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
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)

(-) Description

Title :  A DEHYDRATED FORM OF GLUCOSE ISOMERASE COLLECTED AT 100K.
 
Authors :  J. Sandy
Date :  14 Apr 15  (Deposition) - 23 Mar 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Lobley, J. Sandy, J. Sanchez-Weatherby, M. Mazzorana, T. Krojer R. P. Nowak, T. L. Sorensen
A Generic Protocol For Protein Crystal Dehydration Using Th Hc1B Humidity Controller.
Acta Crystallogr D Struct V. 72 629 2016 Biol
PubMed-ID: 27139626  |  Reference-DOI: 10.1107/S2059798316003065

(-) Compounds

Molecule 1 - XYLOSE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.5
    Engineered: YES
    Expression System: STREPTOMYCES RUBIGINOSUS
    Expression System Taxid: 1929
    Gene: XYLA
    Organism Scientific: STREPTOMYCES RUBIGINOSUS
    Organism Taxid: 1929
    Synonym: GLUCOSE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1FRU4Ligand/IonFRUCTOSE
2GLC4Ligand/IonALPHA-D-GLUCOSE
3MN11Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1FRU8Ligand/IonFRUCTOSE
2GLC8Ligand/IonALPHA-D-GLUCOSE
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , GLC A:407binding site for residue MN A 401
02AC2SOFTWAREGLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , HOH A:514binding site for residue MN A 402
03AC3SOFTWARETHR A:90 , THR A:91 , TYR A:134 , VAL A:135 , HOH A:717binding site for residue MN A 403
04AC4SOFTWAREASP A:150 , HOH A:518 , ASP B:80 , HOH B:502 , HOH B:557 , HOH B:692 , HOH B:709binding site for residue MN A 404
05AC5SOFTWAREASN A:250 , ASP A:264 , HOH A:573 , HOH A:651 , HOH A:733 , HOH A:734binding site for residue MN A 405
06AC6SOFTWARESER A:355 , HOH A:504 , HOH A:507 , HOH A:508 , HOH A:539binding site for residue MN A 406
07AC7SOFTWARETRP A:16 , HIS A:54 , THR A:90 , PHE A:94 , VAL A:135 , TRP A:137 , GLU A:181 , GLU A:217 , HIS A:220 , ASP A:245 , ASP A:287 , MN A:401 , HOH A:514 , HOH A:525 , HOH A:576 , HOH A:616 , HOH A:633 , PHE B:26binding site for residue GLC A 407
08AC8SOFTWAREASP A:150 , ARG A:152 , ASP A:153 , ASP A:156 , HOH A:580 , HOH A:619 , ASP B:81 , HOH B:557binding site for residue GLC A 408
09AC9SOFTWARETRP A:20 , ASP A:24 , PRO A:25 , TYR A:254 , ASP A:255 , GLN A:256 , LYS A:289 , PRO A:291 , HOH A:522 , HOH A:527 , HOH A:535 , HOH A:640 , HOH A:655 , PRO B:187binding site for residue FRU A 409
10AD1SOFTWARETRP A:16 , HIS A:54 , ASP A:57 , PHE A:94 , THR A:95 , LYS A:289 , HOH A:576 , HOH A:601 , PRO B:25 , PHE B:26 , GLY B:27binding site for residue FRU A 410
11AD2SOFTWAREGLU B:181 , GLU B:217 , ASP B:245 , ASP B:287 , GLC B:406binding site for residue MN B 401
12AD3SOFTWAREGLU B:217 , HIS B:220 , ASP B:255 , ASP B:257 , HOH B:530binding site for residue MN B 402
13AD4SOFTWAREHOH A:563 , HOH A:725 , ALA B:339 , HOH B:507 , HOH B:611binding site for residue MN B 403
14AD5SOFTWAREASN B:250 , ASP B:264 , HOH B:568 , HOH B:666 , HOH B:725binding site for residue MN B 404
15AD6SOFTWAREGLY B:138 , HOH B:555 , HOH B:594 , HOH B:736binding site for residue MN B 405
16AD7SOFTWAREPHE A:26 , TRP B:16 , HIS B:54 , PHE B:94 , TRP B:137 , GLU B:181 , GLU B:217 , HIS B:220 , ASP B:245 , ASP B:287 , MN B:401 , GLC B:407 , HOH B:530 , HOH B:574 , HOH B:621 , HOH B:643binding site for residue GLC B 406
17AD8SOFTWAREPRO A:25 , PHE A:26 , TRP B:16 , ASP B:57 , THR B:95 , LYS B:289 , GLC B:406 , HOH B:525 , HOH B:673binding site for residue GLC B 407
18AD9SOFTWAREPRO A:25 , PRO A:187 , TRP B:20 , ASP B:24 , PRO B:25 , TYR B:254 , ASP B:255 , GLN B:256 , LYS B:289 , PRO B:291 , HOH B:504 , HOH B:524 , HOH B:537 , HOH B:542 , HOH B:563 , HOH B:592 , HOH B:599binding site for residue FRU B 408
19AE1SOFTWAREARG A:117 , SER B:64 , SER B:66 , GLU B:67 , LEU B:351 , ASP B:352 , ARG B:354 , GLU B:358 , HOH B:634 , HOH B:644binding site for residue FRU B 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:186 -Pro A:187
2Glu B:186 -Pro B:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZBC)

(-) 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.....ee......hhhhhhhhhhhhhhhhhhhhhhhh...eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zbc A   2 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       


Chain B from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zbc B   2 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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 4ZBC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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
    FRU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ 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 ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:186 - Pro A:187   [ RasMol ]  
    Glu B:186 - Pro B:187   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4zbc
    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
  XYLA_STRRU | P24300
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.1.5
    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
  XYLA_STRRU | P24300
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        XYLA_STRRU | P24300: 1gw9 1mnz 1o1h 1oad 1xib 1xic 1xid 1xie 1xif 1xig 1xih 1xii 1xij 1xis 2g4j 2glk 2gub 2gve 2xis 3cwh 3gnx 3kbj 3kbm 3kbn 3kbs 3kbv 3kbw 3kcj 3kcl 3kco 3n4a 3qys 3qza 3u3h 3xis 4a8i 4a8l 4a8n 4a8r 4duo 4dvo 4e3v 4j4k 4lnc 4qdp 4qdw 4qe1 4qe4 4qe5 4qee 4qeh 4us6 4w4q 4xis 4zb0 4zb2 4zb5 5avh 5avn 5i7g 8xia 9xia

(-) Related Entries Specified in the PDB File

4zb2 ALL STRUCTURES FROM THE SAME STUDY
4zb5 ALL STRUCTURES FROM THE SAME STUDY
4zbo ALL STRUCTURES FROM THE SAME STUDY