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 THE CATALYTIC-DOMAIN OF HUMAN CARBONIC ANHYDRASE IX AT 1.6 ANGSTROM RESOLUTION
 
Authors :  B. P. Mahon, L. Socorro, J. M. Driscoll, R. Mckenna
Date :  21 Sep 15  (Deposition) - 03 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Carbonic Anhydrase Ix, Catalytic Domain, Water Network, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. P. Mahon, A. Bhatt, L. Socorro, J. M. Driscoll, C. Okoh, C. L. Lomelino, M. Y. Mboge, J. J. Kurian, C. Tu, M. Agbandje-Mckenna, S. C. Frost, R. Mckenna
The Structure Of Carbonic Anhydrase Ix Is Adapted For Low-P Catalysis.
Biochemistry V. 55 4642 2016
PubMed-ID: 27439028  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00243

(-) Compounds

Molecule 1 - CARBONIC ANHYDRASE 9
    Chains: A, B
    EC Number: 4.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC-DOMAIN (UNP RESIDUES 140-399)
    Gene: CA9, G250, MN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARBONATE DEHYDRATASE IX,CARBONIC ANHYDRASE IX,CAIX,MEMBRANE ANTIGEN MN,P54/58N,RENAL CELL CARCINOMA-ASSOCIATED ANTIGEN G250,RCC- ASSOCIATED ANTIGEN G250,PMW1

 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, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:226 , HIS A:228 , HIS A:251 , HOH A:606binding site for residue ZN A 401
02AC2SOFTWAREHIS A:140 , TRP A:141 , HIS A:200 , HIS B:244binding site for residue ZN A 402
03AC3SOFTWAREGLN A:224 , HOH A:506 , HOH A:638 , HOH A:755binding site for residue GOL A 403
04AC4SOFTWAREARG A:151 , GLN A:326 , TYR A:327 , GLU A:328 , ILE A:341 , HOH A:512 , HOH A:538 , HOH A:595binding site for residue GOL A 404
05AC5SOFTWAREARG A:151 , VAL A:152 , GLU A:387 , HOH A:521 , HOH A:646 , GLY B:393 , VAL B:394 , ASP B:395binding site for residue GOL A 405
06AC6SOFTWAREARG A:159 , GLN A:338binding site for residue CL A 406
07AC7SOFTWAREGLU A:242 , HOH A:579binding site for residue CL A 407
08AC8SOFTWARELEU A:373 , PHE A:375 , HOH A:575 , HOH A:611 , HOH A:675binding site for residue TRS A 408
09AC9SOFTWAREHIS A:244 , TRP B:141 , HIS B:200 , HOH B:671binding site for residue ZN A 409
10AD1SOFTWAREHIS B:226 , HIS B:228 , HIS B:251 , HOH B:575binding site for residue ZN B 401
11AD2SOFTWAREGLN B:224 , VAL B:253 , HOH B:586 , HOH B:602 , HOH B:611 , HOH B:683binding site for residue GOL B 402
12AD3SOFTWAREPRO B:269 , GLY B:270 , GLU B:328 , HOH B:511binding site for residue GOL B 403
13AD4SOFTWAREPRO A:208 , PHE B:160 , ARG B:384 , HOH B:514 , HOH B:547 , HOH B:707binding site for residue GOL B 404
14AD5SOFTWAREARG B:159 , GLN B:338binding site for residue CL B 405

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:156 -A:336
2B:156 -B:336

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:146 -Pro A:147
2Ser A:162 -Pro A:163
3Leu A:190 -Pro A:191
4Pro A:334 -Pro A:335
5Asp B:146 -Pro B:147
6Ser B:162 -Pro B:163
7Leu B:190 -Pro B:191
8Pro B:334 -Pro B:335

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DVX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DVX)

(-) Exons   (0, 0)

(no "Exon" information available for 5DVX)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh......eehhhhhee.......eee.........eeeee....eeee.....eeeee..eeeeeeeeeeee..........ee......eeeeeeeee....hhhhhh.....eeeeeeeeee....hhhhhhhhhhhhhhh....eeee...hhhhhh......eeeeeee.......eeeeeeee...eeehhhhhhhhhhh........................ee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dvx A 140 HWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELSGFQLPPLPELRLRNNGHSVQLTLPPGLEMKLGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVHLSTKYARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDISALLPSDFSRYFQYEGSLTTPPCAQGVIWTVFNQTVSLSAKQLHTLSDTLWGPGDSRLQLNFRATQPLNGRVIEASFPAGVDSSPR 399
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh......eehhhhhee.......eee.........eeeee....eeee.....eeeee..eeeeeeeeeeee..........ee......eeeeeeeee....hhhhhh.....eeeeeeeeee....hhhhhhhhhhhhhhh....eeee...hhhhhh......eeeeeee.......eeeeeeee...eeehhhhhhhhhhh........................ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dvx B 141 WRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELSGFQLPPLPELRLRNNGHSVQLTLPPGLEMKLGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVHLSTKYARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDISALLPSDFSRYFQYEGSLTTPPCAQGVIWTVFNQTVSLSAKQLHTLSDTLWGPGDSRLQLNFRATQPLNGRVIEASFPAGVD 395
                                   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
   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 5DVX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DVX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DVX)

(-) Gene Ontology  (20, 20)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
    Asp A:146 - Pro A:147   [ RasMol ]  
    Asp B:146 - Pro B:147   [ RasMol ]  
    Leu A:190 - Pro A:191   [ RasMol ]  
    Leu B:190 - Pro B:191   [ RasMol ]  
    Pro A:334 - Pro A:335   [ RasMol ]  
    Pro B:334 - Pro B:335   [ RasMol ]  
    Ser A:162 - Pro A:163   [ RasMol ]  
    Ser B:162 - Pro B:163   [ 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
  5dvx
    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
  CAH9_HUMAN | Q16790
    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)
  4.2.1.1
    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
  CAH9_HUMAN | Q16790
    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
        CAH9_HUMAN | Q16790: 2hkf 3iai 5fl4 5fl5 5fl6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DVX)