2NMX - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF INHIBITOR BINDING TO CARBONIC ANHYDRASE I

Authors :   D. W. Christianson, K. M. Jude

Date :   23 Oct 06 (Deposition) - 24 Apr 07 (Release) - 15 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Metalloenzyme, Hydro Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. K. Srivastava, K. M. Jude, A. L. Banerjee, M. Haldar, S. Manokaran, J. Kooren, S. Mallik, D. W. Christianson
Structural Analysis Of Charge Discrimination In The Binding Of Inhibitors To Human Carbonic Anhydrases I And Ii
J. Am. Chem. Soc. V. 129 5528 2007
PubMed-ID: 17407288 | Reference-DOI: 10.1021/JA068359W

Molecule 1 - CARBONIC ANHYDRASE 1
	Chains	:	A, B
	EC Number	:	4.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B
	Expression System Strain	:	BL21(DE3)RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CARBONIC ANHYDRASE I, CARBONATE DEHYDRATASE I, CA-I

		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 (4, 6)

No.	Name	Count	Type	Full Name
1	M25	2	Ligand/Ion	N-{2-[4-(AMINOSULFONYL)PHENYL]ETHYL}ACETAMIDE
2	NA	1	Ligand/Ion	SODIUM ION
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	M25	1	Ligand/Ion	N-{2-[4-(AMINOSULFONYL)PHENYL]ETHYL}ACETAMIDE
2	NA	-1	Ligand/Ion	SODIUM ION
3	TRS	-1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	M25	1	Ligand/Ion	N-{2-[4-(AMINOSULFONYL)PHENYL]ETHYL}ACETAMIDE
2	NA	-1	Ligand/Ion	SODIUM ION
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:94 , HIS A:96 , HIS A:119 , M25 A:311	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	HIS B:94 , HIS B:96 , HIS B:119 , M25 B:312	BINDING SITE FOR RESIDUE ZN B 302
3	AC3	SOFTWARE	SER B:259 , HOH B:469 , HOH B:481 , HOH B:528 , HOH B:546 , HOH B:557	BINDING SITE FOR RESIDUE NA B 351
4	AC4	SOFTWARE	ALA A:132 , ALA A:135 , TYR A:204 , ALA B:132 , ALA B:135 , TYR B:204	BINDING SITE FOR RESIDUE TRS B 361
5	AC5	SOFTWARE	GLN A:92 , HIS A:94 , HIS A:96 , HIS A:119 , LEU A:198 , THR A:199 , HIS A:200 , TRP A:209 , ZN A:301 , HOH A:704 , HOH A:824 , ALA B:132	BINDING SITE FOR RESIDUE M25 A 311
6	AC6	SOFTWARE	GLN B:92 , HIS B:94 , HIS B:96 , HIS B:119 , LEU B:198 , THR B:199 , HIS B:200 , TRP B:209 , ZN B:302 , HOH B:625 , HOH B:684	BINDING SITE FOR RESIDUE M25 B 312

(no "SS Bond" information available for 2NMX)

Asymmetric Unit

No.	Residues
1	Ser A:29	-	Pro A:30
2	Pro A:201	-	Pro A:202
3	Ser B:29	-	Pro B:30
4	Pro B:201	-	Pro B:202

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001378	H	68	R	CAH1_HUMAN	Unclassified	---	A/B	H	67	R
2	UniProt	VAR_048679	A	143	V	CAH1_HUMAN	Polymorphism	7821248	A/B	A	142	V
3	UniProt	VAR_001379	G	254	R	CAH1_HUMAN	Polymorphism	121909577	A/B	G	253	R

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001378	H	68	R	CAH1_HUMAN	Unclassified	---	A	H	67	R
2	UniProt	VAR_048679	A	143	V	CAH1_HUMAN	Polymorphism	7821248	A	A	142	V
3	UniProt	VAR_001379	G	254	R	CAH1_HUMAN	Polymorphism	121909577	A	G	253	R

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001378	H	68	R	CAH1_HUMAN	Unclassified	---	B	H	67	R
2	UniProt	VAR_048679	A	143	V	CAH1_HUMAN	Polymorphism	7821248	B	A	142	V
3	UniProt	VAR_001379	G	254	R	CAH1_HUMAN	Polymorphism	121909577	B	G	253	R

