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 CATALYTIC DOMAIN OF HUMAN CARBONIC ANHYDRASE ISOZYME XII WITH INHIBITOR
 
Authors :  A. Smirnov, E. Manakova, S. Grazulis
Date :  04 Jun 14  (Deposition) - 15 Apr 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Drug Design, Carbonic Anhydrase, Benzenesulfonamide, Metal-Binding, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Dudutiene, A. Zubriene, A. Smirnov, D. D. Timm, J. Smirnoviene, J. Kazokaite, V. Michailoviene, A. Zaksauskas, E. Manakova, S. Grazulis, D. Matulis
Functionalization Of Fluorinated Benzenesulfonamides And Their Inhibitory Properties Toward Carbonic Anhydrases
Chemmedchem V. 10 662 2015
PubMed-ID: 25758852  |  Reference-DOI: 10.1002/CMDC.201402490

(-) Compounds

Molecule 1 - CARBONIC ANHYDRASE 12
    Chains: A, B, C, D
    EC Number: 4.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-291
    Gene: CA12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARBONATE DEHYDRATASE XII, CARBONIC ANHYDRASE XII, CA-XII, TUMOR ANTIGEN HOM-RCC-3.1.3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2V1F4Ligand/Ion3-(BENZYLAMINO)-2,5,6-TRIFLUORO-4-[(2-PHENYLETHYL)SULFONYL]BENZENESULFONAMIDE
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2V1F2Ligand/Ion3-(BENZYLAMINO)-2,5,6-TRIFLUORO-4-[(2-PHENYLETHYL)SULFONYL]BENZENESULFONAMIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2V1F2Ligand/Ion3-(BENZYLAMINO)-2,5,6-TRIFLUORO-4-[(2-PHENYLETHYL)SULFONYL]BENZENESULFONAMIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:188 , SER A:260 , PHE A:261 , HOH A:426 , HOH A:548 , PRO C:9 , LEU D:25BINDING SITE FOR RESIDUE EDO A 301
02AC2SOFTWAREHIS A:91 , HIS A:93 , HIS A:117 , V1F A:303BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASN A:64 , GLN A:89 , HIS A:91 , HIS A:93 , GLU A:104 , HIS A:117 , ALA A:129 , VAL A:141 , LEU A:197 , THR A:198 , THR A:199 , PRO A:200 , ZN A:302BINDING SITE FOR RESIDUE V1F A 303
04AC4SOFTWAREASP B:156 , SER B:160 , GLN B:221 , HOH B:575BINDING SITE FOR RESIDUE EDO B 301
05AC5SOFTWAREASN B:152 , SER B:154 , GLU B:181BINDING SITE FOR RESIDUE EDO B 302
06AC6SOFTWAREHIS B:91 , HIS B:93 , HIS B:117 , V1F B:304BINDING SITE FOR RESIDUE ZN B 303
07AC7SOFTWAREASN B:64 , GLN B:89 , HIS B:91 , HIS B:93 , HIS B:117 , VAL B:119 , ALA B:129 , SER B:133 , LEU B:197 , THR B:198 , THR B:199 , PRO B:200 , PRO B:201 , TRP B:208 , ZN B:303BINDING SITE FOR RESIDUE V1F B 304
08AC8SOFTWAREHIS C:91 , HIS C:93 , HIS C:117 , V1F C:302BINDING SITE FOR RESIDUE ZN C 301
09AC9SOFTWAREASN C:64 , GLN C:89 , HIS C:91 , HIS C:93 , HIS C:117 , VAL C:119 , ALA C:129 , SER C:130 , SER C:133 , LEU C:197 , THR C:198 , THR C:199 , PRO C:201 , TRP C:208 , ZN C:301 , HOH C:529 , HOH C:578BINDING SITE FOR RESIDUE V1F C 302
10BC1SOFTWAREHIS D:91 , HIS D:93 , HIS D:117 , V1F D:302BINDING SITE FOR RESIDUE ZN D 301
11BC2SOFTWAREASN D:64 , GLN D:89 , HIS D:91 , HIS D:93 , HIS D:117 , VAL D:119 , SER D:133 , LEU D:197 , THR D:198 , THR D:199 , PRO D:200 , TRP D:208 , ZN D:301 , HOH D:526 , HOH D:540BINDING SITE FOR RESIDUE V1F D 302

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:22 -A:202
2B:22 -B:202
3C:22 -C:202
4D:22 -D:202

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ser A:28 -Pro A:29
2Pro A:200 -Pro A:201
3Ser B:28 -Pro B:29
4Pro B:200 -Pro B:201
5Ser C:28 -Pro C:29
6Pro C:200 -Pro C:201
7Ser D:28 -Pro D:29
8Pro D:200 -Pro D:201
9Asp D:253 -Glu D:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QJO)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh......eehhh.eee.......eee........eeeeee....eeee.....eee.....eeeeeeeeee...........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhh.....eeeee..hhhhhh......eeeeee..........eeeeee...eeehhhhhhhhhhh............................eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qjo A   3 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFSQ 263
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262 


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh......eehhh.eee.......eee........eeeeee....eeee.....eee.....eeeeeeeeee...........ee......eeeeeeeee.....hhhhhhh....eeeeeeeeee...hhhhhhhhhhhhhh.....eeeee..hhhhhh......eeeeee..........eeeeee...eeehhhhhhhhhhh............................eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qjo B   3 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFS 262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262


Chain C from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh......eehhh.eee.......eee........eeeeee....eeee.....eee.....eeeeeeeeee...........ee......eeeeeeeee.....hhhhhhh....eeeeeeeeee...hhhhhhhhhhhhhh.....eeeee..hhhhhh......eeeeee..........eeeeee...eeehhhhhhhhhhh............................eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qjo C   3 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFSQ 263
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262 


Chain D from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh......eehhh.eee.......eee........eeeeee....eeee.....eee.....eeeeeeeeee...........ee......eeeeeeeee.....hhhhhhh....eeeeeeeeee......hhhhhhhhhhh.....eeeee..hhhhhh......eeeeee..........eeeeee...eeehhhhhhhhhhh............................eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qjo D   3 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFSQ 263
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
   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 4QJO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    V1F  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp D:253 - Glu D:254   [ RasMol ]  
    Pro A:200 - Pro A:201   [ RasMol ]  
    Pro B:200 - Pro B:201   [ RasMol ]  
    Pro C:200 - Pro C:201   [ RasMol ]  
    Pro D:200 - Pro D:201   [ RasMol ]  
    Ser A:28 - Pro A:29   [ RasMol ]  
    Ser B:28 - Pro B:29   [ RasMol ]  
    Ser C:28 - Pro C:29   [ RasMol ]  
    Ser D:28 - Pro D:29   [ 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
  4qjo
    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
  CAH12_HUMAN | O43570
    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
  CAH12_HUMAN | O43570
    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
        CAH12_HUMAN | O43570: 1jcz 1jd0 4ht2 4kp5 4kp8 4q0l 4qj0 4qjw 4ww8

(-) Related Entries Specified in the PDB File

4qiy 4qiz 4qj0 4qjm 4qjp 4qjw 4qjx 4qtl