3KZA - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GYUBA, A PATCHED CHIMERA OF B-LACTGLOBULIN

Authors :   H. Tsuge, H. Ohtomo, H. Utsunomiya, T. Konuma, M. Ikeguchi

Date :   08 Dec 09 (Deposition) - 22 Dec 10 (Release) - 09 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Artificial Protein, Chimera Protein, Disulfide Bond, Milk Protein, Retinol-Binding, Secreted, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Ohtomo, T. Konuma, H. Utsunoiya, H. Tsuge, M. Ikeguchi
Structure And Stability Of Gyuba, A Patched Chimera Of B-Lactoglobulin
Protein Sci. V. 20 1867 2011
PubMed-ID: 21853497 | Reference-DOI: 10.1002/PRO.720

Molecule 1 - BETA-LACTOGLOBULIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3C
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LGB1
	Organism Common	:	EQUINE, BOVINE
	Organism Scientific	:	EQUUS CABALLUS, BOS TAURUS
	Organism Taxid	:	9796, 9913
	Other Details	:	AN ARTIFICIAL CHIMERA PROTEIN OF BOS-TAURAS AND EQUINE B-LACTOGLOBULIN. THE RESIDUES 1-16, 28-41, 50, 51, 63-65, 74-49, 87, 88, 96-101, 109-116, 125-129, 139-144, 154-162 ARE FROM EQUINE, THE RESIDUES 17-27, 42-49, 52-62, 66-73, 80-86, 89-95, 102-108, 117-124, 130-138, 145-153 ARE FROM BOS-TAURAS.
	Synonym	:	BETA-LG-1, BETA-LACTOGLOBULIN I, BLGI

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3KZA)

(no "Site" information available for 3KZA)

Asymmetric Unit

No.	Residues
1	A:106	-	A:119
2	B:106	-	B:119

(no "Cis Peptide Bond" information available for 3KZA)

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACB_BOVIN_001 *	E	61	Q	LACB_BOVIN	---	---	A/B	E	45	Q
2	UniProt	VAR_LACB_BOVIN_002 *	I	72	L	LACB_BOVIN	---	---	A/B	I	56	L
3	UniProt	VAR_LACB_BOVIN_003 *	Q	75	H	LACB_BOVIN	---	---	A/B	Q	59	H
4	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	A/B	A	118	V
	* ID not provided by source

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

Biological Unit 1 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACB_BOVIN_001 *	E	61	Q	LACB_BOVIN	---	---	A/B	E	45	Q
2	UniProt	VAR_LACB_BOVIN_002 *	I	72	L	LACB_BOVIN	---	---	A/B	I	56	L
3	UniProt	VAR_LACB_BOVIN_003 *	Q	75	H	LACB_BOVIN	---	---	A/B	Q	59	H
4	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	A/B	A	118	V
	* ID not provided by source

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

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACB_BOVIN_001 *	E	61	Q	LACB_BOVIN	---	---	A	E	45	Q
2	UniProt	VAR_LACB_BOVIN_002 *	I	72	L	LACB_BOVIN	---	---	A	I	56	L
3	UniProt	VAR_LACB_BOVIN_003 *	Q	75	H	LACB_BOVIN	---	---	A	Q	59	H
4	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	A	A	118	V
	* ID not provided by source

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

Biological Unit 3 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACB_BOVIN_001 *	E	61	Q	LACB_BOVIN	---	---	B	E	45	Q
2	UniProt	VAR_LACB_BOVIN_002 *	I	72	L	LACB_BOVIN	---	---	B	I	56	L
3	UniProt	VAR_LACB_BOVIN_003 *	Q	75	H	LACB_BOVIN	---	---	B	Q	59	H
4	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	B	A	118	V
	* ID not provided by source

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB_BOVIN	25-38	2	A:10-22 B:10-22
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB1_HORSE	27-40	2	A:9-21 B:9-21

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB_BOVIN	25-38	2	A:10-22 B:10-22
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB1_HORSE	27-40	2	A:9-21 B:9-21

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB_BOVIN	25-38	1	A:10-22 -
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB1_HORSE	27-40	1	A:9-21 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB_BOVIN	25-38	1	- B:10-22
1	LIPOCALIN	PS00213	Lipocalin signature.	LACB1_HORSE	27-40	1	- B:9-21

(no "Exon" information available for 3KZA)

