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 :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI L-ARABINOSE ISOMERASE (ECAI) COMPLEXED WITH RIBITOL
 
Authors :  B. A. Manjasetty, S. K. Burley, S. C. Almo, M. R. Chance, New York Sgx R Center For Structural Genomics (Nysgxrc)
Date :  07 May 12  (Deposition) - 30 May 12  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Structural Genomics, Psi-1, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Isomerase, Sugar Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Manjasetty, S. K. Burley, S. C. Almo, M. R. Chance
Crystal Structure Of Escherichia Coli L-Arabinose Isomerase (Ecai) Complexed With Ribitol
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-ARABINOSE ISOMERASE
    ChainsA, B, C
    EC Number5.3.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET T7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneARAA, B0062, JW0061, UTI89_C0067
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)ABC
Biological Unit 2 (1x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 58)

Asymmetric Unit (4, 58)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2MN3Ligand/IonMANGANESE (II) ION
3MSE51Mod. Amino AcidSELENOMETHIONINE
4RB03Ligand/IonD-RIBITOL
Biological Unit 1 (3, 110)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3MSE102Mod. Amino AcidSELENOMETHIONINE
4RB06Ligand/IonD-RIBITOL
Biological Unit 2 (3, 55)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3MSE51Mod. Amino AcidSELENOMETHIONINE
4RB03Ligand/IonD-RIBITOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:306 , GLU A:333 , HIS A:350 , HIS A:450 , RB0 A:602BINDING SITE FOR RESIDUE MN A 601
2AC2SOFTWAREMSE A:185 , PHE A:279 , GLU A:306 , GLU A:333 , TYR A:335 , HIS A:449 , HIS A:450 , MN A:601 , HOH A:788 , GLN B:16 , LEU B:18 , TYR B:19 , PHE B:83 , GLN B:125 , HIS B:128BINDING SITE FOR RESIDUE RB0 A 602
3AC3SOFTWAREGLU B:306 , GLU B:333 , HIS B:350 , HIS B:450 , RB0 B:602BINDING SITE FOR RESIDUE MN B 601
4AC4SOFTWAREMSE B:185 , PHE B:279 , GLU B:306 , GLU B:333 , HIS B:449 , HIS B:450 , MN B:601 , HOH B:776 , GLN C:16 , TYR C:19 , PHE C:83 , GLN C:125 , HIS C:128BINDING SITE FOR RESIDUE RB0 B 602
5AC5SOFTWARETRP A:491 , VAL A:494 , TRP B:491 , VAL B:494 , TRP C:491 , VAL C:494BINDING SITE FOR RESIDUE ACY B 603
6AC6SOFTWAREGLU C:306 , GLU C:333 , HIS C:350 , HIS C:450 , RB0 C:602BINDING SITE FOR RESIDUE MN C 601
7AC7SOFTWAREGLN A:125 , HIS A:128 , MSE C:185 , PHE C:279 , GLU C:306 , GLU C:333 , HIS C:449 , HIS C:450 , MN C:601BINDING SITE FOR RESIDUE RB0 C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F2D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:432 -Pro A:433
2Gly B:20 -Pro B:21
3Gln B:432 -Pro B:433
4Gln C:432 -Pro C:433

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F2D)

(-) Exons   (0, 0)

(no "Exon" information available for 4F2D)

(-) 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:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4f2da1 A:1-328 automated matches                                                                                                                                                                                                                                                                                                       d4f2da2 A:329-498 automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhh.eeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh..eee.............hhhhhhhhhh..eee...hhhhhhhhhhhhhhh......eeeeeeeeee......eeeee.....hhhhh.....eeee...........eeee.....eeeeeeeeee....eeeeeeeeee..............eeeee..hhhhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f2d A   1 mTIFDNYEVWFVIGSQHLYGPETLRQVTQHAEHVVNALNTEAKLPCKLVLKPLGTTPDEITAICRDANYDDRCAGLVVWLHTFSPAKmWINGLTmLNKPLLQFHTQFNAALPWDSIDmDFmNLNQTAHGGREFGFIGARmRQQHAVVTGHWQDKQAHERIGSWmRQAVSKQDTRHLKVCRFGDNmREVAVTDGDKVAAQIKFGFSVNTWAVGDLVQVVNSISDGDVNALVDEYESCYTmTPATQIHGEKRQNVLEAARIELGmKRFLEQGGFHAFTTTFEDLHGLKQLPGLAVQRLmQQGYGFAGEGDWKTAALLRImKVmSTGLQGGTSFmEDYTYHFEKGNDLVLGSHmLEVCPSIAVEEKPILDVQHLGIGGKDDPARLIFNTQTGPAIVASLIDLGDRYRLLVNCIDTVKTPHSLPKLPVANALWKAQPDLPTASEAWILAGGAHHTVFSHALNLNDmRQFAEmHDIEITVIDNDTRLPAFKDALRWNEVYYGF 498
                            |       10        20        30        40        50        60        70        80       |90    |  100       110       120|      130       140       150       160   |   170       180    |  190       200       210       220       230       240       250       260  |    270       280       290      |300       310       320|      330 |     340       350|      360       370       380       390       400       410       420       430       440       450       460 |     470       480       490        
                            |                                                                                     88-MSE 95-MSE                118-MSE               140-MSE                 164-MSE              185-MSE                                               239-MSE                 263-MSE                           297-MSE              318-MSE       332-MSE            351-MSE                                                                                                        462-MSE |                              
                            1-MSE                                                                                                                 121-MSE                                                                                                                                                                                                 321-MSE                                                                                                                                            468-MSE                          

Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4f2db1 B:1-328 automated matches                                                                                                                                                                                                                                                                                                       d4f2db2 B:329-498 automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.eeeeee.......hhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhh.eeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh..eee.............hhhhhhhhhh..eee...hhhhhhhhhhhhhhh......eeeeeeeeee......eeeee.....hhhhh.....eeee...........eeee.....eeeeeeeeee....eeeeeeeeee..............eeeee..hhhhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f2d B   1 mTIFDNYEVWFVIGSQHLYGPETLRQVTQHAEHVVNALNTEAKLPCKLVLKPLGTTPDEITAICRDANYDDRCAGLVVWLHTFSPAKmWINGLTmLNKPLLQFHTQFNAALPWDSIDmDFmNLNQTAHGGREFGFIGARmRQQHAVVTGHWQDKQAHERIGSWmRQAVSKQDTRHLKVCRFGDNmREVAVTDGDKVAAQIKFGFSVNTWAVGDLVQVVNSISDGDVNALVDEYESCYTmTPATQIHGEKRQNVLEAARIELGmKRFLEQGGFHAFTTTFEDLHGLKQLPGLAVQRLmQQGYGFAGEGDWKTAALLRImKVmSTGLQGGTSFmEDYTYHFEKGNDLVLGSHmLEVCPSIAVEEKPILDVQHLGIGGKDDPARLIFNTQTGPAIVASLIDLGDRYRLLVNCIDTVKTPHSLPKLPVANALWKAQPDLPTASEAWILAGGAHHTVFSHALNLNDmRQFAEmHDIEITVIDNDTRLPAFKDALRWNEVYYGF 498
                            |       10        20        30        40        50        60        70        80       |90    |  100       110       120|      130       140       150       160   |   170       180    |  190       200       210       220       230       240       250       260  |    270       280       290      |300       310       320|      330 |     340       350|      360       370       380       390       400       410       420       430       440       450       460 |     470       480       490        
                            1-MSE                                                                                 88-MSE 95-MSE                118-MSE               140-MSE                 164-MSE              185-MSE                                               239-MSE                 263-MSE                           297-MSE              318-MSE       332-MSE            351-MSE                                                                                                        462-MSE |                              
                                                                                                                                                  121-MSE                                                                                                                                                                                                 321-MSE                                                                                                                                            468-MSE                          

Chain C from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4f2dc1 C:1-328 automated matches                                                                                                                                                                                                                                                                                                       d4f2dc2 C:329-498 automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.eeeeee......hhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhhh.eeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhee.hhhh.......hhhhhhhhhhhhhhhhhhhh..eee.............hhhhhhhhhh..eee...hhhhhhhhhhhhhhh......eeeeeeeeee......eeeee.....hhhhh.....eeee...........eeee.....eeeeeeeeee....eeeeeeeeee.................ee..hhhhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f2d C   1 mTIFDNYEVWFVIGSQHLYGPETLRQVTQHAEHVVNALNTEAKLPCKLVLKPLGTTPDEITAICRDANYDDRCAGLVVWLHTFSPAKmWINGLTmLNKPLLQFHTQFNAALPWDSIDmDFmNLNQTAHGGREFGFIGARmRQQHAVVTGHWQDKQAHERIGSWmRQAVSKQDTRHLKVCRFGDNmREVAVTDGDKVAAQIKFGFSVNTWAVGDLVQVVNSISDGDVNALVDEYESCYTmTPATQIHGEKRQNVLEAARIELGmKRFLEQGGFHAFTTTFEDLHGLKQLPGLAVQRLmQQGYGFAGEGDWKTAALLRImKVmSTGLQGGTSFmEDYTYHFEKGNDLVLGSHmLEVCPSIAVEEKPILDVQHLGIGGKDDPARLIFNTQTGPAIVASLIDLGDRYRLLVNCIDTVKTPHSLPKLPVANALWKAQPDLPTASEAWILAGGAHHTVFSHALNLNDmRQFAEmHDIEITVIDNDTRLPAFKDALRWNEVYYGF 498
                            |       10        20        30        40        50        60        70        80       |90    |  100       110       120|      130       140       150       160   |   170       180    |  190       200       210       220       230       240       250       260  |    270       280       290      |300       310       320|      330 |     340       350|      360       370       380       390       400       410       420       430       440       450       460 |     470       480       490        
                            1-MSE                                                                                 88-MSE 95-MSE                118-MSE               140-MSE                 164-MSE              185-MSE                                               239-MSE                 263-MSE                           297-MSE              318-MSE       332-MSE            351-MSE                                                                                                        462-MSE |                              
                                                                                                                                                  121-MSE                                                                                                                                                                                                 321-MSE                                                                                                                                            468-MSE                          

   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  (2, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F2D)

(-) Gene Ontology  (12, 12)

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
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RB0  [ 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
    Gln A:432 - Pro A:433   [ RasMol ]  
    Gln B:432 - Pro B:433   [ RasMol ]  
    Gln C:432 - Pro C:433   [ RasMol ]  
    Gly B:20 - Pro B:21   [ 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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4f2d
    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
  ARAA_ECOLI | P08202
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.1.4
    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
  ARAA_ECOLI | P08202
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARAA_ECOLI | P082022ajt 2hxg

(-) Related Entries Specified in the PDB File

2ajt APO FORM
2hxg COMPLEXED WITH COFACTOR MN2+ RELATED ID: NYSGXRC-6358A RELATED DB: TARGETTRACK