1YSX - JenaLib

NMR Structure - manually (Jmol Viewer)

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF DOMAIN 3 FROM HUMAN SERUM ALBUMIN COMPLEXED TO AN ANTI-APOPTOTIC LIGAND DIRECTED AGAINST BCL-XL AND BCL-2

Authors :   T. Oltersdorf, S. W. Elmore, A. R. Shoemaker, R. C. Armstrong, D. J. Augeri, B. A. Belli, M. Bruncko, T. L. Deckwerth, J. Dinges, P. J. Hajduk, M. K. Joseph, S. Kitada, S. J. Korsmeyer, A. R. Kunzer, A. Letai, C. Li, M. J. Mitten, D. G. Nettesheim, S. Ng, P. M. Nimmer, J. M. O'Connor, A. Oleksijew, A. M. Petros, J. C. Reed, W. Shen, S. K. Tahir, C. B. Thompson, K. J. Tomaselli, B. Wang, M. D. Wendt, H. Zhang, S. W. Fesik, S. H. Rosenberg

Date :   09 Feb 05 (Deposition) - 07 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

Keywords :   Complex, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Oltersdorf, S. W. Elmore, A. R. Shoemaker, R. C. Armstrong, D. J. Augeri, B. A. Belli, M. Bruncko, T. L. Deckwerth, J. Dinges, P. J. Hajduk, M. K. Joseph, S. Kitada, S. J. Korsmeyer, A. R. Kunzer, A. Letai, C. Li, M. J. Mitten, D. G. Nettesheim, S. Ng, P. M. Nimmer, J. M. O'Connor, A. Oleksijew, A. M. Petros, J. C. Reed, W. Shen, S. K. Tahir, C. B. Thompson, K. J. Tomaselli, B. Wang, M. D. Wendt, H. Zhang, S. W. Fesik, S. H. Rosenberg
An Inhibitor Of Bcl-2 Family Proteins Induces Regression Of Solid Tumours
Nature V. 435 677 2005
PubMed-ID: 15902208 | Reference-DOI: 10.1038/NATURE03579
(for further references see the PDB file header)

Molecule 1 - SERUM ALBUMIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ALB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	4EB	1	Ligand/Ion	4-({2-[(2,4-DIMETHYLPHENYL)SULFANYL]ETHYL}AMINO)-N-[(4'-FLUORO-1,1'-BIPHENYL-4-YL)CARBONYL]-3-NITROBENZENESULFONAMIDE

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:391 , CYS A:392 , LEU A:407 , TYR A:411 , LYS A:414 , VAL A:415 , THR A:422 , LEU A:423 , VAL A:426 , TYR A:452 , LEU A:460 , HIS A:464	BINDING SITE FOR RESIDUE 4EB A 1000

(no "SS Bond" information available for 1YSX)

(no "Cis Peptide Bond" information available for 1YSX)

NMR Structure (18, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_014294	E	420	K	ALBU_HUMAN	Polymorphism	---	A	E	396	K
02	UniProt	VAR_013017	R	434	C	ALBU_HUMAN	Polymorphism	78575701	A	R	410	C
03	UniProt	VAR_014295	K	490	E	ALBU_HUMAN	Polymorphism	1063469	A	K	466	E
04	UniProt	VAR_000534	E	503	K	ALBU_HUMAN	Polymorphism	80259813	A	E	479	K
05	UniProt	VAR_000535	D	518	N	ALBU_HUMAN	Polymorphism	75920790	A	D	494	N
06	UniProt	VAR_000536	E	525	K	ALBU_HUMAN	Polymorphism	75523493	A	E	501	K
07	UniProt	VAR_000537	E	529	K	ALBU_HUMAN	Polymorphism	74826639	A	E	505	K
08	UniProt	VAR_013018	V	557	M	ALBU_HUMAN	Polymorphism	78284052	A	V	533	M
09	UniProt	VAR_000538	K	560	E	ALBU_HUMAN	Polymorphism	77645174	A	K	536	E
10	UniProt	VAR_000539	K	565	E	ALBU_HUMAN	Polymorphism	80345158	A	K	541	E
11	UniProt	VAR_000541	D	574	A	ALBU_HUMAN	Polymorphism	79738788	A	D	550	A
12	UniProt	VAR_000540	D	574	G	ALBU_HUMAN	Polymorphism	79738788	A	D	550	G
13	UniProt	VAR_013019	K	584	E	ALBU_HUMAN	Polymorphism	76671808	A	K	560	E
14	UniProt	VAR_000542	D	587	N	ALBU_HUMAN	Polymorphism	76587671	A	D	563	N
15	UniProt	VAR_000543	E	589	K	ALBU_HUMAN	Polymorphism	75709682	A	E	565	K
16	UniProt	VAR_000544	E	594	K	ALBU_HUMAN	Polymorphism	79228041	A	E	570	K
17	UniProt	VAR_000545	K	597	E	ALBU_HUMAN	Polymorphism	80106970	A	K	573	E
18	UniProt	VAR_000546	K	598	N	ALBU_HUMAN	Polymorphism	75738598	A	K	574	N

