1Y9A - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   ALCOHOL DEHYDROGENASE FROM ENTAMOEBA HISTOLOTICA IN COMPLEX WITH CACODYLATE

Authors :   L. J. Shimon, M. Peretz, E. Goihberg, Y. Burstein, F. Frolow

Date :   15 Dec 04 (Deposition) - 17 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

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

Keywords :   Metal-Binding, Nadp, Oxidoreductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. J. Shimon, E. Goihberg, M. Peretz, Y. Burstein, F. Frolow
Structure Of Alcohol Dehydrogenase From Entamoeba Histolytica.
Acta Crystallogr. , Sect. D V. 62 541 2006
PubMed-ID: 16627948 | Reference-DOI: 10.1107/S0907444906009292
(for further references see the PDB file header)

Molecule 1 - NADP-DEPENDENT ALCOHOL DEHYDROGENASE
	Chains	:	A, C
	EC Number	:	1.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BS-P58
	Expression System Strain	:	TG-I
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ADH1
	Organism Scientific	:	ENTAMOEBA HISTOLYTICA
	Organism Taxid	:	5759

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 17)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CAC	2	Ligand/Ion	CACODYLATE ION
3	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	OHS	2	Mod. Amino Acid	O-(CARBOXYSULFANYL)-4-OXO-L-HOMOSERINE
6	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 22)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	CAC	4	Ligand/Ion	CACODYLATE ION
3	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	OHS	4	Mod. Amino Acid	O-(CARBOXYSULFANYL)-4-OXO-L-HOMOSERINE
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:37 , SER A:39 , HIS A:59 , ASP A:150 , CAC A:1001	BINDING SITE FOR RESIDUE ZN A 1000
02	AC2	SOFTWARE	CYS A:37 , SER A:39 , HIS A:59 , ASP A:150 , THR A:154 , MET A:285 , ZN A:1000 , HOH A:1034	BINDING SITE FOR RESIDUE CAC A 1001
03	AC3	SOFTWARE	ASP A:51 , HIS A:53 , HIS A:202 , HOH A:1330	BINDING SITE FOR RESIDUE ZN A 1002
04	AC4	SOFTWARE	CYS A:22 , PRO A:24 , GLY A:69 , SER A:70 , HOH A:1098	BINDING SITE FOR RESIDUE ACT A 1004
05	AC5	SOFTWARE	HIS A:360 , HOH A:1006 , HOH A:1007	BINDING SITE FOR RESIDUE MG A 1005
06	AC6	SOFTWARE	CYS C:37 , SER C:39 , HIS C:59 , ASP C:150 , CAC C:2001	BINDING SITE FOR RESIDUE ZN C 2000
07	AC7	SOFTWARE	CYS C:37 , SER C:39 , HIS C:59 , TRP C:110 , ASP C:150 , THR C:154 , MET C:285 , ZN C:2000 , HOH C:2018	BINDING SITE FOR RESIDUE CAC C 2001
08	AC8	SOFTWARE	ASP C:51 , HIS C:53	BINDING SITE FOR RESIDUE ZN C 2002
09	AC9	SOFTWARE	CYS C:22 , PRO C:24 , GLY C:69 , SER C:70 , HOH C:2276	BINDING SITE FOR RESIDUE ACT C 2008
10	BC1	SOFTWARE	LYS A:304 , GLY C:167 , ASP C:237 , HOH C:2010 , HOH C:2011	BINDING SITE FOR RESIDUE MG C 2009
11	BC2	SOFTWARE	GLY A:98 , MET A:101 , HIS A:157 , HIS A:287 , HOH A:1025 , HOH A:1165	BINDING SITE FOR RESIDUE EDO A 1003
12	BC3	SOFTWARE	GLY C:98 , MET C:101 , HIS C:157 , HIS C:287 , HOH C:2049 , HOH C:2161	BINDING SITE FOR RESIDUE EDO C 2003
13	BC4	SOFTWARE	ILE C:206 , LYS C:318 , PHE C:324 , ARG C:350 , HOH C:2047	BINDING SITE FOR RESIDUE EDO C 2004
14	BC5	SOFTWARE	HIS C:289 , HIS C:291 , HOH C:2034 , HOH C:2178	BINDING SITE FOR RESIDUE EDO C 2005
15	BC6	SOFTWARE	ASN A:187 , HIS A:188 , HOH A:1142 , HOH A:1143 , ASN C:187 , HIS C:188 , HOH C:2394	BINDING SITE FOR RESIDUE EDO C 2006

(no "SS Bond" information available for 1Y9A)

(no "Cis Peptide Bond" information available for 1Y9A)

(no "SAP(SNP)/Variant" information available for 1Y9A)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	ADH1_ENTHI	58-72	2	A:58-72 C:58-72

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	ADH1_ENTHI	58-72	4	A:58-72 C:58-72

(no "Exon" information available for 1Y9A)

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
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Chain A from PDB  Type:PROTEIN  Length:360
 aligned with ADH1_ENTHI | P35630 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:360
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
           ADH1_ENTHI     1 MKGLAMLGIGRIGWIEKKIPECGPLDALVRPLALAPCTSDTHTVWAGAIGDRHDMILGHEAVGQIVKVGSLVKRLKVGDKVIVPAITPDWGEEESQRGYPMHSGGMLGGWKFSNFKDGVFSEVFHVNEADANLALLPRDIKPEDAVMLSDMVTTGFHGAELANIKLGDTVCVIGIGPVGLMSVAGANHLGAGRIFAVGSRKHCCDIALEYGATDIINYKNGDIVEQILKATDGKGVDKVVIAGGDVHTFAQAVKMIKPGSDIGNVNYLGEGDNIDIPRSEWGVGMGHKHIHGGLTPGGRVRMEKLASLISTGKLDTSKLITHRFEGLEKVEDALMLMKNKPADLIKPVVRIHYDDEDTLH 360
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1y9aA01 A:1-161,A:293-360 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                  1y9aA02 A:162-292 NAD(P)-binding Rossmann-like Domain                                                                              1y9aA01 A:1-161,A:293-360                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....eeeee..........eeeeeeee..hhhhhhhhhhh.....eeee....eeeeeeee...........eeee........hhhhhh.hhhhh....................eee.hhhhhhee.....hhhhhh...hhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh....eeee....hhhhhhhhh...eeehhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee................hhhhh..eeeee....hhhhhhhhhhhhhhh...hhhh.eeeeee...hhhhhhhhhhhh.....eeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ADH_ZINC       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y9a A   1 MKGLAMLGIGRIGWIEKKIPECGPLDALVRPLALAPCTSDTHTVWAGAIGDRHDMILGHEAVGQIVKVGSLVKRLKVGDKVIVPAITPDWGEEESQRGYPMHSGGMLGGWKFSNFKDGVFSEVFHVNEADANLALLPRDIKPEDAVMLSDMVTTGFHGAELANIKLGDTVCVIGIGPVGLMSVAGANHLGAGRIFAVGSRKHCCDIALEYGATDIINYKNGDIVEQILKATDGKGVDKVVIAGGdVHTFAQAVKMIKPGSDIGNVNYLGEGDNIDIPRSEWGVGMGHKHIHGGLTPGGRVRMEKLASLISTGKLDTSKLITHRFEGLEKVEDALMLMKNKPADLIKPVVRIHYDDEDTLH 360
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    |  250       260       270       280       290       300       310       320       330       340       350       360
                                                                                                                                                                                                                                                                              245-OHS

Chain C from PDB  Type:PROTEIN  Length:360
 aligned with ADH1_ENTHI | P35630 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:360
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
           ADH1_ENTHI     1 MKGLAMLGIGRIGWIEKKIPECGPLDALVRPLALAPCTSDTHTVWAGAIGDRHDMILGHEAVGQIVKVGSLVKRLKVGDKVIVPAITPDWGEEESQRGYPMHSGGMLGGWKFSNFKDGVFSEVFHVNEADANLALLPRDIKPEDAVMLSDMVTTGFHGAELANIKLGDTVCVIGIGPVGLMSVAGANHLGAGRIFAVGSRKHCCDIALEYGATDIINYKNGDIVEQILKATDGKGVDKVVIAGGDVHTFAQAVKMIKPGSDIGNVNYLGEGDNIDIPRSEWGVGMGHKHIHGGLTPGGRVRMEKLASLISTGKLDTSKLITHRFEGLEKVEDALMLMKNKPADLIKPVVRIHYDDEDTLH 360
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1y9aC01 C:1-161,C:293-360 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                  1y9aC02 C:162-292 NAD(P)-binding Rossmann-like Domain                                                                              1y9aC01 C:1-161,C:293-360                                            CATH domains
           Pfam domains (1) -----------------------ADH_N-1y9aC01 C:24-134                                                                                         ------------------------------------------ADH_zinc_N-1y9aC03 C:177-310                                                                                                          -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------ADH_N-1y9aC02 C:24-134                                                                                         ------------------------------------------ADH_zinc_N-1y9aC04 C:177-310                                                                                                          -------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee....eeeee..........eeeeeeee..hhhhhhhhhh......eeee....eeeeeeee...........eeee........hhhhhh.hhhhh....................eee.hhhhhhee.....hhhhhhh..hhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhh...eeee....hhhhhhhhhh....eeeeee.....hhhhhhhhheeeeeeeee................hhhhh..eeeee.....hhhhhhhhhhhhhh....hhh.eeeeee..hhhhhhhhhhhhh.....eeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ADH_ZINC       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y9a C   1 MKGLAMLGIGRIGWIEKKIPECGPLDALVRPLALAPCTSDTHTVWAGAIGDRHDMILGHEAVGQIVKVGSLVKRLKVGDKVIVPAITPDWGEEESQRGYPMHSGGMLGGWKFSNFKDGVFSEVFHVNEADANLALLPRDIKPEDAVMLSDMVTTGFHGAELANIKLGDTVCVIGIGPVGLMSVAGANHLGAGRIFAVGSRKHCCDIALEYGATDIINYKNGDIVEQILKATDGKGVDKVVIAGGdVHTFAQAVKMIKPGSDIGNVNYLGEGDNIDIPRSEWGVGMGHKHIHGGLTPGGRVRMEKLASLISTGKLDTSKLITHRFEGLEKVEDALMLMKNKPADLIKPVVRIHYDDEDTLH 360
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    |  250       260       270       280       290       300       310       320       330       340       350       360
                                                                                                                                                                                                                                                                              245-OHS

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 1Y9A)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Entamoeba histolytica. Organism_taxid: 5759. (2)

1a	1y9aA02	A:162-292
1b	1y9aC02	C:162-292

Architecture: Alpha-Beta Complex (3881)

Topology: Quinone Oxidoreductase; Chain A, domain 1 (131)

Homologous Superfamily: Medium-chain alcohol dehydrogenases, catalytic domain (131)

Entamoeba histolytica. Organism_taxid: 5759. (2)

2a	1y9aA01	A:1-161,A:293-360
2b	1y9aC01	C:1-161,C:293-360

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GroES (70)

Family: ADH_N (62)

Entamoeba histolytica (2)

1a	ADH_N-1y9aC01	C:24-134
1b	ADH_N-1y9aC02	C:24-134

Clan: NADP_Rossmann (1239)

Family: ADH_zinc_N (75)

Entamoeba histolytica (2)

2a	ADH_zinc_N-1y9aC03	C:177-310
2b	ADH_zinc_N-1y9aC04	C:177-310

Asymmetric Unit(hide GO term definitions)

Chain A,C (ADH1_ENTHI | P35630)

molecular function
	GO:0050009	isopropanol dehydrogenase (NADP+) activity	Catalysis of the reaction: NADP(+) + propan-2-ol = acetone + H(+) + NADPH.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y9a)

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	1y9a
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(no "Related Entries Specified in the PDB File" available for 1Y9A)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 17)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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