Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE LIGANDED STRUCTURE OF C. BESCII FAMILY 3 PECTATE LYASE
 
Authors :  P. M. Alahuhta, V. V. Lunin
Date :  26 Apr 12  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Pl3, Parallel Beta-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. M. Alahuhta, V. V. Lunin
The Liganded Structure Of C. Bescii Family 3 Pectate Lyase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PECTATE LYASE
    ChainsA, B
    EC Number4.2.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 268-460
    GeneATHE_1854
    Organism ScientificCALDICELLULOSIRUPTOR BESCII
    Organism Taxid521460
    StrainDSM 6725 / Z-1320

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 20)

Asymmetric Unit (6, 20)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ADA1Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
3CA9Ligand/IonCALCIUM ION
4DGU2Ligand/IonD-GALACTURONIC ACID
5MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6UNG2Ligand/Ion4-O-(4-DEOXY-BETA-L-THREO-HEX-4-ENOPYRANURONOSYL)-ALPHA-D-GALACTOPYRANURONIC ACID
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ADA1Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
3CA-1Ligand/IonCALCIUM ION
4DGU1Ligand/IonD-GALACTURONIC ACID
5MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6UNG1Ligand/Ion4-O-(4-DEOXY-BETA-L-THREO-HEX-4-ENOPYRANURONOSYL)-ALPHA-D-GALACTOPYRANURONIC ACID
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ADA-1Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
3CA-1Ligand/IonCALCIUM ION
4DGU1Ligand/IonD-GALACTURONIC ACID
5MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6UNG1Ligand/Ion4-O-(4-DEOXY-BETA-L-THREO-HEX-4-ENOPYRANURONOSYL)-ALPHA-D-GALACTOPYRANURONIC ACID
Biological Unit 3 (5, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ADA1Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
3CA-1Ligand/IonCALCIUM ION
4DGU1Ligand/IonD-GALACTURONIC ACID
5MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6UNG1Ligand/Ion4-O-(4-DEOXY-BETA-L-THREO-HEX-4-ENOPYRANURONOSYL)-ALPHA-D-GALACTOPYRANURONIC ACID

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:310 , HOH A:331 , HOH A:336 , HOH A:353BINDING SITE FOR RESIDUE CA A 201
02AC2SOFTWAREASP A:64 , GLU A:84 , ASP A:85 , DGU A:210 , HOH A:352 , HOH A:482BINDING SITE FOR RESIDUE CA A 202
03AC3SOFTWAREGLN A:37 , GLU A:84 , ASP A:107 , UNG A:209 , HOH A:309 , HOH A:409 , HOH A:444BINDING SITE FOR RESIDUE CA A 203
04AC4SOFTWAREGLU A:39 , GLU A:84 , UNG A:209 , DGU A:210 , HOH A:483BINDING SITE FOR RESIDUE CA A 204
05AC5SOFTWAREGLU A:167 , ADA A:211 , HOH A:367 , HOH A:492 , HOH A:505 , HOH A:506BINDING SITE FOR RESIDUE CA A 205
06AC6SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , HOH A:360 , THR B:0 , ASN B:1BINDING SITE FOR RESIDUE MPD A 206
07AC7SOFTWAREHOH A:447 , HOH A:475 , ASN B:1 , LEU B:6 , MPD B:205BINDING SITE FOR RESIDUE MPD A 207
08AC8SOFTWARELYS A:119 , GLU A:147 , PRO A:164 , TYR A:193 , HOH A:404 , HOH A:522BINDING SITE FOR RESIDUE MPD A 208
09AC9SOFTWAREGLU A:39 , LYS A:54 , GLU A:84 , ASP A:107 , LYS A:108 , GLN A:111 , LYS A:130 , ARG A:133 , ASN A:135 , GLY A:136 , LYS A:160 , CA A:203 , CA A:204 , DGU A:210 , HOH A:409 , HOH A:444 , HOH A:483 , HOH A:485 , HOH A:487 , HOH A:489 , HOH A:513 , HOH A:514 , HOH A:515BINDING SITE FOR RESIDUE UNG A 209
10BC1SOFTWAREGLU A:39 , GLU A:84 , ASP A:85 , GLN A:111 , ASN A:113 , ASN A:135 , CA A:202 , CA A:204 , UNG A:209 , HOH A:352 , HOH A:364 , HOH A:482 , HOH A:487BINDING SITE FOR RESIDUE DGU A 210
11BC2SOFTWARELYS A:141 , LYS A:160 , SER A:161 , ASP A:162 , GLU A:167 , TRP A:169 , GLU A:183 , PRO A:185 , CA A:205 , HOH A:363 , HOH A:367 , HOH A:456 , HOH A:471 , HOH A:505 , HOH A:506BINDING SITE FOR RESIDUE ADA A 211
12BC3SOFTWAREASN A:137 , THR A:139 , ASP B:148BINDING SITE FOR RESIDUE ACT A 212
13BC4SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:303 , HOH B:322 , HOH B:334 , HOH B:337BINDING SITE FOR RESIDUE CA B 201
14BC5SOFTWAREGLN B:37 , GLU B:84 , ASP B:107 , UNG B:206 , HOH B:317 , HOH B:429 , HOH B:432BINDING SITE FOR RESIDUE CA B 202
15BC6SOFTWAREASP B:64 , GLU B:84 , ASP B:85 , DGU B:207 , HOH B:341 , HOH B:422BINDING SITE FOR RESIDUE CA B 203
16BC7SOFTWAREGLU B:39 , GLU B:84 , UNG B:206 , DGU B:207 , HOH B:431BINDING SITE FOR RESIDUE CA B 204
17BC8SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , MPD A:207 , LEU B:6 , ILE B:12 , TYR B:20 , HOH B:314BINDING SITE FOR RESIDUE MPD B 205
18BC9SOFTWARELYS A:103 , HOH A:500 , GLU B:39 , GLU B:84 , ASP B:107 , LYS B:108 , GLN B:111 , LYS B:130 , ARG B:133 , ASN B:135 , GLY B:136 , CA B:202 , CA B:204 , DGU B:207 , HOH B:429 , HOH B:431 , HOH B:437 , HOH B:439 , HOH B:443 , HOH B:444 , HOH B:445BINDING SITE FOR RESIDUE UNG B 206
19CC1SOFTWARELYS A:26 , GLU A:80 , HOH A:377 , HOH A:502 , GLU B:39 , GLU B:84 , ASP B:85 , GLN B:111 , ASN B:113 , CA B:203 , CA B:204 , UNG B:206 , HOH B:341 , HOH B:422 , HOH B:439BINDING SITE FOR RESIDUE DGU B 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EW9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:60 -Pro A:61
2Ala B:60 -Pro B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EW9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EW9)

(-) Exons   (0, 0)

(no "Exon" information available for 4EW9)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eee....eeeeeeeeeee...............eee....eeeeeee.......eee...eeeeeeee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeee...ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ew9 A  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     

Chain B from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eee....eeeeeeeeeee...............eee....eeeeeee.......eee...eeee..ee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeee...ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ew9 B  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     

   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 4EW9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EW9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EW9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ADA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DGU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNG  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:60 - Pro A:61   [ RasMol ]  
    Ala B:60 - Pro B:61   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ew9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B9MKT4_CALBD | B9MKT4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.2.2.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  B9MKT4_CALBD | B9MKT4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B9MKT4_CALBD | B9MKT43t9g 4yz0 4yza 4yzq 4yzx 4z03 4z05 4z06

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4EW9)