C:73 , GLY C:74 , ARG C:77 , HIS C:92 , ASN C:98 , PHE C:100 , HOH C:316 , HOH C:337 , HOH C:360 , HOH C:362BINDING SITE FOR RESIDUE 2GP C 310
07AC7SOFTWARETYR D:38 , HIS D:40 , LYS D:41 , TYR D:42 , ASN D:43 , ASN D:44 , TYR D:45 , GLU D:46 , GLU D:58 , ASN D:98 , PHE D:100 , HOH D:352 , HOH D:353BINDING SITE FOR RESIDUE 2GP D 311
08BI1AUTHORTYR A:42 , ASN A:43 , ASN A:44 , TYR A:45 , GLU A:46BINDING SITE.
09BI2AUTHORTYR B:42 , ASN B:43 , ASN B:44 , TYR B:45 , GLU B:46BINDING SITE.
10BI3AUTHORTYR C:42 , ASN C:43 , ASN C:44 , TYR C:45 , GLU C:46BINDING SITE.
11BI4AUTHORTYR D:42 , ASN D:43 , ASN D:44 , TYR D:45 , GLU D:46BINDING SITE.
12CA1AUTHORASP C:49SITE.
13CA2AUTHORASP D:49SITE.
14CT1AUTHORTYR A:38 , HIS A:40 , GLU A:58 , ARG A:77 , HIS A:92ACTIVE SITE.
15CT2AUTHORTYR B:38 , HIS B:40 , GLU B:58 , ARG B:77 , HIS B:92ACTIVE SITE.
16CT3AUTHORTYR C:38 , HIS C:40 , GLU C:58 , ARG C:77 , HIS C:92ACTIVE SITE.
17CT4AUTHORTYR D:38 , HIS D:40 , GLU D:58 , ARG D:77 , HIS D:92ACTIVE SITE.

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:2 -A:10
2A:6 -A:103
3B:2 -B:10
4B:6 -B:103
5C:2 -C:10
6C:6 -C:103
7D:2 -D:10
8D:6 -D:103

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:38 -Pro A:39
2Ser A:54 -Pro A:55
3Tyr B:38 -Pro B:39
4Ser B:54 -Pro B:55
5Tyr C:38 -Pro C:39
6Ser C:54 -Pro C:55
7Tyr D:38 -Pro D:39
8Ser D:54 -Pro D:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HOH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HOH)

(-) Exons   (0, 0)

(no "Exon" information available for 5HOH)

(-) 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:104
                                                                                                                                        
               SCOP domains d5hoha_ A: RNase T1                                                                                      SCOP domains
               CATH domains 5hohA00 A:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5hoh A   1 ACDYTCGSACYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHAGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain B from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains d5hohb_ B: RNase T1                                                                                      SCOP domains
               CATH domains 5hohB00 B:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5hoh B   1 ACDYTCGSACYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHAGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain C from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains d5hohc_ C: RNase T1                                                                                      SCOP domains
               CATH domains 5hohC00 C:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5hoh C   1 ACDYTCGSACYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHAGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain D from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains d5hohd_ D: RNase T1                                                                                      SCOP domains
               CATH domains 5hohD00 D:1-104  [code=3.10.450.30, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhhhhhhhhhhhhh......................................................................eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5hoh D   1 ACDYTCGSACYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHAGASGNNFVECT 104
                                    10        20        30        40        50        60        70        80        90       100
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HOH)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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  5hoh
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  RNT1_ASPOR | P00651
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  3.1.27.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNT1_ASPOR | P00651: 1b2m 1bir 1bu4 1bvi 1ch0 1det 1fys 1fzu 1g02 1gsp 1hyf 1hz1 1i0v 1i0x 1i2e 1i2f 1i2g 1i3f 1i3i 1iyy 1lov 1low 1loy 1lra 1q9e 1rga 1rgc 1rgk 1rgl 1rhl 1rls 1rn1 1rn4 1rnt 1trp 1trq 1tto 1ygw 2aad 2aae 2bir 2bu4 2gsp 2hoh 2rnt 3bir 3bu4 3gsp 3hoh 3rnt 3syu 3urp 4bir 4bu4 4gsp 4hoh 4odk 4rnt 5bir 5bu4 5gsp 5rnt 6gsp 6rnt 7gsp 7rnt 8rnt 9rnt

(-) Related Entries Specified in the PDB File

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