1YB1 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN 17-BETA-HYDROXYSTEROID DEHYDROGENASE TYPE XI

Authors :   P. Lukacik, G. Bunkoczi, K. Kavanagh, S. Ng, F. Von Delft, J. Bray, A. Ed C. Arrowsmith, M. Sundstrom, U. Oppermann, Structural Genomics Co (Sgc)

Date :   18 Dec 04 (Deposition) - 28 Dec 04 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Short Chain Dehydrogenase, Hydroxysteroid Dehydrogenase, Human, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Lukacik, G. Bunkoczi, K. Kavanagh, S. Ng, F. Von Delft, J. Bray, A. Edwards, C. Arrowsmith, M. Sundstrom, U. Oppermann
Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase Type Xi.
To Be Published
PubMed: search

Molecule 1 - 17-BETA-HYDROXYSTEROID DEHYDROGENASE TYPE XI
	Chains	:	A, B
	EC Number	:	1.1.1.62
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P11 (PET11 DERIVATIVE)
	Expression System Strain	:	ROSETTA 2 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DHRS8
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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 (4, 11)

No.	Name	Count	Type	Full Name
1	AOI	2	Ligand/Ion	ANDROSTERONE
2	CL	6	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	AOI	2	Ligand/Ion	ANDROSTERONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	AOI	4	Ligand/Ion	ANDROSTERONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:214 , PHE A:215 , SER A:256 , HOH A:724	BINDING SITE FOR RESIDUE CL A 401
02	AC2	SOFTWARE	ASP A:62 , ILE A:63 , CL A:405 , HOH A:780	BINDING SITE FOR RESIDUE CL A 402
03	AC3	SOFTWARE	ASN B:214 , PHE B:215 , SER B:256 , HOH B:665	BINDING SITE FOR RESIDUE CL B 403
04	AC4	SOFTWARE	ILE B:43	BINDING SITE FOR RESIDUE CL B 404
05	AC5	SOFTWARE	CYS A:89 , CL A:402 , HOH A:792	BINDING SITE FOR RESIDUE CL A 405
06	AC6	SOFTWARE	HOH A:793 , GLN B:128	BINDING SITE FOR RESIDUE CL B 406
07	AC7	SOFTWARE	GLY A:42 , ILE A:43 , ALA A:168 , ALA A:169 , HOH A:741 , HOH A:748 , HOH A:818	BINDING SITE FOR RESIDUE SO4 A 702
08	AC8	SOFTWARE	ARG A:92 , HOH A:793 , HOH A:849 , THR B:127 , PRO B:130	BINDING SITE FOR RESIDUE SO4 A 703
09	AC9	SOFTWARE	ILE A:267 , HOH A:704 , SER B:122 , LYS B:148 , THR B:155 , LEU B:194 , GLU B:197 , HOH B:602 , HOH B:641	BINDING SITE FOR RESIDUE AOI B 601
10	BC1	SOFTWARE	GLU A:197 , LEU B:178 , HOH B:618	BINDING SITE FOR RESIDUE AOI A 602
11	BC2	SOFTWARE	ILE B:63 , VAL B:87 , ASP B:88 , CYS B:89 , SER B:90 , GLY B:117 , VAL B:138 , HOH B:629	BINDING SITE FOR RESIDUE GOL B 501

(no "SS Bond" information available for 1YB1)

Asymmetric Unit

No.	Residues
1	Gly A:229	-	Pro A:230
2	Gly B:229	-	Pro B:230

(no "SAP(SNP)/Variant" information available for 1YB1)

(no "PROSITE Motif" information available for 1YB1)

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000358290	1a	ENSE00001405112	chr4:88312538-88312013	526	DHB11_HUMAN	1-70	70	2	A:25-65 B:25-65	41 41
1.3	ENST00000358290	3	ENSE00001432115	chr4:88303514-88303407	108	DHB11_HUMAN	71-106	36	2	A:66-101 B:66-101	36 36
1.4b	ENST00000358290	4b	ENSE00001422137	chr4:88295982-88295851	132	DHB11_HUMAN	107-150	44	2	A:102-145 B:102-145	44 44
1.7	ENST00000358290	7	ENSE00001418052	chr4:88293967-88293861	107	DHB11_HUMAN	151-186	36	2	A:146-181 (gaps) B:146-181 (gaps)	36 36
1.9	ENST00000358290	9	ENSE00001405922	chr4:88278568-88278431	138	DHB11_HUMAN	186-232	47	2	A:181-227 B:181-227	47 47
1.11a	ENST00000358290	11a	ENSE00001432509	chr4:88261758-88261642	117	DHB11_HUMAN	232-271	40	2	A:227-266 B:227-266	40 40
1.12e	ENST00000358290	12e	ENSE00001428384	chr4:88258518-88257762	757	DHB11_HUMAN	271-300	30	2	A:266-268 B:266-268	3 3

