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Description

Title :   THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA

Authors :   I. Grishkovskaya, G. V. Avvakumov, G. L. Hammond, Y. A. Muller

Date :   13 Nov 01 (Deposition) - 15 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Shbg, Dht, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Grishkovskaya, G. V. Avvakumov, G. L. Hammond, Y. A. Muller
Resolution Of A Disordered Region At The Entrance Of The Human Sex Hormone-Binding Globulin Steroid-Binding Site.
J. Mol. Biol. V. 318 621 2002
PubMed-ID: 12054810 | Reference-DOI: 10.1016/S0022-2836(02)00169-9
(for further references see the PDB file header)

Compounds

Molecule 1 - SEX HORMONE-BINDING GLOBULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL LG-DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	DHT	1	Ligand/Ion	5-ALPHA-DIHYDROTESTOSTERONE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	DHT	2	Ligand/Ion	5-ALPHA-DIHYDROTESTOSTERONE

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:41 , SER A:42 , GLY A:58 , ASP A:65 , TRP A:66 , ASN A:82 , VAL A:105 , LYS A:134 , LEU A:171 , HOH A:318	BINDING SITE FOR RESIDUE DHT A 301

SS Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	A:164	-	A:188

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016182	P	185	L	SHBG_HUMAN	Polymorphism	6258	A	P	156	L

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016182	P	185	L	SHBG_HUMAN	Polymorphism	6258	A	P	156	L

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

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LAM_G_DOMAIN	PS50025	Laminin G domain profile.	SHBG_HUMAN	45-217	1	A:16-188

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LAM_G_DOMAIN	PS50025	Laminin G domain profile.	SHBG_HUMAN	45-217	2	A:16-188

Exons (4, 4)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000380450	2b	ENSE00001943779	chr17:7533468-7533601	134	SHBG_HUMAN	1-37	37	0	-	-
1.3	ENST00000380450	3	ENSE00001650558	chr17:7533734-7533825	92	SHBG_HUMAN	38-68	31	1	A:12-39	28
1.4	ENST00000380450	4	ENSE00000887379	chr17:7533998-7534187	190	SHBG_HUMAN	68-131	64	1	A:39-102	64
1.5	ENST00000380450	5	ENSE00000887381	chr17:7534518-7534679	162	SHBG_HUMAN	132-185	54	1	A:103-156	54
1.6	ENST00000380450	6	ENSE00000887383	chr17:7534907-7535066	160	SHBG_HUMAN	186-239	54	1	A:157-188	32
1.7	ENST00000380450	7	ENSE00000887385	chr17:7535197-7535333	137	SHBG_HUMAN	239-284	46	0	-	-
1.8	ENST00000380450	8	ENSE00000887386	chr17:7536070-7536277	208	SHBG_HUMAN	285-354	70	0	-	-
1.9b	ENST00000380450	9b	ENSE00001828732	chr17:7536522-7536701	180	SHBG_HUMAN	354-402	49	0	-	-

Sequences/Alignments

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:177
 aligned with SHBG_HUMAN | P04278 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:177
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
           SHBG_HUMAN    41 DPPAVHLSNGPGQEPIAVMTFDLTKITKTSSSFEVRTWDPEGVIFYGDTNPKDDWFMLGLRDGRPEIQLHNHWAQLTVGAGPRLDDGRWHQVEVKMEGDSVLLEVDGEEVLRLRQVSGPLTSKRHPIMRIALGGLLFPASNLRLPLVPALDGCLRRDSWLDKQAEISASAPTSLRSC 217
               SCOP domains d1kdka_ A: Sex hormone-binding globulin                                                                                                                                           SCOP domains
               CATH domains 1kdkA00 A:12-188  [code=2.60.120.200, no name defined]                                                                                                                            CATH domains
               Pfam domains ----------------------------------Laminin_G_1-1kdkA01 A:46-176                                                                                                       ------------ Pfam domains
         Sec.struct. author ....ee..........eeeeee.......eeeeeeee....eeeeeeeee...eeeeeeee..eeeeeee....eeeee..........eeeeeeee..eeeeee..eeeeee.............eeeeee.....hhhhh.........eeeeeeee.hhh.eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------L-------------------------------- SAPs(SNPs)
                    PROSITE ----LAM_G_DOMAIN  PDB: A:16-188 UniProt: 45-217                                                                                                                                   PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:12-39      ---------------------------------------------------------------Exon 1.5  PDB: A:103-156 UniProt: 132-185             Exon 1.6  PDB: A:157-188         Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.4  PDB: A:39-102 UniProt: 68-131                         -------------------------------------------------------------------------------------- Transcript 1 (2)
                 1kdk A  12 DPPAVHLSNGPGQEPIAVMTFDLTKITKTSSSFEVRTWDPEGVIFYGDTNPKDDWFMLGLRDGRPEIQLHNHWAQLTVGAGPRLDDGRWHQVEVKMEGDSVLLEVDGEEVLRLRQVSGPLTSKRHPIMRIALGGLLFPASNLRLPLVPALDGCLRRDSWLDKQAEISASAPTSLRSC 188
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Laminin G-like module (37)

Protein domain: Sex hormone-binding globulin (9)

Human (Homo sapiens) [TaxId: 9606] (9)

d1kdka_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Human (Homo sapiens) (49)

1kdkA00

A:12-188

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Laminin_G_1 (15)

Homo sapiens (Human) (7)

Laminin_G_1-1kdkA01

A:46-176

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A (SHBG_HUMAN | P04278)

molecular function
	GO:0005497	androgen binding	Interacting selectively and non-covalently with any androgen, male sex hormones.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0005496	steroid binding	Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
cellular component
	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.
	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.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	SHBG_HUMAN \| P04278	:	1d2s 1f5f 1kdm 1lhn 1lho 1lhu 1lhv 1lhw

Related Entries Specified in the PDB File

1d2s	1D2S CRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAIN OF SHBG IN COMPLEX WITH DIHYDROTESTOSTERONE
1f5f	CRYSTAL STRUCTURE OF THE N-TERMINAL G-DOMAIN OF SHBG IN COMPLEX WITH ZINC