2FJ9 - JenaLib

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Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF THE UNLIGANDED HUMAN ACBP

Authors :   J. P. Taskinen, D. M. Van Aalten, J. Knudsen, R. K. Wierenga

Date :   02 Jan 06 (Deposition) - 31 Oct 06 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Fatty Acid Metabolism, Acbp, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. P. Taskinen, D. M. Van Aalten, J. Knudsen, R. K. Wierenga
High Resolution Crystal Structures Of Unliganded And Liganded Human Liver Acbp Reveal A New Mode Of Binding For The Acyl-Coa Ligand.
Proteins V. 66 229 2006
PubMed-ID: 17044054 | Reference-DOI: 10.1002/PROT.21124

Molecule 1 - ACYL-COA-BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DBI
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ACBP, DIAZEPAM-BINDING INHIBITOR, DBI, ENDOZEPINE, EP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	PB	1	Ligand/Ion	LEAD (II) ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PB	-1	Ligand/Ion	LEAD (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PB	-1	Ligand/Ion	LEAD (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:61 , ASP A:69 , CL A:89 , HOH A:1101 , HOH A:1156	BINDING SITE FOR RESIDUE PB A 1
2	AC2	SOFTWARE	GLU A:11 , HIS A:15 , HOH A:1277	BINDING SITE FOR RESIDUE ZN A 88
3	AC3	SOFTWARE	PB A:1 , GLU A:61 , ASP A:69 , HOH A:1034	BINDING SITE FOR RESIDUE CL A 89
4	AC4	SOFTWARE	ASP A:22 , GLU A:43	BINDING SITE FOR RESIDUE CL A 90

(no "SS Bond" information available for 2FJ9)

(no "Cis Peptide Bond" information available for 2FJ9)

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048160	D	39	N	ACBP_HUMAN	Polymorphism	8192504	A	D	39	N
2	UniProt	VAR_048161	M	71	V	ACBP_HUMAN	Polymorphism	8192506	A	M	71	V
3	UniProt	VAR_048162	G	86	R	ACBP_HUMAN	Polymorphism	8192507	A	G	86	R

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_048160	D	39	N	ACBP_HUMAN	Polymorphism	8192504	A	D	39	N
2	UniProt	VAR_048161	M	71	V	ACBP_HUMAN	Polymorphism	8192506	A	M	71	V
3	UniProt	VAR_048162	G	86	R	ACBP_HUMAN	Polymorphism	8192507	A	G	86	R

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

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048160	D	39	N	ACBP_HUMAN	Polymorphism	8192504	A	D	39	N
2	UniProt	VAR_048161	M	71	V	ACBP_HUMAN	Polymorphism	8192506	A	M	71	V
3	UniProt	VAR_048162	G	86	R	ACBP_HUMAN	Polymorphism	8192507	A	G	86	R

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACB_2	PS51228	Acyl-CoA-binding (ACB) domain profile.	ACBP_HUMAN	2-87	1	A:2-87
2	ACB_1	PS00880	Acyl-CoA-binding (ACB) domain signature.	ACBP_HUMAN	20-38	1	A:20-38

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACB_2	PS51228	Acyl-CoA-binding (ACB) domain profile.	ACBP_HUMAN	2-87	1	A:2-87
2	ACB_1	PS00880	Acyl-CoA-binding (ACB) domain signature.	ACBP_HUMAN	20-38	1	A:20-38

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACB_2	PS51228	Acyl-CoA-binding (ACB) domain profile.	ACBP_HUMAN	2-87	2	A:2-87
2	ACB_1	PS00880	Acyl-CoA-binding (ACB) domain signature.	ACBP_HUMAN	20-38	2	A:20-38

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000355857	1a	ENSE00001883996	chr2:120124497-120124636	140	ACBP_HUMAN	1-3	3	1	A:2-3	2
1.5a	ENST00000355857	5a	ENSE00001202551	chr2:120125764-120125881	118	ACBP_HUMAN	4-43	40	1	A:4-43	40
1.6b	ENST00000355857	6b	ENSE00001020634	chr2:120128316-120128378	63	ACBP_HUMAN	43-64	22	1	A:43-64	22
1.7f	ENST00000355857	7f	ENSE00001931282	chr2:120129821-120130126	306	ACBP_HUMAN	64-87	24	1	A:64-87	24

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:86
 aligned with ACBP_HUMAN | P07108 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:86
                                    11        21        31        41        51        61        71        81      
            ACBP_HUMAN    2 SQAEFEKAAEEVRHLKTKPSDEEMLFIYGHYKQATVGDINTERPGMLDFTGKAKWDAWNELKGTSKEDAMKAYINKVEELKKKYGI 87
               SCOP domains d2fj9a_ A: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------N-------------------------------V--------------R- SAPs(SNPs)
                PROSITE (1) ACB_2  PDB: A:2-87 UniProt: 2-87                                                       PROSITE (1)
                PROSITE (2) ------------------ACB_1  PDB: A:20-38------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.Exon 1.5a  PDB: A:4-43 UniProt: 4-43    --------------------Exon 1.7f  PDB: A:64-87  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.6b  PDB: A:43-6----------------------- Transcript 1 (2)
                  2fj9 A  2 SQAEFEKAAEEVRHLKTKPSDEEMLFIYGHYKQATVGDINTERPGMLDFTGKAKWDAWNELKGTSKEDAMKAYINKVEELKKKYGI 87
                                    11        21        31        41        51        61        71        81

Legend:		→ Mismatch	(orange background)
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	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 alpha proteins (14657)

Fold: Acyl-CoA binding protein-like (48)

Superfamily: Acyl-CoA binding protein (15)

Family: Acyl-CoA binding protein (10)

Protein domain: automated matches (3)

Human (Homo sapiens) [TaxId: 9606] (3)

d2fj9a_

(no "CATH Domain" information available for 2FJ9)

(no "Pfam Domain" information available for 2FJ9)

Asymmetric Unit(hide GO term definitions)

Chain A (ACBP_HUMAN | P07108)

molecular function
	GO:0030156	benzodiazepine receptor binding	Interacting selectively and non-covalently with the peripheral benzodiazepine receptor (PBR).
	GO:0000062	fatty-acyl-CoA binding	Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0036042	long-chain fatty acyl-CoA binding	Interacting selectively and non-covalently with a long-chain fatty acyl-CoA. A long-chain fatty acyl-CoA is any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
	GO:0036151	phosphatidylcholine acyl-chain remodeling	Remodeling the acyl chains of phosphatidylcholine, through sequential deacylation and re-acylation reactions, to generate phosphatidylcholine containing different types of fatty acid acyl chains.
	GO:0018345	protein palmitoylation	The covalent attachment of a palmitoyl group to a protein.
	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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	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:0097038	perinuclear endoplasmic reticulum	The portion of endoplasmic reticulum, the intracellular network of tubules and cisternae, that occurs near the nucleus. The lumen of the perinuclear endoplasmic reticulum is contiguous with the nuclear envelope lumen (also called perinuclear space), the region between the inner and outer nuclear membranes.

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Description

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Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

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