2VDX - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED CORTICOSTEROID BINDING GLOBULIN

Authors :   A. Zhou, Z. Wei, R. J. Read

Date :   13 Oct 07 (Deposition) - 06 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

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

Keywords :   Transport Protein, Cortisol Binding Globulin, Glycoprotein, Lipid-Binding, Steroid-Binding, Disease Mutation, Cbg, Serpin, Cleaved, Secreted, Cortisol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Zhou, Z. Wei, P. L. Stanley, R. J. Read, P. E. Stein, R. W. Carrell
The S-To-R Transition Of Corticosteroid-Binding Globulin And The Mechanism Of Hormone Release.
J. Mol. Biol. V. 380 244 2008
PubMed-ID: 18513745 | Reference-DOI: 10.1016/J.JMB.2008.05.012

Molecule 1 - CORTICOSTEROID-BINDING GLOBULIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI,
	Expression System Plasmid	:	PSUMO3-CBG
	Expression System Strain	:	BL21(DE3)
	Expression System Variant	:	PSUMO3 FUSION SYSTEM
	Expression System Vector	:	PSUMO3
	Fragment	:	RESIDUES 33-405
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CBG, TRANSCORTIN, SERPIN A6, HUMAN CORTICOSTEROID-BINDING GLOBULIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:235 , GLY A:237 , HOH A:2058 , HOH A:2098 , HOH A:2099 , HOH A:2101	BINDING SITE FOR RESIDUE NA A1384
2	AC2	SOFTWARE	SER A:215 , SER A:216 , HOH A:2079 , HOH A:2084	BINDING SITE FOR RESIDUE NA A1385
3	AC3	SOFTWARE	TYR B:235 , GLY B:237 , HOH B:2023 , HOH B:2085 , HOH B:2086	BINDING SITE FOR RESIDUE NA B1384
4	AC4	SOFTWARE	LEU A:93 , LYS A:96 , HOH A:2029	BINDING SITE FOR RESIDUE NA A1386

(no "SS Bond" information available for 2VDX)

(no "Cis Peptide Bond" information available for 2VDX)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_007111	L	115	H	CBG_HUMAN	Disease (CBG deficiency)	113418909	A/B	L	93	H
2	UniProt	VAR_024350	S	246	A	CBG_HUMAN	Polymorphism	2228541	A/B	S	224	A
3	UniProt	VAR_016223	D	389	N	CBG_HUMAN	Disease (CBG deficiency)	28929488	A/B	D	367	N

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_007111	L	115	H	CBG_HUMAN	Disease (CBG deficiency)	113418909	A	L	93	H
2	UniProt	VAR_024350	S	246	A	CBG_HUMAN	Polymorphism	2228541	A	S	224	A
3	UniProt	VAR_016223	D	389	N	CBG_HUMAN	Disease (CBG deficiency)	28929488	A	D	367	N

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_007111	L	115	H	CBG_HUMAN	Disease (CBG deficiency)	113418909	B	L	93	H
2	UniProt	VAR_024350	S	246	A	CBG_HUMAN	Polymorphism	2228541	B	S	224	A
3	UniProt	VAR_016223	D	389	N	CBG_HUMAN	Disease (CBG deficiency)	28929488	B	D	367	N

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	CBG_HUMAN	377-387	2	A:355-365 B:355-365

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	CBG_HUMAN	377-387	1	A:355-365 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	CBG_HUMAN	377-387	1	- B:355-365

(no "Exon" information available for 2VDX)

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:366
 aligned with CBG_HUMAN | P08185 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:368
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        
            CBG_HUMAN    38 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDTAGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 405
               SCOP domains d2vdxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2vdxA01 A:16-184,A:280-333 Antithrombin, subunit I, domain 2                                                                                                             2vdxA02 A:185-279,A:339-382 Alpha-1-antitrypsin, domain 1                                      2vdxA01 A:16-184,A:280-333                            -----2vdxA02 A:1 85-279,A:339-382                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh..........-.....eeeeeeeeeeee.....hhhhheeeeeeee..eeeeeeeeeeeeeeeeee.....eeeeeee....eeeeeeee...hhhhhhhh.hhhhhhhhhhhheeeeeeeeee..eeeeeeehhhhhhhh..hhhhh.............eeeeeeeeeeeeee...eeeeeeeeeeeeee.-..eeee....eeeeeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------N---------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vdx A  16 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFSG-DSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTTQANFSRITQDAQLKSSKVVHKAVLQLNEEGTEAAGAMFLEAIPR-KPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 383
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165| |    175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345   | | 355       365       375        
                                                                                                                                                                                166 |                                                                                                                                                                                  349 |                                
                                                                                                                                                                                  168                                                                                                                                                                                    351

Chain B from PDB  Type:PROTEIN  Length:360
 aligned with CBG_HUMAN | P08185 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:368
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        
            CBG_HUMAN    38 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDTAGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 405
               SCOP domains d2vdxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2vdxB01 B:16-184,B:280-333 Antithrombin, subunit I, domain 2                                                                                                             2vdxB02 B:185-279,B:339-382 Alpha-1-antitrypsin, domain 1                                      2vdxB01 B:16-184,B:280-333                            -----2vdxB02 B:1 85-279,B:339-382                - CATH domains
           Pfam domains (1) ---Serpin-2vdxB01 B:19-382                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) ---Serpin-2vdxB02 B:19-382                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh-----..eeeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..........--....eeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeee.....eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh.............eeeeeeeeeeeeee...eeeeeeeeeeeeee.-..eeee....eeeeeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------N---------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vdx B  16 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLF-----SLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFSG--SPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTTQANFSRITQDAQLKSSKVVHKAVLQLNEEGTEAAGAMFLEAIPR-KPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 383
                                    25        35        45        55        65        75        85        |-    |  105       115       125       135       145       155       165|  |   175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345   | | 355       365       375        
                                                                                                         94   100                                                               166  |                                                                                                                                                                                 349 |                                
                                                                                                                                                                                   169                                                                                                                                                                                   351

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: Multi-domain proteins (alpha and beta) (2421)

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: automated matches (20)

Protein domain: automated matches (20)

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

1a	d2vdxa_	A:
1b	d2vdxb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Antithrombin; Chain I, domain 2 (100)

Homologous Superfamily: Antithrombin, subunit I, domain 2 (100)

Human (Homo sapiens) (80)

1a	2vdxA01	A:16-184,A:280-333
1b	2vdxB01	B:16-184,B:280-333

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Alpha-1-antitrypsin; domain 1 (101)

Homologous Superfamily: Alpha-1-antitrypsin, domain 1 (101)

Human (Homo sapiens) (81)

2a	2vdxA02	A:185-279,A:339-382
2b	2vdxB02	B:185-279,B:339-382

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Serpin] (63)

Family: Serpin (63)

Homo sapiens (Human) (41)

1a	Serpin-2vdxB01	B:19-382
1b	Serpin-2vdxB02	B:19-382

Asymmetric Unit(hide GO term definitions)

Chain A,B (CBG_HUMAN | P08185)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
	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.
biological process
	GO:0008211	glucocorticoid metabolic process	The chemical reactions and pathways involving glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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	CBG_HUMAN \| P08185	:	2vdy 4bb2 4c41 4c49

2vdy	CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED CORTICOSTEROID BINDING GLOBULIN COMPLEXED WITH CORTISOL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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