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALBUMIN_1	PS00212	Albumin domain signature.	ALBU_HUMAN	185-209 377-401 575-599	1	- - A:551-575

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000295897	2a	ENSE00002075693	chr4:74269956-74270123	168	ALBU_HUMAN	1-27	27	0	-	-
1.3a	ENST00000295897	3a	ENSE00001076782	chr4:74270833-74270890	58	ALBU_HUMAN	27-46	20	0	-	-
1.4b	ENST00000295897	4b	ENSE00001076799	chr4:74272346-74272478	133	ALBU_HUMAN	46-90	45	0	-	-
1.5a	ENST00000295897	5a	ENSE00001076811	chr4:74274311-74274522	212	ALBU_HUMAN	91-161	71	0	-	-
1.7d	ENST00000295897	7d	ENSE00001076808	chr4:74275072-74275204	133	ALBU_HUMAN	161-205	45	0	-	-
1.8a	ENST00000295897	8a	ENSE00001076797	chr4:74276029-74276126	98	ALBU_HUMAN	206-238	33	0	-	-
1.9a	ENST00000295897	9a	ENSE00001076788	chr4:74277713-74277842	130	ALBU_HUMAN	238-281	44	0	-	-
1.10b	ENST00000295897	10b	ENSE00001076792	chr4:74279137-74279351	215	ALBU_HUMAN	282-353	72	0	-	-
1.11a	ENST00000295897	11a	ENSE00001076805	chr4:74280752-74280884	133	ALBU_HUMAN	353-397	45	0	-	-
1.12	ENST00000295897	12	ENSE00001076781	chr4:74281973-74282070	98	ALBU_HUMAN	398-430	33	1	A:385-406	22
1.13b	ENST00000295897	13b	ENSE00001076796	chr4:74283248-74283386	139	ALBU_HUMAN	430-476	47	1	A:406-452	47
1.14b	ENST00000295897	14b	ENSE00001076790	chr4:74283805-74284028	224	ALBU_HUMAN	477-551	75	1	A:453-527	75
1.16b	ENST00000295897	16b	ENSE00001076802	chr4:74285224-74285356	133	ALBU_HUMAN	551-595	45	1	A:527-571	45
1.18a	ENST00000295897	18a	ENSE00001076795	chr4:74285971-74286038	68	ALBU_HUMAN	596-609	14	1	A:572-584	13
1.20j	ENST00000295897	20j	ENSE00001823230	chr4:74286809-74287129	321	ALBU_HUMAN	-	0	0	-	-

NMR Structure

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:200
 aligned with ALBU_HUMAN | P02768 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:200
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608
           ALBU_HUMAN   409 QNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALG 608
               SCOP domains ----d1ysxa1 A:389-584 Serum albumin                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Serum_albumin-1ysxA01 A:388-568                                                                                                                                                      ---------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhh...................hhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) -----------K-------------C-------------------------------------------------------E------------K--------------N------K---K---------------------------M--E----E--------A---------E--N-K----K--EN---------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------G---------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------ALBUMIN_1  PDB: A:551-575--------- PROSITE
           Transcript 1 (1) Exon 1.12 [INCOMPLETE]----------------------------------------------Exon 1.14b  PDB: A:453-527 UniProt: 477-551                                --------------------------------------------Exon 1.18a    Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.13b  PDB: A:406-452 UniProt: 430-476    --------------------------------------------------------------------------Exon 1.16b  PDB: A:527-571 UniProt: 551-595  ------------- Transcript 1 (2)
                 1ysx A 385 QNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALG 584
                                   394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Serum albumin-like (99)

Superfamily: Serum albumin-like (99)

Family: Serum albumin-like (75)

Protein domain: Serum albumin (69)

Human (Homo sapiens) [TaxId: 9606] (69)

d1ysxa1

A:389-584

(no "CATH Domain" information available for 1YSX)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Serum_albumin (23)

Family: Serum_albumin (23)

Homo sapiens (Human) (22)

Serum_albumin-1ysxA01

A:388-568

NMR Structure(hide GO term definitions)

Chain A (ALBU_HUMAN | P02768)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0051087	chaperone binding	Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0005504	fatty acid binding	Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0015643	toxic substance binding	Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0015721	bile acid and bile salt transport	The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0009267	cellular response to starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
	GO:0019836	hemolysis by symbiont of host erythrocytes	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0042157	lipoprotein metabolic process	The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
	GO:0051659	maintenance of mitochondrion location	Any process in which a mitochondrion is maintained in a specific location within a cell and prevented from moving elsewhere.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0043069	negative regulation of programmed cell death	Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0046010	positive regulation of circadian sleep/wake cycle, non-REM sleep	Any process that activates or increases the duration or quality of non-rapid eye movement (NREM) sleep.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0046689	response to mercury ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
	GO:0007584	response to nutrient	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
	GO:0010033	response to organic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0070541	response to platinum ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platinum stimulus.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
	GO:0043252	sodium-independent organic anion transport	The directed, sodium-independent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0005604	basement membrane	A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

NMR Structure
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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (18, 18)

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Exons (5, 5)

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