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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN CARBONIC ANHYDRASE ISOZYME XII WITH 3-[(PYRIMIDIN-2-YLSULFANYL)ACETYL]BENZENESULFONAMIDE
 
Authors :  A. Smirnov, E. Manakova, S. Grazulis
Date :  13 May 13  (Deposition) - 06 Nov 13  (Release) - 06 Nov 13  (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 :  E. Capkauskaite, A. Zubriene, A. Smirnov, J. Torresan, M. Kisonaite, J. Kazokaite, J. Gylyte, V. Michailoviene, V. Jogaite, E. Manakova, S. Grazulis, S. Tumkevicius, D. Matulis
Benzenesulfonamides With Pyrimidine Moiety As Inhibitors Of Human Carbonic Anhydrases I, Ii, Vi, Vii, Xii, And Xiii
Bioorg. Med. Chem. V. 21 6937 2013
PubMed-ID: 24103428  |  Reference-DOI: 10.1016/J.BMC.2013.09.029

(-) 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: CATALYTIC DOMAIN, 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  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2E1G3Ligand/Ion3-[(PYRIMIDIN-2-YLSULFANYL)ACETYL]BENZENESULFONAMIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN4Ligand/IonZINC ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2E1G2Ligand/Ion3-[(PYRIMIDIN-2-YLSULFANYL)ACETYL]BENZENESULFONAMIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DMS-1Ligand/IonDIMETHYL SULFOXIDE
2E1G1Ligand/Ion3-[(PYRIMIDIN-2-YLSULFANYL)ACETYL]BENZENESULFONAMIDE
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:91 , HIS A:93 , HIS A:117 , E1G A:302BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREGLN A:89 , HIS A:91 , HIS A:93 , HIS A:117 , VAL A:119 , SER A:133 , LEU A:197 , THR A:198 , THR A:199 , PRO A:201 , ZN A:301BINDING SITE FOR RESIDUE E1G A 302
03AC3SOFTWAREPHE A:151 , HOH A:584 , LYS C:18BINDING SITE FOR RESIDUE DMS A 303
04AC4SOFTWAREHIS B:91 , HIS B:93 , HIS B:117 , E1G B:302BINDING SITE FOR RESIDUE ZN B 301
05AC5SOFTWAREGLN B:89 , HIS B:91 , HIS B:93 , HIS B:117 , VAL B:119 , SER B:133 , LEU B:197 , THR B:198 , THR B:199 , PRO B:201 , TRP B:208 , ZN B:301 , HOH B:580BINDING SITE FOR RESIDUE E1G B 302
06AC6SOFTWARETRP B:4 , ASN B:64 , HIS B:66 , GLN B:89 , HIS B:91 , THR B:199 , HOH B:566BINDING SITE FOR RESIDUE PEG B 303
07AC7SOFTWAREASP B:156 , SER B:160 , HOH B:513BINDING SITE FOR RESIDUE EDO B 304
08AC8SOFTWAREHIS C:91 , HIS C:93 , HIS C:117BINDING SITE FOR RESIDUE ZN C 301
09AC9SOFTWAREHIS D:91 , HIS D:93 , HIS D:117 , E1G D:302BINDING SITE FOR RESIDUE ZN D 301
10BC1SOFTWAREGLN 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:201 , ZN D:301 , PEG D:303 , HOH D:535BINDING SITE FOR RESIDUE E1G D 302
11BC2SOFTWARETRP D:4 , ASN D:64 , HIS D:66 , SER D:67 , GLN D:89 , HIS D:91 , THR D:199 , E1G D:302 , HOH D:422 , HOH D:533BINDING SITE FOR RESIDUE PEG D 303

(-) 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  (8, 8)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KP8)

(-) Exons   (0, 0)

(no "Exon" information available for 4KP8)

(-) 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 d4kp8a_ A: Carbonic anhydrase                                                                                                                                                                                                                                         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
                 4kp8 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d4kp8b_ B: Carbonic anhydrase                                                                                                                                                                                                                                       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...eeehhhhhhhhhhhh...........................eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kp8 B   4 WTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFS 262
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253         


Chain C from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains d4kp8c_ C: Carbonic anhydrase                                                                                                                                                                                                                                         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
                 4kp8 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains d4kp8d_ D: Carbonic anhydrase                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh......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
                 4kp8 D   4 WTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFSQ 263
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KP8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KP8)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAH12_HUMAN | O43570: 1jcz 1jd0 4ht2 4kp5 4q0l 4qj0 4qjo 4qjw 4ww8

(-) Related Entries Specified in the PDB File

4kni 4knj 4knm 4knn 4kp5