3DA2 - JenaLib

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Title :   X-RAY STRUCTURE OF HUMAN CARBONIC ANHYDRASE 13 IN COMPLEX WITH INHIBITOR

Authors :   E. S. Pilka, S. S. Picaud, W. W. Yue, O. N. F. King, J. E. Bray, P. Filippako A. K. Roos, A. C. W. Pike, F. Von Delft, C. H. Arrowsmith, M. Wikstrom, A. M. Edwards, C. Bountra, U. Oppermann, Structural Genomics Conso (Sgc)

Date :   28 May 08 (Deposition) - 15 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Carbonic Anhydrase, Sulfonamide, Sgc, Structural Genomics, Structural Genomics Consortium, Lyase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. S. Pilka, S. S. Picaud, W. W. Yue, O. N. F. King, J. E. Bray, P. Filippakopoulos, A. K. Roos, A. C. W. Pike, F. Von Delft, C. H. Arrowsmith, M. Wikstrom, A. M. Edwards, C. Bountra, U. Oppermann
X-Ray Structure Of Human Carbonic Anhydrase 13 In Complex With Inhibitor.
To Be Published
PubMed: search

Molecule 1 - CARBONIC ANHYDRASE 13
	Chains	:	A, B
	EC Number	:	4.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CA13
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CARBONIC ANHYDRASE XIII, CARBONATE DEHYDRATASE XIII, CA- XIII

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	4MD	2	Ligand/Ion	N-(4-CHLOROBENZYL)-N-METHYLBENZENE-1,4-DISULFONAMIDE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	4MD	1	Ligand/Ion	N-(4-CHLOROBENZYL)-N-METHYLBENZENE-1,4-DISULFONAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	4MD	1	Ligand/Ion	N-(4-CHLOROBENZYL)-N-METHYLBENZENE-1,4-DISULFONAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:95 , HIS A:97 , HIS A:120	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	HIS B:95 , HIS B:97 , HIS B:120	BINDING SITE FOR RESIDUE ZN B 301
3	AC3	SOFTWARE	ARG B:90	BINDING SITE FOR RESIDUE CL B 302
4	AC4	SOFTWARE	ALA B:259 , PHE B:261	BINDING SITE FOR RESIDUE CL B 303
5	AC5	SOFTWARE	GLN A:93 , HIS A:95 , HIS A:97 , HIS A:120 , PHE A:132 , ALA A:136 , HIS A:137 , LEU A:199 , THR A:200	BINDING SITE FOR RESIDUE 4MD A 401
6	AC6	SOFTWARE	GLN B:93 , HIS B:95 , HIS B:97 , HIS B:120 , PHE B:132 , ALA B:136 , HIS B:137 , LEU B:199 , THR B:200 , PRO B:203 , TRP B:210	BINDING SITE FOR RESIDUE 4MD B 401

(no "SS Bond" information available for 3DA2)

Asymmetric Unit

No.	Residues
1	Ser A:30	-	Pro A:31
2	Pro A:202	-	Pro A:203
3	Ser B:30	-	Pro B:31
4	Pro B:202	-	Pro B:203

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059207	N	68	S	CAH13_HUMAN	Polymorphism	4740046	A/B	N	68	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059207	N	68	S	CAH13_HUMAN	Polymorphism	4740046	A	N	68	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059207	N	68	S	CAH13_HUMAN	Polymorphism	4740046	B	N	68	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	CAH13_HUMAN	4-261	1	A:4-261
2	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH13_HUMAN	106-122	2	A:106-122 B:106-122

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	CAH13_HUMAN	4-261	1	A:4-261
2	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH13_HUMAN	106-122	1	A:106-122 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	CAH13_HUMAN	4-261	0	-
2	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH13_HUMAN	106-122	1	- B:106-122

(no "Exon" information available for 3DA2)

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:262
 aligned with CAH13_HUMAN | Q8N1Q1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                             1                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
          CAH13_HUMAN     - -MSRLSWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASF 261
               SCOP domains d3da2a_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3da2A00 A:0-261 Carbonic Anhydrase II                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh......eehhhhhee......eeee.hhh.eeeeee....eeeee.......eeee......eeeeeeeeee..........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee......hhhhhh..........eee....hhhhhh.....eeeeee..........eeeeee...eeehhhhhhhhhh............................ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ALPHA_CA_2  PDB: A:4-261 UniProt: 4-261                                                                                                                                                                                                                            PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------ALPHA_CA_1       ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3da2 A   0 SMSRLSWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASF 261
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with CAH13_HUMAN | Q8N1Q1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
          CAH13_HUMAN     5 SWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASF 261
               SCOP domains d3da2b_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3da2B00 B:5-261 Carbonic Anhydrase II                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh......eehhhhhee......eeee.hhh.eeeeee....eeeee.......eeee......eeeeeeeeee..........ee......eeeeeeeee.....hhhhhhh....eeeeeeeeee.....hhhhhhhhhhhhh....eee....hhhhhh.....eeeeee..........eeeeee...eeehhhhhhhhh.............................ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ALPHA_CA_2  PDB: - UniProt: 4-261                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------ALPHA_CA_1       ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3da2 B   5 SWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASF 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Carbonic anhydrase (525)

Superfamily: Carbonic anhydrase (525)

Family: Carbonic anhydrase (513)

Protein domain: automated matches (14)

Human (Homo sapiens) [TaxId: 9606] (14)

1a	d3da2a_	A:
1b	d3da2b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Carbonic Anhydrase II (332)

Homologous Superfamily: Carbonic Anhydrase II (332)

Homo sapiens. Organism_taxid: 9606. (1)

1a	3da2B00	B:5-261
1b	3da2A00	A:0-261

(no "Pfam Domain" information available for 3DA2)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CAH13_HUMAN | Q8N1Q1)

molecular function
	GO:0004089	carbonate dehydratase activity	Catalysis of the reaction: H2CO3 = CO2 + H2O.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0015701	bicarbonate transport	The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

Asymmetric Unit
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Ligands, Modified Residues, Ions (3, 6)

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SS Bonds (0, 0)

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