1M49 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-2 COMPLEXED WITH SP-1985

Authors :   M. A. Arkin, M. Randal, W. L. Delano, J. Hyde, T. N. Luong, J. D. Oslob, D. R. Raphael, L. Taylor, J. Wang, R. S. Mcdowell, J. A. Wells, A. C. Braisted

Date :   02 Jul 02 (Deposition) - 31 Jul 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Cytokine, Four-Helix Bundle, Small Molecule Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Arkin, M. Randal, W. L. Delano, J. Hyde, T. N. Luong, J. D. Oslob, D. R. Raphael, L. Taylor, J. Wang, R. S. Mcdowell, J. A. Wells, A. C. Braisted
Binding Of Small Molecules To An Adaptive Protein-Protein Interface
Proc. Natl. Acad. Sci. Usa V. 100 1603 2003
PubMed-ID: 12582206 | Reference-DOI: 10.1073/PNAS.252756299
(for further references see the PDB file header)

Molecule 1 - INTERLEUKIN-2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PRSET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IL-2, T-CELL GROWTH FACTOR, TCGF, ALDESLEUKIN

		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	CMM	2	Ligand/Ion	2-[2-(1-CARBAMIMIDOYL-PIPERIDIN-3-YL)-ACETYLAMINO]-3-{4-[2-(3-OXALYL-1H-INDOL-7-YL)ETHYL]-PHENYL}-PROPIONIC ACID METHYL ESTER

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CMM	1	Ligand/Ion	2-[2-(1-CARBAMIMIDOYL-PIPERIDIN-3-YL)-ACETYLAMINO]-3-{4-[2-(3-OXALYL-1H-INDOL-7-YL)ETHYL]-PHENYL}-PROPIONIC ACID METHYL ESTER

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CMM	1	Ligand/Ion	2-[2-(1-CARBAMIMIDOYL-PIPERIDIN-3-YL)-ACETYLAMINO]-3-{4-[2-(3-OXALYL-1H-INDOL-7-YL)ETHYL]-PHENYL}-PROPIONIC ACID METHYL ESTER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:35 , ARG A:38 , MET A:39 , THR A:41 , PHE A:42 , LYS A:43 , TYR A:45 , THR A:51 , GLU A:62 , PRO A:65 , ALA A:73 , GLN A:126 , SER A:127 , SER A:130 , HOH A:208 , HOH A:240 , HOH A:248	BINDING SITE FOR RESIDUE CMM A 201
2	AC2	SOFTWARE	GLU A:60 , LYS A:64 , GLU A:67 , ARG A:83 , ILE A:86 , SER A:87 , ASN A:90 , VAL A:91 , ARG B:38 , THR B:41 , PHE B:42 , LYS B:43 , TYR B:45 , GLU B:62 , PRO B:65 , LEU B:72 , HOH B:228 , HOH B:229	BINDING SITE FOR RESIDUE CMM B 202

Asymmetric Unit

No.	Residues
1	A:58	-	A:105
2	B:58	-	B:105

(no "Cis Peptide Bond" information available for 1M49)

(no "SAP(SNP)/Variant" information available for 1M49)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERLEUKIN_2	PS00424	Interleukin-2 signature.	IL2_HUMAN	71-83	2	A:51-63 B:51-63

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERLEUKIN_2	PS00424	Interleukin-2 signature.	IL2_HUMAN	71-83	1	A:51-63 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERLEUKIN_2	PS00424	Interleukin-2 signature.	IL2_HUMAN	71-83	1	- B:51-63

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000226730	1a	ENSE00001293064	chr4:123377880-123377449	432	IL2_HUMAN	1-49	49	2	A:4-29 B:4-29	26 26
1.1c	ENST00000226730	1c	ENSE00000935280	chr4:123377358-123377299	60	IL2_HUMAN	50-69	20	2	A:30-49 B:34-49	20 16
1.2	ENST00000226730	2	ENSE00000935278	chr4:123375008-123374865	144	IL2_HUMAN	70-117	48	2	A:50-97 (gaps) B:50-97 (gaps)	48 48
1.3b	ENST00000226730	3b	ENSE00001138256	chr4:123373017-123372625	393	IL2_HUMAN	118-153	36	2	A:98-132 B:102-133	35 32

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:123
 aligned with IL2_HUMAN | P60568 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:129
                                    33        43        53        63        73        83        93       103       113       123       133       143         
            IL2_HUMAN    24 SSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFCQSIISTL 152
               SCOP domains d1m49a_ A: Interleukin-2 (IL-2)                                                                                                   SCOP domains
               CATH domains 1m49A00 A:4-132  [code=1.20.1250.10, no name defined]                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.------hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------INTERLEUKIN_2--------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: A:4-29    Exon 1.1c           Exon 1.2  PDB: A:50-97 (gaps) UniProt: 70-117   Exon 1.3b  PDB: A:98-132            Transcript 1
                 1m49 A   4 SSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQ------RPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFCQSIISTL 132
                                    13        23        33        43        53        63        73|      |83        93       103       113       123         
                                                                                                 74     81

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with IL2_HUMAN | P60568 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:130
                                    33        43        53        63        73        83        93       103       113       123       133       143       153
            IL2_HUMAN    24 SSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFCQSIISTLT 153
               SCOP domains d1m49b_ B: Interleukin-2 (    IL-2)                                                                                                SCOP domains
               CATH domains 1m49B00 B:4-133  [code=1.2    0.1250.10, no name defined]                                                                          CATH domains
           Pfam domains (1) IL2-1m49B01 B:4-130                                                                                                            --- Pfam domains (1)
           Pfam domains (2) IL2-1m49B02 B:4-130                                                                                                            --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..-----hhhhhhhhhhhhhhhhh----...........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------INTERLEUKIN_2---------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: B:4-29    Exon 1.1c           Exon 1.2  PDB: B:50-97 (gaps) UniProt: 70-117   Exon 1.3b  PDB: B:102-133            Transcript 1
                 1m49 B   4 SSSTKKTQLQLEHLLLDLQMILNGIN----PKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQS-----RPRDLISNINVIVLELK----TFMCEYADETATIVEFLNRWITFCQSIISTLT 133
                                    13        23     |   -|       43        53        63        73 |     |83        93   |   103       113       123       133
                                                    29   34                                       75    81              97  102

Legend:		→ Mismatch	(orange background)
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		→ 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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: 4-helical cytokines (168)

Superfamily: 4-helical cytokines (168)

Family: Short-chain cytokines (78)

Protein domain: Interleukin-2 (IL-2) (16)

Human (Homo sapiens) [TaxId: 9606] (16)

1a	d1m49a_	A:
1b	d1m49b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Growth Hormone; Chain: A; (136)

Homologous Superfamily: [code=1.20.1250.10, no name defined] (130)

Human (Homo sapiens) (110)

1a	1m49A00	A:4-132
1b	1m49B00	B:4-133

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 4H_Cytokine (48)

Family: IL2 (11)

Homo sapiens (Human) (11)

1a	IL2-1m49B01	B:4-130
1b	IL2-1m49B02	B:4-130

Asymmetric Unit(hide GO term definitions)

Chain A,B (IL2_HUMAN | P60568)

molecular function
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0043208	glycosphingolipid binding	Interacting selectively and non-covalently with glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0005134	interleukin-2 receptor binding	Interacting selectively and non-covalently with the interleukin-2 receptor.
	GO:0031851	kappa-type opioid receptor binding	Interacting selectively and non-covalently with a kappa-type opioid receptor.
	GO:0019209	kinase activator activity	Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	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:0097192	extrinsic apoptotic signaling pathway in absence of ligand	A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0030101	natural killer cell activation	The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor.
	GO:0002903	negative regulation of B cell apoptotic process	Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell apoptotic process.
	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:0045822	negative regulation of heart contraction	Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	GO:0050672	negative regulation of lymphocyte proliferation	Any process that stops, prevents or reduces the rate or extent of lymphocyte proliferation.
	GO:0001933	negative regulation of protein phosphorylation	Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
	GO:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0045582	positive regulation of T cell differentiation	Any process that activates or increases the frequency, rate or extent of T cell differentiation.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
	GO:0042104	positive regulation of activated T cell proliferation	Any process that activates or increases the rate or extent of activated T cell proliferation.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
	GO:0060999	positive regulation of dendritic spine development	Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
	GO:0051024	positive regulation of immunoglobulin secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0032729	positive regulation of interferon-gamma production	Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032740	positive regulation of interleukin-17 production	Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
	GO:0048304	positive regulation of isotype switching to IgG isotypes	Any process that activates or increases the frequency, rate or extent of isotype switching to IgG isotypes.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0045591	positive regulation of regulatory T cell differentiation	Any process that activates or increases the frequency, rate or extent of differentiation of regulatory T cells.
	GO:0034105	positive regulation of tissue remodeling	Any process that activates or increases the frequency, rate, or extent of tissue remodeling.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0007205	protein kinase C-activating G-protein coupled receptor signaling pathway	The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of protein kinase C (PKC). PKC is activated by second messengers including diacylglycerol (DAG).
	GO:0046013	regulation of T cell homeostatic proliferation	Any process that modulates the frequency, rate or extent of resting T cell proliferation.
	GO:0045471	response to ethanol	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 ethanol stimulus.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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1m47	1M47 IS THE CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-2
1m48	1M48 IS THE CRYSTAL STRUCTURE OF HUMAN IL-2 COMPLEXED WITH (R)-N-[2-[1-(AMINOIMINOMETHYL)-3-PIPERIDINYL]-1-OXOETHYL]- 4-(PHENYLETHYNYL)-L-PHENYLALANINE METHYL ESTER
1m4a	1M4A IS THE CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-2 Y31C COVALENTLY MODIFIED AT C31 WITH (1H-INDOL-3-YL)-(2-MERCAPTO -ETHOXYIMINO)-ACETIC ACID
1m4b	1M4B IS THE CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-2 K43C COVALENTLY MODIFIED AT C43 WITH 2-[2-(2-CYCLOHEXYL-2- GUANIDINO-ACETYLAMINO)-ACETYLAMINO]-N-(3-MERCAPTO-PROPYL)- PROPIONAMIDE
1m4c	1M4C IS THE CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-2

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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Exons (4, 8)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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Gene Ontology (48, 48)

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