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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN ALCOHOL DEHYDROGENASE BETA-1-BETA-1 ISOFORM COMPLEXED WITH N-BENZYLFORMAMIDE DETERMINED TO 1.6 ANGSTROM RESOLUTION

Authors :   B. J. Gibbons, T. D. Hurley

Date :   23 Jul 04 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. J. Gibbons, T. D. Hurley
Structure Of Three Class I Human Alcohol Dehydrogenases Complexed With Isoenzyme Specific Formamide Inhibitors
Biochemistry V. 43 12555 2004
PubMed-ID: 15449945 | Reference-DOI: 10.1021/BI0489107
(for further references see the PDB file header)

Molecule 1 - ALCOHOL DEHYDROGENASE BETA CHAIN
	Chains	:	A, B
	EC Number	:	1.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK2233
	Expression System Strain	:	DH5-ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ADH1B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ALCOHOL DEHYDROGENASE BETA-1-BETA-1 ISOFORM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	BNF	2	Ligand/Ion	N-BENZYLFORMAMIDE
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:97 , CYS A:100 , CYS A:103 , CYS A:111	BINDING SITE FOR RESIDUE ZN A 375
2	AC2	SOFTWARE	CYS A:46 , HIS A:67 , CYS A:174 , NAD A:1377 , BNF A:1378	BINDING SITE FOR RESIDUE ZN A 376
3	AC3	SOFTWARE	CYS B:97 , CYS B:100 , CYS B:103 , CYS B:111	BINDING SITE FOR RESIDUE ZN B 375
4	AC4	SOFTWARE	CYS B:46 , HIS B:67 , CYS B:174 , NAD B:2377 , BNF B:2378	BINDING SITE FOR RESIDUE ZN B 376
5	AC5	SOFTWARE	SER A:1 , LYS A:5 , HOH A:1613 , HOH A:1725 , THR B:127 , ARG B:128 , HOH B:2483 , HOH B:2545 , HOH B:2817	BINDING SITE FOR RESIDUE PO4 B 400
6	AC6	SOFTWARE	ARG A:47 , THR A:48 , HIS A:51 , PHE A:93 , CYS A:174 , THR A:178 , GLY A:199 , LEU A:200 , GLY A:201 , GLY A:202 , VAL A:203 , ASP A:223 , ILE A:224 , LYS A:228 , VAL A:268 , ILE A:269 , ARG A:271 , VAL A:292 , GLY A:293 , VAL A:294 , ALA A:317 , VAL A:318 , TYR A:319 , LEU A:362 , ARG A:369 , ZN A:376 , BNF A:1378 , HOH A:1397 , HOH A:1413 , HOH A:1425 , HOH A:1426 , HOH A:1448 , HOH A:1471 , HOH A:1515 , HOH A:1719 , HOH A:1839	BINDING SITE FOR RESIDUE NAD A 1377
7	AC7	SOFTWARE	ARG B:47 , THR B:48 , HIS B:51 , PHE B:93 , CYS B:174 , THR B:178 , GLY B:199 , LEU B:200 , GLY B:201 , GLY B:202 , VAL B:203 , ASP B:223 , ILE B:224 , LYS B:228 , VAL B:268 , ILE B:269 , ARG B:271 , VAL B:292 , VAL B:294 , ALA B:317 , VAL B:318 , TYR B:319 , LEU B:362 , ARG B:369 , ZN B:376 , BNF B:2378 , HOH B:2428 , HOH B:2446 , HOH B:2470 , HOH B:2476 , HOH B:2491 , HOH B:2503 , HOH B:2579 , HOH B:2873	BINDING SITE FOR RESIDUE NAD B 2377
8	AC8	SOFTWARE	CYS A:46 , THR A:48 , HIS A:67 , PHE A:93 , CYS A:174 , ZN A:376 , NAD A:1377	BINDING SITE FOR RESIDUE BNF A 1378
9	AC9	SOFTWARE	CYS B:46 , THR B:48 , HIS B:67 , PHE B:93 , LEU B:116 , CYS B:174 , ZN B:376 , NAD B:2377	BINDING SITE FOR RESIDUE BNF B 2378

(no "SS Bond" information available for 1U3U)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:61	-	Pro A:62
2	Leu B:61	-	Pro B:62

Asymmetric/Biological Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_000426	R	48	H	ADH1B_HUMAN	Polymorphism	1229984	A/B	R	47	H
2	UniProt	VAR_019322	N	57	K	ADH1B_HUMAN	Polymorphism	1041969	A/B	N	56	K
3	UniProt	VAR_019323	T	60	S	ADH1B_HUMAN	Polymorphism	6413413	A/B	T	59	S
4	UniProt	VAR_000427	R	370	C	ADH1B_HUMAN	Polymorphism	2066702	A/B	R	369	C

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_ZINC	PS00059	Zinc-containing alcohol dehydrogenases signature.	ADH1B_HUMAN	67-81	2	A:66-80 B:66-80

Asymmetric/Biological Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000305046	1b	ENSE00001383360	chr4:100242556-100242471	86	ADH1B_HUMAN	1-6	6	2	A:1-5 B:1-5	5 5
1.2c	ENST00000305046	2c	ENSE00001624682	chr4:100240043-100239942	102	ADH1B_HUMAN	7-40	34	2	A:6-39 B:6-39	34 34
1.3a	ENST00000305046	3a	ENSE00001600077	chr4:100239341-100239203	139	ADH1B_HUMAN	41-87	47	2	A:40-86 B:40-86	47 47
1.4b	ENST00000305046	4b	ENSE00001655834	chr4:100237459-100237372	88	ADH1B_HUMAN	87-116	30	2	A:86-115 B:86-115	30 30
1.5b	ENST00000305046	5b	ENSE00001727418	chr4:100237274-100237055	220	ADH1B_HUMAN	116-189	74	2	A:115-188 B:115-188	74 74
1.6	ENST00000305046	6	ENSE00001736990	chr4:100235238-100234978	261	ADH1B_HUMAN	190-276	87	2	A:189-275 B:189-275	87 87
1.7	ENST00000305046	7	ENSE00001711573	chr4:100232813-100232678	136	ADH1B_HUMAN	277-322	46	2	A:276-321 B:276-321	46 46
1.8	ENST00000305046	8	ENSE00001682168	chr4:100232060-100231922	139	ADH1B_HUMAN	322-368	47	2	A:321-367 B:321-367	47 47
1.9d	ENST00000305046	9d	ENSE00002069705	chr4:100229021-100226121	2901	ADH1B_HUMAN	368-375	8	2	A:367-374 B:367-374	8 8

Asymmetric/Biological 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:374
 aligned with ADH1B_HUMAN | P00325 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:374
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371    
          ADH1B_HUMAN     2 STAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVTPLPVILGHEAAGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRVCKNPESNYCLKNDLGNPRGTLQDGTRRFTCRGKPIHHFLGTSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVNVAKVTPGSTCAVFGLGGVGLSAVMGCKAAGAARIIAVDINKDKFAKAKELGATECINPQDYKKPIQEVLKEMTDGGVDFSFEVIGRLDTMMASLLCCHEACGTSVIVGVPPASQNLSINPMLLLTGRTWKGAVYGGFKSKEGIPKLVADFMAKKFSLDALITHVLPFEKINEGFDLLHSGKSIRTVLTF 375
               SCOP domains d1u3ua1 A:1-162,A:339-374 Alcohol dehydrogenase                                                                                                                   d1u3ua2 A:163-338 Alcohol dehydrogenase                                                                                                                                         d1u3ua1 A:1-162,A:339-374            SCOP domains
               CATH domains 1u3uA01 A:1-178,A:318-374 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                                   1u3uA02 A:179-317 NAD(P)-binding Rossmann-like Domain                                                                                      1u3uA01 A:1-178,A:318-374                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.......eeeeeee......eeeeeeeeee.hhhhhhhhh........ee...eeeeeeeee...........eeee........hhhhhh........................eee..eee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhhh.....eeee.........eee.hhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh....hhh.eeeeee..hhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H--------K--S---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C----- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------ADH_ZINC       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.1b Exon 1.2c  PDB: A:6-39            Exon 1.3a  PDB: A:40-86 UniProt: 41-87         ----------------------------Exon 1.5b  PDB: A:115-188 UniProt: 116-189                                Exon 1.6  PDB: A:189-275 UniProt: 190-276                                              Exon 1.7  PDB: A:276-321 UniProt: 277-322     ---------------------------------------------1.9d     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.4b  PDB: A:86-115      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:321-367 UniProt: 322-368      ------- Transcript 1 (2)
                 1u3u A   1 STAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVTPLPVILGHEAAGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRVCKNPESNYCLKNDLGNPRGTLQDGTRRFTCRGKPIHHFLGTSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVNVAKVTPGSTCAVFGLGGVGLSAVMGCKAAGAARIIAVDINKDKFAKAKELGATECINPQDYKKPIQEVLKEMTDGGVDFSFEVIGRLDTMMASLLCCHEACGTSVIVGVPPASQNLSINPMLLLTGRTWKGAVYGGFKSKEGIPKLVADFMAKKFSLDALITHVLPFEKINEGFDLLHSGKSIRTVLTF 374
                                    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       370

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with ADH1B_HUMAN | P00325 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:374
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371    
          ADH1B_HUMAN     2 STAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVTPLPVILGHEAAGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRVCKNPESNYCLKNDLGNPRGTLQDGTRRFTCRGKPIHHFLGTSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVNVAKVTPGSTCAVFGLGGVGLSAVMGCKAAGAARIIAVDINKDKFAKAKELGATECINPQDYKKPIQEVLKEMTDGGVDFSFEVIGRLDTMMASLLCCHEACGTSVIVGVPPASQNLSINPMLLLTGRTWKGAVYGGFKSKEGIPKLVADFMAKKFSLDALITHVLPFEKINEGFDLLHSGKSIRTVLTF 375
               SCOP domains d1u3ub1 B:1-162,B:339-374 Alcohol dehydrogenase                                                                                                                   d1u3ub2 B:163-338 Alcohol dehydrogenase                                                                                                                                         d1u3ub1 B:1-162,B:339-374            SCOP domains
               CATH domains 1u3uB01 B:1-178,B:318-374 Medium-chain alcohol dehydrogenases, catalytic domain                                                                                                   1u3uB02 B:179-317 NAD(P)-binding Rossmann-like Domain                                                                                      1u3uB01 B:1-178,B:318-374                                 CATH domains
           Pfam domains (1) --------------------------------ADH_N-1u3uB01 B:33-160                                                                                                          -----------------------------------------ADH_zinc_N-1u3uB03 B:202-334                                                                                                         ---------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------ADH_N-1u3uB02 B:33-160                                                                                                          -----------------------------------------ADH_zinc_N-1u3uB04 B:202-334                                                                                                         ---------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeeeeeee.......eeeeeee......eeeeeeeeee.hhhhhhhhh........ee...eeeeeeeee...........eeee........hhhhhh........................eee..eee...........eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeehhhhh..hhhhhhhhhh.....eeee...hhhhhhhhhhhh.....eeee.........eee.hhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh....hhh.eeeeee..hhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H--------K--S---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C----- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------ADH_ZINC       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.1b Exon 1.2c  PDB: B:6-39            Exon 1.3a  PDB: B:40-86 UniProt: 41-87         ----------------------------Exon 1.5b  PDB: B:115-188 UniProt: 116-189                                Exon 1.6  PDB: B:189-275 UniProt: 190-276                                              Exon 1.7  PDB: B:276-321 UniProt: 277-322     ---------------------------------------------1.9d     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.4b  PDB: B:86-115      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:321-367 UniProt: 322-368      ------- Transcript 1 (2)
                 1u3u B   1 STAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVTPLPVILGHEAAGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRVCKNPESNYCLKNDLGNPRGTLQDGTRRFTCRGKPIHHFLGTSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVNVAKVTPGSTCAVFGLGGVGLSAVMGCKAAGAARIIAVDINKDKFAKAKELGATECINPQDYKKPIQEVLKEMTDGGVDFSFEVIGRLDTMMASLLCCHEACGTSVIVGVPPASQNLSINPMLLLTGRTWKGAVYGGFKSKEGIPKLVADFMAKKFSLDALITHVLPFEKINEGFDLLHSGKSIRTVLTF 374
                                    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       370

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/Biological 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)

Human (Homo sapiens) (188)

1a	1u3uA02	A:179-317
1b	1u3uB02	B:179-317

Architecture: Alpha-Beta Complex (3881)

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

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

Human (Homo sapiens) (30)

2a	1u3uA01	A:1-178,A:318-374
2b	1u3uB01	B:1-178,B:318-374

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GroES (70)

Family: ADH_N (62)

Homo sapiens (Human) (18)

1a	ADH_N-1u3uB01	B:33-160
1b	ADH_N-1u3uB02	B:33-160

Clan: NADP_Rossmann (1239)

Family: ADH_zinc_N (75)

Homo sapiens (Human) (24)

2a	ADH_zinc_N-1u3uB03	B:202-334
2b	ADH_zinc_N-1u3uB04	B:202-334

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ADH1B_HUMAN | P00325)

molecular function
	GO:0004022	alcohol dehydrogenase (NAD) activity	Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + H+.
	GO:0004024	alcohol dehydrogenase activity, zinc-dependent	Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + H+, requiring the presence of zinc.
	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:0006069	ethanol oxidation	An ethanol metabolic process in which ethanol is converted to acetyl-CoA via acetaldehyde and acetate.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	1u3u
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	1.1.1.1
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UniProtKB/Swiss-Prot
	ADH1B_HUMAN \| P00325	:	1deh 1hdx 1hdy 1hdz 1hsz 1htb 1u3v 3hud

1hsz	HUMAN ALCOHOL DEHYDROGENASE, BETA-1-BETA-1 ISOENZYME
1u3t	HUMAN ALCOHOL DEHYDROGENASE ALPHA-ALPHA ISOFORM COMPLEXED WITH N-CYCLOPENTYL-N-CYCLOBUTYLFORMAMIDE DETERMINED TO 2.5 ANGSTROM RESOLUTION
1u3v	HUMAN ALCOHOL DEHYDROGENASE BETA-1-BETA-1 ISOFORM COMPLEXED WITH N-HEPTYLFORMAMIDE DETERMINED TO 1.65 ANGSTROM RESOLUTION
1u3w	HUMAN ALCOHOL DEHYDROGENASE GAMMA-2-GAMMA-2 ISOFORM COMPLEXED WITH N-1-METHYLHEPTYLFORMAMIDE DETERMINED TO 1.45 ANGSTROM RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (1, 2)

Exons (9, 18)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

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