1Y5R - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF MURINE 11B-HYDROXYSTEROID DEHYDROGENASE COMPLEXED WITH CORTICOSTERONE

Authors :   J. Zhang, T. D. Osslund, M. H. Plant, C. L. Clogston, R. E. Nybo, F. Xiong, J. M. Delaney, S. Jordan

Date :   02 Dec 04 (Deposition) - 17 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

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

Reference :   J. Zhang, T. D. Osslund, M. H. Plant, C. L. Clogston, R. E. Nybo, F. Xiong, J. M. Delaney, S. Jordan
Crystal Structure Of Murine 11-Hydroxysteroid Dehydrogenase 1: An Important Therapeutic Target For Diabetes
Biochemistry V. 44 6948 2005
PubMed-ID: 15865440 | Reference-DOI: 10.1021/BI047599Q
(for further references see the PDB file header)

Molecule 1 - CORTICOSTEROID 11-BETA-DEHYDROGENASE, ISOZYME 1
	Chains	:	A, B
	EC Number	:	1.1.1.146
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAMG21
	Expression System Strain	:	GM221
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HSD11B1
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	11-DH, 11-BETA-HYDROXYSTEROID DEHYDROGENASE 1, 11- BETA-HSD1, 11BETA- HSD1A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	C0R	2	Ligand/Ion	CORTICOSTERONE
2	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	C0R	2	Ligand/Ion	CORTICOSTERONE
2	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	C0R	4	Ligand/Ion	CORTICOSTERONE
2	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	C0R A:11 , GLY A:41 , SER A:43 , LYS A:44 , GLY A:45 , ILE A:46 , ALA A:65 , ARG A:66 , SER A:67 , THR A:92 , MET A:93 , ASN A:119 , ILE A:121 , ILE A:168 , SER A:169 , SER A:170 , TYR A:183 , LYS A:187 , LEU A:215 , GLY A:216 , LEU A:217 , ILE A:218 , THR A:220 , THR A:222 , ALA A:223	BINDING SITE FOR RESIDUE NDP A 1
2	AC2	SOFTWARE	C0R B:12 , GLY B:41 , SER B:43 , LYS B:44 , GLY B:45 , ILE B:46 , ARG B:66 , SER B:67 , THR B:92 , MET B:93 , ASN B:119 , HIS B:120 , ILE B:121 , ILE B:168 , SER B:169 , SER B:170 , TYR B:183 , LYS B:187 , LEU B:215 , GLY B:216 , LEU B:217 , ILE B:218 , THR B:220 , THR B:222 , ALA B:223	BINDING SITE FOR RESIDUE NDP B 2
3	AC3	SOFTWARE	NDP A:1 , ILE A:121 , SER A:170 , GLN A:177 , TYR A:183 , THR A:222	BINDING SITE FOR RESIDUE C0R A 11
4	AC4	SOFTWARE	NDP B:2 , ILE B:121 , THR B:124 , SER B:170 , GLN B:177 , ILE B:180 , TYR B:183 , LEU B:217 , ILE B:227	BINDING SITE FOR RESIDUE C0R B 12

(no "SS Bond" information available for 1Y5R)

(no "Cis Peptide Bond" information available for 1Y5R)

(no "SAP(SNP)/Variant" information available for 1Y5R)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHI1_MOUSE	170-198	2	A:170-198 B:170-198

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHI1_MOUSE	170-198	2	A:170-198 B:170-198

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHI1_MOUSE	170-198	4	A:170-198 B:170-198

(no "Exon" information available for 1Y5R)

