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
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)

(-) Description

Title :  C. BESCII FAMILY 3 PECTATE LYASE DOUBLE MUTANT K108A/R133A IN COMPLEX WITH ALPHA-D-GALACTOPYRANURONIC ACID
 
Authors :  P. M. Alahuhta, V. V. Lunin
Date :  25 Mar 15  (Deposition) - 23 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pl3, Parallel Beta-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Alahuhta, L. E. Taylor, R. Brunecky, D. W. Sammond, W. Michener, M. W. Adams, M. E. Himmel, Y. J. Bomble, V. Lunin
The Catalytic Mechanism And Unique Low Ph Optimum Of Caldicellulosiruptor Bescii Family 3 Pectate Lyase.
Acta Crystallogr. , Sect. D V. 71 1946 2015
PubMed-ID: 26327384  |  Reference-DOI: 10.1107/S1399004715013760

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A, B
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ATHE_1854
    Mutation: YES
    Organism Scientific: CALDICELLULOSIRUPTOR BESCII (STRAIN ATCC BAA- 1888 / DSM 6725 / Z-1320)
    Organism Taxid: 521460
    Strain: ATCC BAA-1888 / DSM 6725 / Z-1320

 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  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1ADA2Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA8Ligand/IonCALCIUM ION
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1ADA1Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADA1Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD-1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:37 , GLU A:84 , ASP A:107 , CA A:202 , HOH A:366 , HOH A:376 , HOH A:469binding site for residue CA A 201
02AC2SOFTWAREGLU A:39 , GLU A:84 , CA A:201 , ADA A:205 , HOH A:324 , HOH A:469binding site for residue CA A 202
03AC3SOFTWAREASP A:64 , GLU A:84 , ASP A:85 , ADA A:205 , HOH A:339 , HOH A:363binding site for residue CA A 203
04AC4SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:371 , HOH A:389 , HOH A:478binding site for residue CA A 204
05AC5SOFTWAREGLU A:39 , GLU A:84 , ASP A:85 , GLN A:111 , ASN A:113 , ASN A:135 , CA A:202 , CA A:203 , HOH A:304 , HOH A:329 , HOH A:339 , HOH A:363 , HOH A:450binding site for residue ADA A 205
06AC6SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , MPD A:207 , HOH A:364 , ASN B:1binding site for residue MRD A 206
07AC7SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , MRD A:206 , HOH A:364 , THR B:0 , ASN B:1binding site for residue MPD A 207
08AC8SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , LEU B:6 , ILE B:12 , TYR B:20 , HOH B:424binding site for residue MPD A 208
09AC9SOFTWARELYS A:119 , TYR A:145 , GLU A:147 , SER A:186 , SER A:188 , TYR A:193binding site for residue MPD A 209
10AD1SOFTWAREGLN B:37 , GLU B:84 , ASP B:107 , CA B:202 , HOH B:368 , HOH B:437 , HOH B:469binding site for residue CA B 201
11AD2SOFTWAREGLU B:39 , GLU B:84 , CA B:201 , ADA B:205 , HOH B:351 , HOH B:469binding site for residue CA B 202
12AD3SOFTWAREASP B:64 , GLU B:84 , ASP B:85 , ADA B:205 , HOH B:330 , HOH B:380binding site for residue CA B 203
13AD4SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:369 , HOH B:400 , HOH B:487binding site for residue CA B 204
14AD5SOFTWAREHOH A:322 , GLU B:39 , GLU B:84 , ASP B:85 , GLN B:111 , ASN B:113 , ASN B:135 , CA B:202 , CA B:203 , HOH B:330 , HOH B:339 , HOH B:357 , HOH B:376 , HOH B:380 , HOH B:435 , HOH B:450binding site for residue ADA B 205
15AD6SOFTWAREASN A:137 , THR A:139 , ASP B:148 , ASN B:172 , HOH B:307 , HOH B:417binding site for residue MPD B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z06)

(-) 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 4Z06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z06)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z06)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee...eee....eeeeeeeeeee...............eee....eeeeeee.......eee...eeee..ee.......eee....eeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z06 A  -4 HHVGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFQLNAPCTFKVKNFTATNIGKLVAQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185        


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
                 4z06 B  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFQLNAPCTFKVKNFTATNIGKLVAQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 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 4Z06)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z06)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z06)

(-) 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
    ADA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ 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 ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4z06
    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
  B9MKT4_CALBD | B9MKT4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.2.2.2
    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
  B9MKT4_CALBD | B9MKT4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B9MKT4_CALBD | B9MKT4: 3t9g 4ew9 4yz0 4yza 4yzq 4yzx 4z03 4z05

(-) Related Entries Specified in the PDB File

4yz0 4yza 4yzq 4yzx 4z03 4z05