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(-) Description

Title :  DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N-ACETYLGLUCOSAMINIDASE, STRH
 
Authors :  B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston
Date :  25 Jun 12  (Deposition) - 10 Jul 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston
Inhibition Of The Family 20 Glycoside Hydrolase Catalytic Modules In The Streptococcus Pneumoniae Exo-Beta-D-N- Acetylglucosaminidase, Strh.
Org. Biomol. Chem. V. 11 7907 2013
PubMed-ID: 24132305  |  Reference-DOI: 10.1039/C3OB41579A

(-) Compounds

Molecule 1 - BETA-N-ACETYLHEXOSAMINIDASE
    ChainsA, B
    EC Number3.2.1.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET28A
    Expression System Vector TypePLASMID
    FragmentCATALYTIC MODULE, RESIDUES 627-1064
    Organism ScientificSTREPTOCOCCUS PNEUMONIAE
    Organism Taxid170187
    StrainTIGR4
    SynonymGLYCOSIDE HYDROLASE 20

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3OAN2Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3OAN1Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3OAN1Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:641 , HIS B:742 , ASP B:804 , GLU B:805 , TRP B:872 , TRP B:876 , TYR B:879 , TYR B:902 , ILE B:904 , TRP B:951 , ASP B:953 , HOH B:3040BINDING SITE FOR RESIDUE OAN B2041
02AC2SOFTWAREARG A:641 , HIS A:742 , ASP A:804 , GLU A:805 , TRP A:872 , TRP A:876 , TYR A:879 , TYR A:902 , ILE A:904 , TRP A:951 , ASP A:953 , ACT A:2043 , HOH A:3044BINDING SITE FOR RESIDUE OAN A2040
03AC3SOFTWARETYR B:854 , GLN B:862 , LYS B:865 , LYS B:890BINDING SITE FOR RESIDUE ACT B2042
04AC4SOFTWARETYR B:705 , ASP B:744 , HOH B:3062 , HOH B:3065BINDING SITE FOR RESIDUE ACT B2043
05AC5SOFTWAREGLN A:1039 , HOH A:3271BINDING SITE FOR RESIDUE ACT A2041
06AC6SOFTWARETYR A:854 , GLN A:862 , LYS A:865 , LYS A:890 , HOH A:3176BINDING SITE FOR RESIDUE ACT A2042
07AC7SOFTWAREARG A:641 , GLU A:805 , ASN A:808 , OAN A:2040BINDING SITE FOR RESIDUE ACT A2043
08AC8SOFTWAREARG B:641 , GLU B:805 , ASN B:808BINDING SITE FOR RESIDUE ACT B2044
09AC9SOFTWAREGLN A:648 , TYR A:959 , GLU A:961BINDING SITE FOR RESIDUE EDO A2044
10BC1SOFTWARESER B:657 , GLY B:660 , TYR B:661 , LYS B:729 , ASP B:730 , ILE B:731 , ARG B:980 , HOH B:3030 , HOH B:3031 , HOH B:3273BINDING SITE FOR RESIDUE EDO B2045
11BC2SOFTWAREILE B:904 , LEU B:905 , GLY B:906 , GLN B:907 , ARG B:954BINDING SITE FOR RESIDUE EDO B2046
12BC3SOFTWARETYR A:705 , ASP A:744 , HOH A:3067BINDING SITE FOR RESIDUE EDO A2045
13BC4SOFTWAREHIS B:761 , ASP B:771 , LEU B:772 , TYR B:806BINDING SITE FOR RESIDUE EDO B2047
14BC5SOFTWAREALA A:760 , HIS A:761 , ASP A:771 , LEU A:772 , TYR A:806BINDING SITE FOR RESIDUE EDO A2046
15BC6SOFTWAREGLU A:751 , GLY A:754 , LYS A:756 , ASN A:757 , HOH A:3273BINDING SITE FOR RESIDUE EDO A2047
16BC7SOFTWARETYR A:903 , GLN A:907 , LEU A:916 , GLU A:963 , HOH A:3185BINDING SITE FOR RESIDUE EDO A2048
17BC8SOFTWAREGLY B:906 , ARG B:954 , ALA B:957 , GLU B:958 , HOH B:3227BINDING SITE FOR RESIDUE EDO B2048

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AZG)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:739 -Pro A:740
2Tyr A:936 -Pro A:937
3Ser B:739 -Pro B:740
4Tyr B:936 -Pro B:937

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AZG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AZG)

(-) 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:411
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:418
                                   631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031        
          STRH_STRPN    622 AKREVEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGGGFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKIPTNLEGYSKESLEALDAAKTALNYNLNRNKQAELDTLVANLKAALQ 1039
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhheeeeeee......hhhhhhhhhhhhhhhh..eeeeeee............eee..eeehhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.....eee...eeeeee...hhhhhhhhhhhhhhhhhhhh....eee......hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeee....hhhhh.........eeee...........hhhhhhhh..eeee.hhhhhee...hhhhh..hhhhhhhhhhhh................eeeeeeeee........hhhhhhhhhhhhhhh........hhhhhhhhh..-------..hhhhhhhhhhhh........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4azg A  622 RGSHMEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGGGFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKI-------SKESLEALDAAKTALNYNLNRNKQAELDTLVANLKAALQ 1039
                                   631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991 |    1001      1011      1021      1031        
                                                                                                                                                                                                                                                                                                                                                                                                             993    1001                                      

Chain B from PDB  Type:PROTEIN  Length:414
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:419
                                   631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031         
          STRH_STRPN    622 AKREVEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGGGFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKIPTNLEGYSKESLEALDAAKTALNYNLNRNKQAELDTLVANLKAALQG 1040
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhheeeeeee......hhhhhhhhhhhhhhhh..eeeeeee.....ee.....eee..eeehhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhh.....eee...eeeeee...hhhhhhhhhhhhhhhhhhhh....eeeee....hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeee....hhhhh.........eeee...........hhhhhhhh..eeee.hhhhhee...hhhhh..hhhhhhhhhhhh................eeeeeeeee........hhhhhhhhhhhhhhh........hhhhhhhhh...-----.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4azg B  622 RGSHMEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGGGFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKIP-----YSKESLEALDAAKTALNYNLNRNKQAELDTLVANLKAALQG 1040
                                   631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991  |   1001      1011      1021      1031         
                                                                                                                                                                                                                                                                                                                                                                                                              994  1000                                        

   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  (0, 0)

(no "SCOP Domain" information available for 4AZG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (STRH_STRPN | P49610)
molecular function
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        STRH_STRPN | P496102ltj 2yl5 2yl6 2yl8 2yl9 2yla 2yll 4az5 4az6 4az7 4azb 4azc 4azh 4azi

(-) Related Entries Specified in the PDB File

2yl5 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl6 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl8 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl9 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yla INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yll INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
4az5 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4az6 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4az7 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azh DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azi DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH