2AKQ - JenaLib

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Title :   THE STRUCTURE OF BOVINE B-LACTOGLOBULIN A IN CRYSTALS GROWN AT VERY LOW IONIC STRENGTH

Authors :   J. J. Adams, B. F. Anderson, G. E. Norris, L. K. Creamer, G. B. Jameson

Date :   03 Aug 05 (Deposition) - 16 Aug 05 (Release) - 27 May 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   B-Lactoglbulin, X-Ray, Crystal Lattice, Low Ionic Strength, Pseudo-Merohedral Twinning, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Adams, B. F. Anderson, G. E. Norris, L. K. Creamer, G. B. Jameson
Structure Of Bovine Beta-Lactoglobulin (Variant A) At Very Low Ionic Strength
J. Struct. Biol. V. 154 246 2006
PubMed-ID: 16540345 | Reference-DOI: 10.1016/J.JSB.2005.12.010
(for further references see the PDB file header)

Molecule 1 - BETA-LACTOGLOBULIN VARIANT A
	Chains	:	A, B, C, D
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	BETA-LG, ALLERGEN BOS D 5
	Tissue	:	MAMMARY GLAND

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C
Biological Unit 3 (2x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2AKQ)

(no "Site" information available for 2AKQ)

Asymmetric Unit

No.	Residues
1	A:66	-	A:160
2	A:106	-	A:119
3	B:66	-	B:160
4	B:106	-	B:119
5	C:66	-	C:160
6	C:106	-	C:119
7	D:66	-	D:160
8	D:106	-	D:119

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

Asymmetric Unit (5, 20)

								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/C/D	E	45	Q
2	UniProt	VAR_LACB_BOVIN_002 *	I	72	L	LACB_BOVIN	---	---	A/B/C/D	I	56	L
3	UniProt	VAR_LACB_BOVIN_003 *	Q	75	H	LACB_BOVIN	---	---	A/B/C/D	Q	59	H
4	UniProt	VAR_LACB_BOVIN_004 *	G	80	D	LACB_BOVIN	---	---	A/B/C/D	D	64	D
5	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	A/B/C/D	V	118	V
	* ID not provided by source

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

Biological Unit 1 (5, 10)

								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_004 *	G	80	D	LACB_BOVIN	---	---	A/B	D	64	D
5	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	A/B	V	118	V
	* ID not provided by source

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

Biological Unit 2 (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACB_BOVIN_001 *	E	61	Q	LACB_BOVIN	---	---	C	E	45	Q
2	UniProt	VAR_LACB_BOVIN_002 *	I	72	L	LACB_BOVIN	---	---	C	I	56	L
3	UniProt	VAR_LACB_BOVIN_003 *	Q	75	H	LACB_BOVIN	---	---	C	Q	59	H
4	UniProt	VAR_LACB_BOVIN_004 *	G	80	D	LACB_BOVIN	---	---	C	D	64	D
5	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	C	V	118	V
	* ID not provided by source

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

Biological Unit 3 (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACB_BOVIN_001 *	E	61	Q	LACB_BOVIN	---	---	D	E	45	Q
2	UniProt	VAR_LACB_BOVIN_002 *	I	72	L	LACB_BOVIN	---	---	D	I	56	L
3	UniProt	VAR_LACB_BOVIN_003 *	Q	75	H	LACB_BOVIN	---	---	D	Q	59	H
4	UniProt	VAR_LACB_BOVIN_004 *	G	80	D	LACB_BOVIN	---	---	D	D	64	D
5	UniProt	VAR_LACB_BOVIN_005 *	A	134	V	LACB_BOVIN	---	---	D	V	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	4	A:9-22 B:9-22 C:9-22 D:9-22

Biological Unit 1 (1, 2)

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

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	2	- - C:9-22 -

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	2	- - - D:9-22

(no "Exon" information available for 2AKQ)

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:156
 aligned with LACB_BOVIN | P02754 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:156
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
           LACB_BOVIN    21 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 176
               SCOP domains d2akqa_ A: beta-Lactoglobulin                                                                                                                                SCOP domains
               CATH domains 2akqA00 A:5-160  [code=2.40.128.20, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh.ee.eeeeeee.hhhhhh........eeeeeee.....eeeeeeee....eeeeeeeeee.....eee.......eeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhhh....eeee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------Q----------L--H----D-----------------------------------------------------V------------------------------------------ SAPs(SNPs)
                    PROSITE ----LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2akq A   5 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with LACB_BOVIN | P02754 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:156
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
           LACB_BOVIN    21 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 176
               SCOP domains d2akqb_ B: beta-Lactoglobulin                                                                                                                                SCOP domains
               CATH domains 2akqB00 B:5-160  [code=2.40.128.20, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh.ee.eeeeeee.hhhhhh........eeeeeee.....eeeeeeee....eeeeeeee.......ee........eeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhhh....eeee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------Q----------L--H----D-----------------------------------------------------V------------------------------------------ SAPs(SNPs)
                    PROSITE ----LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2akq B   5 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with LACB_BOVIN | P02754 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:156
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
           LACB_BOVIN    21 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 176
               SCOP domains d2akqc_ C: beta-Lactoglobulin                                                                                                                                SCOP domains
               CATH domains 2akqC00 C:5-160  [code=2.40.128.20, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh.ee.eeeeeee.hhhhhh........eeeeeee.....eeeeeeee....eeeeeeeeee.....eeeeee..eeeeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhhh....eeee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------Q----------L--H----D-----------------------------------------------------V------------------------------------------ SAPs(SNPs)
                    PROSITE ----LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2akq C   5 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154

Chain D from PDB  Type:PROTEIN  Length:156
 aligned with LACB_BOVIN | P02754 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:156
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
           LACB_BOVIN    21 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 176
               SCOP domains d2akqd_ D: beta-Lactoglobulin                                                                                                                                SCOP domains
               CATH domains 2akqD00 D:5-160  [code=2.40.128.20, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh.ee.eeeeeee.hhhhhh........eeeeeee.....eeeeeeee....eeeeeeeeee.....eee.......eeeeeee....eeeeeee...hhhhh.eeeeee.....hhhhhhhhhhhhhh....eeee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------Q----------L--H----D-----------------------------------------------------V------------------------------------------ SAPs(SNPs)
                    PROSITE ----LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2akq D   5 QTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQC 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154

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: beta-Lactoglobulin (41)

Cow (Bos taurus) [TaxId: 9913] (39)

1a	d2akqa_	A:
1b	d2akqb_	B:
1c	d2akqc_	C:
1d	d2akqd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.20, no name defined] (352)

Cattle (Bos taurus) (38)

1a	2akqA00	A:5-160
1b	2akqB00	B:5-160
1c	2akqC00	C:5-160
1d	2akqD00	D:5-160

(no "Pfam Domain" information available for 2AKQ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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.

Asymmetric Unit
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Biological Units
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1beb	BOVINE BETA-LACTOGLOBULIN, LATTICE X (TRICLINIC)
1bso	BOVINE BETA-LACTOGLOBULIN, VARIANT A, LATTICE Z (TRIGONAL) WITH BOUND 12-BROMODODECANOIC ACID
3blg	BOVINE BETA-LACTOGLOBULIN, VARIANT A, LATTICE Z (TRIGONAL) AT PH 6.2

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (8, 8)

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