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 IBPAFIC2-H3717A IN COMPLEX WITH ADENYLYLATED CDC42
 
Authors :  J. Xiao, J. E. Dixon
Date :  18 Jan 13  (Deposition) - 20 Feb 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fic Domain, Adenosine Monophosphate-Protein Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xiao, C. A. Worby, S. Mattoo, B. Sankaran, J. E. Dixon
Structural Basis Of Fic-Mediated Adenylylation.
Nat. Struct. Mol. Biol. V. 17 1004 2010
PubMed-ID: 20622875  |  Reference-DOI: 10.1038/NSMB.1867

(-) Compounds

Molecule 1 - ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE AND CYSTEINE PROTEASE IBPA
    Chains: A, B
    EC Number: 2.7.7.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FIDO 2 DOMAIN (UNP RESIDUES 3482-3797)
    Gene: IBPA, P76, HSM_1489
    Mutation: YES
    Organism Scientific: HAEMOPHILUS SOMNUS
    Organism Taxid: 228400
    Strain: 2336
    Synonym: HMW IGBP, P120, ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE IBPA, AMPYLATOR IBPA, CYSTEINE PROTEASE IBPA, PROTEIN P76 IGBP, 76 KDA ANTIGEN
 
Molecule 2 - CELL DIVISION CONTROL PROTEIN 42 HOMOLOG
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDC42
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: G25K GTP-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:3660 , LEU A:3661 , HOH A:4112 , HOH A:4113 , HOH A:4117 , LYS B:3532BINDING SITE FOR RESIDUE SO4 A 3801
02AC2SOFTWARELYS A:3532 , ARG B:3660 , LEU B:3661 , HOH B:4034 , HOH B:4080 , HOH B:4088BINDING SITE FOR RESIDUE SO4 B 3801
03AC3SOFTWARELYS B:3670 , GLU B:3671 , ALA B:3673 , ILE B:3714 , GLU B:3721 , GLY B:3722 , ASN B:3723 , GLY B:3724 , ARG B:3728 , GLU B:3751 , PRO B:3752 , ILE B:3755 , GLN B:3757 , HOH B:4137 , TYR C:32 , HOH C:324BINDING SITE FOR RESIDUE AMP C 201
04AC4SOFTWAREGLU B:3671 , ASN B:3672 , ALA C:13 , VAL C:14 , GLY C:15 , LYS C:16 , THR C:17 , CYS C:18 , PHE C:28 , GLN C:116 , ASP C:118 , LEU C:119 , SER C:158 , ALA C:159 , LEU C:160 , MG C:203 , HOH C:302 , HOH C:305 , HOH C:308 , HOH C:316 , HOH C:328 , HOH C:342 , HOH C:345BINDING SITE FOR RESIDUE GDP C 202
05AC5SOFTWARETHR C:17 , THR C:35 , GDP C:202 , HOH C:302 , HOH C:345BINDING SITE FOR RESIDUE MG C 203
06AC6SOFTWARELYS B:3759 , SER B:3761 , HOH B:4138 , HOH B:4143 , SER C:86 , PRO C:87 , SER C:88 , GLN C:134 , HOH C:404BINDING SITE FOR RESIDUE SO4 C 204
07AC7SOFTWARELYS A:3670 , GLU A:3671 , ALA A:3673 , ILE A:3714 , GLU A:3721 , GLY A:3722 , ASN A:3723 , GLY A:3724 , ARG A:3728 , GLU A:3751 , PRO A:3752 , ILE A:3755 , GLN A:3757 , HOH A:4118 , TYR D:32 , HOH D:366BINDING SITE FOR RESIDUE AMP D 201
08AC8SOFTWAREGLU A:3671 , ASN A:3672 , ASP D:11 , ALA D:13 , VAL D:14 , GLY D:15 , LYS D:16 , THR D:17 , CYS D:18 , PHE D:28 , GLN D:116 , ASP D:118 , LEU D:119 , SER D:158 , ALA D:159 , LEU D:160 , MG D:203 , HOH D:302 , HOH D:306 , HOH D:308 , HOH D:312 , HOH D:330 , HOH D:340 , HOH D:387 , HOH D:395BINDING SITE FOR RESIDUE GDP D 202
09AC9SOFTWARETHR D:17 , THR D:35 , GDP D:202 , HOH D:302 , HOH D:340 , HOH D:387BINDING SITE FOR RESIDUE MG D 203
10BC1SOFTWARELYS A:3759 , SER A:3761 , SER D:86 , PRO D:87 , SER D:88 , GLN D:134 , HOH D:381 , HOH D:389 , HOH D:402BINDING SITE FOR RESIDUE SO4 D 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ITR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ITR)

(-) 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:299
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...............ee.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...........hhhhh...........hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4itr A 3488 VNYQDLEDNLNLKGLISLEDDRNANFESNVLKNEKFLDEAREISKKSIPEATVKQMSHLPEFDDILTEGAKKVESRINKAITFRPSVEEFSEIQDLVKTLPKTKVIEDLSTKTNEITEALAATSKTIQRTPELKEQLKTAIEDFLQNSQGKPLTVQMIENLNHGLRPDEGEGRLLYKKENLTKENAVFSSPEAAKIQLAETVDFINRAKNEGIEPSVVGALVYQRLIAYAPFAEGNGRMARVIVNKILLDAGYPAFTKFSDEFEPQIIPQTKASTKSATSSEVVVEFLKELAKKGSKED 3786
                                  3497      3507      3517      3527      3537      3547      3557      3567      3577      3587      3597      3607      3617      3627      3637      3647      3657      3667      3677      3687      3697      3707      3717      3727      3737      3747      3757      3767      3777         


Chain B from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...............ee.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...........hhhhh...........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4itr B 3488 VNYQDLEDNLNLKGLISLEDDRNANFESNVLKNEKFLDEAREISKKSIPEATVKQMSHLPEFDDILTEGAKKVESRINKAITFRPSVEEFSEIQDLVKTLPKTKVIEDLSTKTNEITEALAATSKTIQRTPELKEQLKTAIEDFLQNSQGKPLTVQMIENLNHGLRPDEGEGRLLYKKENLTKENAVFSSPEAAKIQLAETVDFINRAKNEGIEPSVVGALVYQRLIAYAPFAEGNGRMARVIVNKILLDAGYPAFTKFSDEFEPQIIPQTKASTKSATSSEVVVEFLKELAKKGS 3783
                                  3497      3507      3517      3527      3537      3547      3557      3567      3577      3587      3597      3607      3617      3627      3637      3647      3657      3667      3677      3687      3697      3707      3717      3727      3737      3747      3757      3767      3777      


Chain C from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                 
               SCOP domains d4itrc_ C: CDC42                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhh......ee.....eeeeeee..eeeeeeee....hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4itr C    3 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALE  178
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      


Chain D from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                  
               SCOP domains d4itrd_ D: CDC42                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhh......ee.....eeeeeee..eeeeeeee....hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4itr D    3 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEP  179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (127, 129)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4itr)
 

(-) 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
  4itr
    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
  CDC42_HUMAN | P60953
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  IBPA_HISS2 | Q06277
    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)
  2.7.7.1
    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
  CDC42_HUMAN | P60953
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IBPA_HISS2 | Q06277
    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
        CDC42_HUMAN | P60953: 1a4r 1aje 1am4 1an0 1cee 1cf4 1doa 1e0a 1ees 1grn 1gzs 1ki1 1kz7 1kzg 1nf3 2ase 2dfk 2kb0 2ngr 2odb 2qrz 2wm9 2wmn 2wmo 3gcg 3qbv 3vhl 4did 4js0 4yc7 4ydh 5cjp 5fi1 5hzk
        IBPA_HISS2 | Q06277: 3n3u

(-) Related Entries Specified in the PDB File

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