Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE (X01 MUTANT)
 
Authors :  D. H. Kwan, I. Constantinescu, R. Chapanian, M. A. Higgins, E. Samain, A. B. Boraston, J. N. Kizhakkedathu, S. G. Withers
Date :  11 Nov 14  (Deposition) - 26 Nov 14  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycoside Hydrolase, Blood Group Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Kwan, I. Constantinescu, R. Chapanian, M. A. Higgins, M. Koetzler, E. Samain, A. B. Boraston, J. N. Kizhakkedathu, S. G. Withers
Towards Efficient Enzymes For The Generation Of Universal Blood Through Structure-Guided Directed Evolution.
J. Am. Chem. Soc. V. 137 5695 2015
PubMed-ID: 25870881  |  Reference-DOI: 10.1021/JA5116088

(-) Compounds

Molecule 1 - GLYCOSIDE HYDROLASE
    Chains: A
    EC Number: 3.2.1.102
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET29
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 423-1005
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Strain: SP3-BS71

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4GAL1Ligand/IonBETA-D-GALACTOSE
5SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:467 , LYS A:731 , ARG A:735 , HOH A:3984BINDING SITE FOR RESIDUE SO4 A2010
2AC2SOFTWAREGLN A:448 , SER A:823 , THR A:824 , HOH A:3723 , HOH A:3726 , HOH A:3727 , HOH A:3985BINDING SITE FOR RESIDUE SO4 A2011
3AC3SOFTWARESER A:537 , THR A:538 , HOH A:3177 , HOH A:3186 , HOH A:3271 , HOH A:3843BINDING SITE FOR RESIDUE SO4 A2012
4AC4SOFTWAREGLY A:631 , ASP A:633 , SER A:634 , GLY A:766 , THR A:774 , ARG A:776 , GLU A:777 , THR A:779BINDING SITE FOR RESIDUE EDO A2013
5AC5SOFTWAREGLY A:443 , GLU A:444 , ASN A:447 , ASP A:482 , HOH A:3054 , HOH A:3127 , HOH A:3987 , HOH A:3988BINDING SITE FOR RESIDUE EDO A2014
6AC6SOFTWAREASP A:481 , ASP A:482 , TYR A:530 , HOH A:3977 , HOH A:3978 , HOH A:3989 , HOH A:3990BINDING SITE FOR RESIDUE EDO A2015
7AC7SOFTWARETYR A:440 , HIS A:479 , ASP A:481 , THR A:523 , THR A:557 , GLU A:558 , THR A:626 , TRP A:659 , GLU A:663 , GLU A:710 , HIS A:711 , PRO A:712 , LYS A:927 , HOH A:3116 , HOH A:3215 , HOH A:3460 , HOH A:3509 , HOH A:3548 , HOH A:3976 , HOH A:3977 , HOH A:3978 , HOH A:3979 , HOH A:3980 , HOH A:3981 , HOH A:3982 , HOH A:3983BINDING SITE FOR POLY-SACCHARIDE RESIDUES A2G A2007 THROUGH FUC A2009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D6E)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:710 -His A:711

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D6E)

(-) Exons   (0, 0)

(no "Exon" information available for 4D6E)

(-) 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:578
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhh..........hhhhhhhhh...hhh.eeeeee........hhhhhhhhhhhhhhhhh............eeeeeee.hhh...hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhh..eeeee.....hhhhhhh.....hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhh..............hhhhhh...hhhhhhhhhhhhhh....eeeeehhhhhhee..eehhhhhhhhhhhhhhhhhh...hhhhhhhhh.eeee.hhhhhhhhhhhh.....................ee..........eeee..hhhhhhhhhhhhhhhhhh........eeeee..eeeee.........eeeeeee..eeeeeee....eeeeeee..eeeeeee.....hhhhhh...hhhhhhh....hhhhhhhhhhhhh.........eeeeeeee......eeeeeee........eeeee....eeeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4d6e A  421 EVDKRREINNEHPLLMMPLYANGEEFNQGKYTFWGGDTLTGKWENIPDDLKPYTVIQLHPDDLPKRDGAARDFYEHMLEEAAKYVNPKTGKNEPIPVILTVYTAGNMPYYTSAHWLSTSWIDKMYQKYPNLHGIFSTESYWIWANDIENKAADYLKVSAKNGGYFIWAEQNVGSAIEKAFGKNGKIAFQKSVDKYWKNLIFMFKNTPAAEGNDSTTESYMKGLWLSNHTYQWGGLMDTWKWYETGKWKLFASGNIGKSQGDRQWLTEPESMLGEEALGVYLNGGVVYNFEHPAYTYGVNNKESLLFSEVIKEFFRYVIAHPAPSKEKVLEDTKVFIHGDYSNKGNGKFFVNVNTDREQTPLYMTGRYNVIPAIPGVLKTDKLIQIKEITSPEFSSTQARKEYLNKLYPMNYEGDIFAQKLDNRWFVYNYKVNENVKQTGKLKFNSLEMNVEFEPHTYGIFERISNGLKVNLNNFRTNKDSLWSNAQDANQAKKLPQLTKKGAIKWIEEHYIKDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTITINSNGNLEFELHFLEH 1006
                                   430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800 ||    818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998        
                                                                                                                                                                                                                                                                                                                                                                                                                       802|                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                        811
   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 4D6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D6E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D6E)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4D6E)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    A2G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:710 - His A:711   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4d6e
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.102
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4D6E)

(-) Related Entries Specified in the PDB File

4d6c CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98)
4d6d CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE
4d6f CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TETRASACCHARIDE (E558A, X01 MUTANT)
4d6g CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE (L19 MUTANT)
4d6h CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 1 BLOOD GROUP A-TETRASACCHARIDE (E558A X02 MUTANT)
4d6i CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 1 BLOOD GROUP A-TETRASACCHARIDE (E558A L19 MUTANT)
4d6j CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 2 BLOOD GROUP A-TETRASACCHARIDE (E558A X01 MUTANT)