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:243
 aligned with DHB11_HUMAN | Q8NBQ5 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:244
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
          DHB11_HUMAN    30 RRKSVTGEIVLITGAGHGIGRLTAYEFAKLKSKLVLWDINKHGLEETAAKCKGLGAKVHTFVVDCSNREDIYSSAKKVKAEIGDVSILVNNAGVVYTSDLFATQDPQIEKTFEVNVLAHFWTTKAFLPAMTKNNHGHIVTVASAAGHVSVPFLLAYCSSKFAAVGFHKTLTDELAALQITGVKTTCLCPNFVNTGFIKNPSTSLGPTLEPEEVVNRLMHGILTEQKMIFIPSSIAFLTTLERIL 273
               SCOP domains d1yb1a_ A: 17-beta-hydroxysteroid dehydrogenase type XI                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....-..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhh....hhhhhh...hhhhhhhhhhhhhhh...eeee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:25-65 UniProt: 1-70    Exon 1.3  PDB: A:66-101             Exon 1.4b  PDB: A:102-145 UniProt: 107-150  Exon 1.7  PDB: A:146-181 (gaps)     ---------------------------------------------Exon 1.11a  PDB: A:227-266              -- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:181-227 UniProt: 186-232      --------------------------------------1.1 Transcript 1 (2)
                 1yb1 A  25 RRKSVTGEIVLITGAGHGIGRLTAYEFAKLKSKLVLWDINKHGLEETAAKCKGLGAKVHTFVVDCSNREDIYSSAKKVKAEIGDVSILVNNAGVVYTSDLFATQDPQIEKTFEVNVLAHFWTTKAFLPAMTKNNHGHIVTVASAA-HVSVPFLLAYCSSKFAAVGFHKTLTDELAALQITGVKTTCLCPNFVNTGFIKNPSTSLGPTLEPEEVVNRLMHGILTEQKMIFIPSSIAFLTTLERIL 268
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164    | |174       184       194       204       214       224       234       244       254       264    
                                                                                                                                                                          169 |                                                                                                 
                                                                                                                                                                            171

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with DHB11_HUMAN | Q8NBQ5 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:244
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
          DHB11_HUMAN    30 RRKSVTGEIVLITGAGHGIGRLTAYEFAKLKSKLVLWDINKHGLEETAAKCKGLGAKVHTFVVDCSNREDIYSSAKKVKAEIGDVSILVNNAGVVYTSDLFATQDPQIEKTFEVNVLAHFWTTKAFLPAMTKNNHGHIVTVASAAGHVSVPFLLAYCSSKFAAVGFHKTLTDELAALQITGVKTTCLCPNFVNTGFIKNPSTSLGPTLEPEEVVNRLMHGILTEQKMIFIPSSIAFLTTLERIL 273
               SCOP domains d1yb1b_ B: 17-beta-hydroxysteroid dehydrogenase type XI                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------adh_short-1yb1B01 B:32-199                                                                                                                                              --------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------adh_short-1yb1B02 B:32-199                                                                                                                                              --------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...--..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhh....hhhhhh...hhhhhhhhhhhhhhh...eeee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:25-65 UniProt: 1-70    Exon 1.3  PDB: B:66-101             Exon 1.4b  PDB: B:102-145 UniProt: 107-150  Exon 1.7  PDB: B:146-181 (gaps)     ---------------------------------------------Exon 1.11a  PDB: B:227-266              -- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:181-227 UniProt: 186-232      --------------------------------------1.1 Transcript 1 (2)
                 1yb1 B  25 RRKSVTGEIVLITGAGHGIGRLTAYEFAKLKSKLVLWDINKHGLEETAAKCKGLGAKVHTFVVDCSNREDIYSSAKKVKAEIGDVSILVNNAGVVYTSDLFATQDPQIEKTFEVNVLAHFWTTKAFLPAMTKNNHGHIVTVASA--HVSVPFLLAYCSSKFAAVGFHKTLTDELAALQITGVKTTCLCPNFVNTGFIKNPSTSLGPTLEPEEVVNRLMHGILTEQKMIFIPSSIAFLTTLERIL 268
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164   |  |174       184       194       204       214       224       234       244       254       264    
                                                                                                                                                                         168  |                                                                                                 
                                                                                                                                                                            171

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: 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: 17-beta-hydroxysteroid dehydrogenase type XI (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1yb1a_	A:
1b	d1yb1b_	B:

(no "CATH Domain" information available for 1YB1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Homo sapiens (Human) (21)

1a	adh_short-1yb1B01	B:32-199
1b	adh_short-1yb1B02	B:32-199

Asymmetric Unit(hide GO term definitions)

Chain A,B (DHB11_HUMAN | Q8NBQ5)

molecular function
	GO:0004303	estradiol 17-beta-dehydrogenase activity	Catalysis of the reaction: estradiol-17-beta + NADP+ = estrone + NADPH + 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.
	GO:0016229	steroid dehydrogenase activity	Catalysis of an oxidation-reduction (redox) reaction in which one substrate is a sterol derivative.
biological process
	GO:0006710	androgen catabolic process	The chemical reactions and pathways resulting in the breakdown of androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.
	GO:0006703	estrogen biosynthetic process	The chemical reactions and pathways resulting in the formation of estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.
	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: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:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:229 - Pro A:230	[ RasMol ]
		Gly B:229 - Pro B:230	[ RasMol ]

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	1yb1
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Description

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Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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