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:149
 aligned with LACB1_HORSE | P02758 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:155
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          LACB1_HORSE    21 IPQTMQDLDLQEVAGKWHSVAMAASDISLLDSESAPLRVYIEKLRPTPEDNLEIILREGENKGCAEKKIFAEKTESPAEFKINYLDEDTVFALDTDYKNYLFLCMKNAATPGQSLVCQYLARTQMVDEEIMEKFRRALQPLPGRVQIVPDLTRMA 175
               SCOP domains d3kzaa_ A: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhee.eeeeeee.hhhhh.........eeeeeee.....eeeeee.------..eeeeeee.....eeeeee..eeeeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------Q----------L--H----------------------------------------------------------V--------------------------------------- SAPs(SNPs)
                PROSITE (2) ------LIPOCALIN     --------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kza A   3 IPQTMQDLDLQEVAGTWYSLAMAASDISLLDSESAPLRVYVEELKPTPEGDLEILLQK------AQKKIIAEKTESPAEFKIDALDENKVLVLDTDYKNYLLFCMENAATPGQSLACQALVRTQMVDDEALEKFDKALQPLPMHIRLSFNPTRMA 157
                                    12        22        32        42        52       | -    |   72        82        92       102       112       122       132       142       152     
                                                                                    60     67

Chain A from PDB  Type:PROTEIN  Length:149
 aligned with LACB_BOVIN | P02754 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:155
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168     
           LACB_BOVIN    19 VTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLE 173
               SCOP domains d3kzaa_ A: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhee.eeeeeee.hhhhh.........eeeeeee.....eeeeee.------..eeeeeee.....eeeeee..eeeeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------Q----------L--H----------------------------------------------------------V--------------------------------------- SAPs(SNPs)
                    PROSITE ------LIPOCALIN     --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kza A   3 IPQTMQDLDLQEVAGTWYSLAMAASDISLLDSESAPLRVYVEELKPTPEGDLEILLQK------AQKKIIAEKTESPAEFKIDALDENKVLVLDTDYKNYLLFCMENAATPGQSLACQALVRTQMVDDEALEKFDKALQPLPMHIRLSFNPTRMA 157
                                    12        22        32        42        52       | -    |   72        82        92       102       112       122       132       142       152     
                                                                                    60     67

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with LACB1_HORSE | P02758 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:155
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          LACB1_HORSE    21 IPQTMQDLDLQEVAGKWHSVAMAASDISLLDSESAPLRVYIEKLRPTPEDNLEIILREGENKGCAEKKIFAEKTESPAEFKINYLDEDTVFALDTDYKNYLFLCMKNAATPGQSLVCQYLARTQMVDEEIMEKFRRALQPLPGRVQIVPDLTRMA 175
               SCOP domains d3kzab_ B: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhee.eeeeeee.hhhhh.........eeeeeee.....eeeeee.------..eeeee.......eeeeee..eeeeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------Q----------L--H----------------------------------------------------------V--------------------------------------- SAPs(SNPs)
                PROSITE (2) ------LIPOCALIN     --------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kza B   3 IPQTMQDLDLQEVAGTWYSLAMAASDISLLDSESAPLRVYVEELKPTPEGDLEILLQK------AQKKIIAEKTESPAEFKIDALDENKVLVLDTDYKNYLLFCMENAATPGQSLACQALVRTQMVDDEALEKFDKALQPLPMHIRLSFNPTRMA 157
                                    12        22        32        42        52       | -    |   72        82        92       102       112       122       132       142       152     
                                                                                    60     67

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with LACB_BOVIN | P02754 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:155
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168     
           LACB_BOVIN    19 VTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLE 173
               SCOP domains d3kzab_ B: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhee.eeeeeee.hhhhh.........eeeeeee.....eeeeee.------..eeeee.......eeeeee..eeeeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------Q----------L--H----------------------------------------------------------V--------------------------------------- SAPs(SNPs)
                    PROSITE ------LIPOCALIN     --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kza B   3 IPQTMQDLDLQEVAGTWYSLAMAASDISLLDSESAPLRVYVEELKPTPEGDLEILLQK------AQKKIIAEKTESPAEFKIDALDENKVLVLDTDYKNYLLFCMENAATPGQSLACQALVRTQMVDDEALEKFDKALQPLPMHIRLSFNPTRMA 157
                                    12        22        32        42        52       | -    |   72        82        92       102       112       122       132       142       152     
                                                                                    60     67

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: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Retinol binding protein-like (261)

Protein domain: automated matches (36)

Horse (Equus caballus) [TaxId: 9796] (1)

1a	d3kzaa_	A:
1b	d3kzab_	B:

(no "CATH Domain" information available for 3KZA)

(no "Pfam Domain" information available for 3KZA)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LACB_BOVIN | P02754)

molecular function
	GO:0019841	retinol binding	Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
	GO:0036094	small molecule binding	Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
biological process
	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: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.

Chain A,B (LACB1_HORSE | P02758)

molecular function
	GO:0019841	retinol binding	Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
	GO:0036094	small molecule binding	Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0032725	positive regulation of granulocyte macrophage colony-stimulating factor production	Any process that activates or increases the frequency, rate, or extent of granulocyte macrophage colony-stimulating factor production.
	GO:2000667	positive regulation of interleukin-13 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-13 secretion.
	GO:2000778	positive regulation of interleukin-6 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
	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: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.

Asymmetric Unit
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(no "Cis Peptide Bonds" information available for 3kza)

Biological Units
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	3kza
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(no "Related Entries Specified in the PDB File" available for 3KZA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

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Exons (0, 0)

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