3B0O - JenaLib

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Title :   CRYSTAL STRUCTURE OF ALPHA-LACTALBUMIN

Authors :   K. Makabe, K. Kuwajima

Date :   10 Jun 11 (Deposition) - 13 Jun 12 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.61

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

Keywords :   Calcium Binding Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Makabe, T. Nakamura, K. Kuwajima
Structural Insights Into The Stability Perturbations Induce By N-Terminal Variation In Human And Goat Alpha-Lactalbumin
Protein Eng. Des. Sel. V. 26 165 2013
PubMed-ID: 23155056 | Reference-DOI: 10.1093/PROTEIN/GZS093

Molecule 1 - ALPHA-LACTALBUMIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LALBA, LYZL7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LACTOSE SYNTHASE B PROTEIN, LYSOZYME-LIKE PROTEIN 7

		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, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:79 , ASP A:82 , ASP A:84 , ASP A:87 , ASP A:88 , HOH A:128	BINDING SITE FOR RESIDUE CA A 124
2	AC2	SOFTWARE	LYS B:79 , ASP B:82 , ASP B:84 , ASP B:87 , ASP B:88 , HOH B:132 , HOH B:133	BINDING SITE FOR RESIDUE CA B 124

Asymmetric Unit

No.	Residues
1	A:6	-	A:120
2	A:28	-	A:111
3	A:61	-	A:77
4	A:73	-	A:91
5	B:6	-	B:120
6	B:28	-	B:111
7	B:61	-	B:77
8	B:73	-	B:91

(no "Cis Peptide Bond" information available for 3B0O)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024526	I	46	V	LALBA_HUMAN	Polymorphism	2232565	A/B	I	27	V

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024526	I	46	V	LALBA_HUMAN	Polymorphism	2232565	A	I	27	V

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024526	I	46	V	LALBA_HUMAN	Polymorphism	2232565	B	I	27	V

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LALBA_HUMAN	20-142	2	A:2-120 B:2-120
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LALBA_HUMAN	92-110	2	A:73-91 B:73-91

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LALBA_HUMAN	20-142	1	A:2-120 -
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LALBA_HUMAN	92-110	1	A:73-91 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LALBA_HUMAN	20-142	1	- B:2-120
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LALBA_HUMAN	92-110	1	- B:73-91

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000301046	1	ENSE00001113957	chr12:48963829-48963671	159	LALBA_HUMAN	1-45	45	2	A:1-26 B:1-26	26 26
1.2	ENST00000301046	2	ENSE00001113961	chr12:48963023-48962865	159	LALBA_HUMAN	45-98	54	2	A:26-79 B:26-79	54 54
1.3	ENST00000301046	3	ENSE00001113959	chr12:48962375-48962300	76	LALBA_HUMAN	98-123	26	2	A:79-104 B:79-104	26 26
1.4	ENST00000301046	4	ENSE00001113958	chr12:48961800-48961468	333	LALBA_HUMAN	123-142	20	2	A:104-120 B:104-120	17 17

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:120
 aligned with LALBA_HUMAN | P00709 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:120
                                    29        39        49        59        69        79        89        99       109       119       129       139
          LALBA_HUMAN    20 KQFTKCELSQLLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNESTEYGLFQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKILDIKGIDYWLAHKALCTEKLEQWLC 139
               SCOP domains d3b0oa_ A: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....eee....ee...................hhhhhhh..hhhhhhhhhhhhhhh.hhhhhh.hhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------V--------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: A:2-120 UniProt: 20-142                                                                     PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-26     ----------------------------------------------------Exon 1.3  PDB: A:79-104   ---------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.2  PDB: A:26-79 UniProt: 45-98                 ------------------------Exon 1.4          Transcript 1 (2)
                 3b0o A   1 MQFTKCELSQLLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNESTEYGLFQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKILDIKGIDYWLAHKALCTEKLEQWLC 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with LALBA_HUMAN | P00709 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:120
                                    29        39        49        59        69        79        89        99       109       119       129       139
          LALBA_HUMAN    20 KQFTKCELSQLLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNESTEYGLFQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKILDIKGIDYWLAHKALCTEKLEQWLC 139
               SCOP domains d3b0ob_ B: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eeee....ee...................hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------V--------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: B:2-120 UniProt: 20-142                                                                     PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:1-26     ----------------------------------------------------Exon 1.3  PDB: B:79-104   ---------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.2  PDB: B:26-79 UniProt: 45-98                 ------------------------Exon 1.4          Transcript 1 (2)
                 3b0o B   1 MQFTKCELSQLLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNESTEYGLFQISNKLWCKSSQVPQSRNICDISCDKFLDDDITDDIMCAKKILDIKGIDYWLAHKALCTEKLEQWLC 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

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) (23004)

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: C-type lysozyme (738)

Protein domain: automated matches (17)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d3b0oa_	A:
1b	d3b0ob_	B:

(no "CATH Domain" information available for 3B0O)

(no "Pfam Domain" information available for 3B0O)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LALBA_HUMAN | P00709)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004461	lactose synthase activity	Catalysis of the reaction: UDP-galactose + D-glucose = UDP + lactose.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0005989	lactose biosynthetic process	The chemical reactions and pathways resulting in the formation of lactose, the disaccharide galactopyranosyl-glucose.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	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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	LALBA_HUMAN \| P00709	:	1a4v 1b9o 1cb3 1hml 3b0i 4l41

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

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Exons (4, 8)

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