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:265
 aligned with DHI1_MOUSE | P50172 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284     
           DHI1_MOUSE    25 EEFRPEMLQGKKVIVTGASKGIGREMAYHLSKMGAHVVLTARSEEGLQKVVSRCLELGAASAHYIAGTMEDMTFAEQFIVKAGKLMGGLDMLILNHITQTSLSLFHDDIHSVRRVMEVNFLSYVVMSTAALPMLKQSNGSIAVISSLAGKMTQPMIAPYSASKFALDGFFSTIRTELYITKVNVSITLCVLGLIDTETAMKEISGIINAQASPKEECALEIIKGTALRKSEVYYDKSPLTPILLGNPGRKIMEFFSLRYYNKDMF 289
               SCOP domains d1y5ra_ A: 11-beta-hydroxysteroid dehydrogenase 1                                                                                                                                                                                                                         SCOP domains
               CATH domains 1y5rA00 A:25-289 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeee...hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhh........hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:170-198    ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y5r A  25 EEFRPEMLQGKKVIVTGASKGIGREMAYHLSKMGAHVVLTARSEEGLQKVVSRCLELGAASAHYIAGTMEDMTFAEQFIVKAGKLMGGLDMLILNHITQTSLSLFHDDIHSVRRVMEVNFLSYVVMSTAALPMLKQSNGSIAVISSLAGKMTQPMIAPYSASKFALDGFFSTIRTELYITKVNVSITLCVLGLIDTETAMKEISGIINAQASPKEECALEIIKGTALRKSEVYYDKSPLTPILLGNPGRKIMEFFSLRYYNKDMF 289
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with DHI1_MOUSE | P50172 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284     
           DHI1_MOUSE    25 EEFRPEMLQGKKVIVTGASKGIGREMAYHLSKMGAHVVLTARSEEGLQKVVSRCLELGAASAHYIAGTMEDMTFAEQFIVKAGKLMGGLDMLILNHITQTSLSLFHDDIHSVRRVMEVNFLSYVVMSTAALPMLKQSNGSIAVISSLAGKMTQPMIAPYSASKFALDGFFSTIRTELYITKVNVSITLCVLGLIDTETAMKEISGIINAQASPKEECALEIIKGTALRKSEVYYDKSPLTPILLGNPGRKIMEFFSLRYYNKDMF 289
               SCOP domains d1y5rb_ B: 11-beta-hydroxysteroid dehydrogenase 1                                                                                                                                                                                                                         SCOP domains
               CATH domains 1y5rB00 B:25-289 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ----------adh_short-1y5rB01 B:35-202                                                                                                                                              --------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------adh_short-1y5rB02 B:35-202                                                                                                                                              --------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhh...eeee.....hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhh.........hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:170-198    ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y5r B  25 EEFRPEMLQGKKVIVTGASKGIGREMAYHLSKMGAHVVLTARSEEGLQKVVSRCLELGAASAHYIAGTMEDMTFAEQFIVKAGKLMGGLDMLILNHITQTSLSLFHDDIHSVRRVMEVNFLSYVVMSTAALPMLKQSNGSIAVISSLAGKMTQPMIAPYSASKFALDGFFSTIRTELYITKVNVSITLCVLGLIDTETAMKEISGIINAQASPKEECALEIIKGTALRKSEVYYDKSPLTPILLGNPGRKIMEFFSLRYYNKDMF 289
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284

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: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: 11-beta-hydroxysteroid dehydrogenase 1 (34)

Mouse (Mus musculus) [TaxId: 10090] (5)

1a	d1y5ra_	A:
1b	d1y5rb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

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

House mouse (Mus musculus) (11)

1a	1y5rA00	A:25-289
1b	1y5rB00	B:25-289

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Mus musculus (Mouse) (3)

1a	adh_short-1y5rB01	B:35-202
1b	adh_short-1y5rB02	B:35-202

Asymmetric Unit(hide GO term definitions)

Chain A,B (DHI1_MOUSE | P50172)

molecular function
	GO:0070524	11-beta-hydroxysteroid dehydrogenase (NADP+) activity	Catalysis of the reaction: an 11-beta-hydroxysteroid + NADP+ = an 11-oxosteroid + NADPH + H+.
	GO:0003845	11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity	Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD(P)+ = an 11-oxosteroid + NAD(P)H + H(+).
	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.
biological process
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0030324	lung development	The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
	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.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	1y5r
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	DHI1_MOUSE \| P50172
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	DHI1_MOUSE \| P50172	:	1y5m 3gmd 4k26 4nmh

1y5m	THE PROTEIN WITH A DETERGENT MOLECULE BOUND IN THE STEROID BINDING POCKET

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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