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.	CAH1_HUMAN	4-261	1	A:3-260
2	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH1_HUMAN	106-122	2	A:105-121 B:105-121

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.	CAH1_HUMAN	4-261	1	A:3-260
2	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH1_HUMAN	106-122	1	A:105-121 -

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.	CAH1_HUMAN	4-261	0	-
2	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH1_HUMAN	106-122	1	- B:105-121

(no "Exon" information available for 2NMX)

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:258
 aligned with CAH1_HUMAN | P00915 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:258
                                    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        
           CAH1_HUMAN     4 PDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF 261
               SCOP domains d2nmxa_ A: Carbonic anhydrase                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2nmxA00 A:3-260 Carbonic Anhydrase II                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh......ee.....ee......eeee.hhh.eeeeee....eeeee.......eeee......eeeeeeeeee..........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhh.....eee....hhhhhh.....eeeeee..........eeeeee...eeehhhhhhhhhh............................ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------R--------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------R------- SAPs(SNPs)
                PROSITE (1) ALPHA_CA_2  PDB: A:3-260 UniProt: 4-261                                                                                                                                                                                                                            PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------ALPHA_CA_1       ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nmx A   3 PDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF 260
                                    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

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with CAH1_HUMAN | P00915 from UniProtKB/Swiss-Prot  Length:261

    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       
           CAH1_HUMAN     5 DWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF 261
               SCOP domains d2nmxb_ B: Carbonic anhydrase                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2nmxB00 B:4-260 Carbonic Anhydrase II                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) -Carb_anhydrase-2nmxB01 B:5-259                                                                                                                                                                                                                                 - Pfam domains (1)
           Pfam domains (2) -Carb_anhydrase-2nmxB02 B:5-259                                                                                                                                                                                                                                 - Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhh......eehhhhhee......eeee.hhh.eeeeee....eeeee.......eeee......eeeeeeeeee..........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhh.....eee....hhhhhh.....eeeeee..........eeeeee...eeehhhhhhhhhh............................ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------R--------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------R------- SAPs(SNPs)
                PROSITE (1) ALPHA_CA_2  PDB: - UniProt: 4-261                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------ALPHA_CA_1       ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nmx B   4 DWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF 260
                                    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

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Carbonic anhydrase (525)

Superfamily: Carbonic anhydrase (525)

Family: Carbonic anhydrase (513)

Protein domain: Carbonic anhydrase (499)

Human (Homo sapiens), erythrocytes, isozyme I [TaxId: 9606] (18)

1a	d2nmxa_	A:
1b	d2nmxb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Carbonic Anhydrase II (332)

Homologous Superfamily: Carbonic Anhydrase II (332)

Human (Homo sapiens) (309)

1a	2nmxB00	B:4-260
1b	2nmxA00	A:3-260

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Carb_anhydrase] (168)

Family: Carb_anhydrase (168)

Homo sapiens (Human) (157)

1a	Carb_anhydrase-2nmxB01	B:5-259
1b	Carb_anhydrase-2nmxB02	B:5-259

Asymmetric Unit(hide GO term definitions)

Chain A,B (CAH1_HUMAN | P00915)

molecular function
	GO:0004064	arylesterase activity	Catalysis of the reaction: a phenyl acetate + H2O = a phenol + acetate.
	GO:0004089	carbonate dehydratase activity	Catalysis of the reaction: H2CO3 = CO2 + H2O.
	GO:0016836	hydro-lyase activity	Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Pro A:201 - Pro A:202	[ RasMol ]
		Pro B:201 - Pro B:202	[ RasMol ]
		Ser A:29 - Pro A:30	[ RasMol ]
		Ser B:29 - Pro B:30	[ RasMol ]

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2nn1	STRUCTURE OF INHIBITOR BINDING TO CARBONIC ANHYDRASE I
2nn7	STRUCTURE OF INHIBITOR BINDING TO CARBONIC ANHYDRASE I
2nng	STRUCTURE OF INHIBITOR BINDING TO CARBONIC ANHYDRASE II
2nno	STRUCTURE OF INHIBITOR BINDING TO CARBONIC ANHYDRASE II
2nns	STRUCTURE OF INHIBITOR BINDING TO CARBONIC ANHYDRASE II
2nnv	STRUCTURE OF INHIBITOR BINDING TO CARBONIC ANHYDRASE II

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