1F42

THE P40 DOMAIN OF HUMAN INTERLEUKIN-12

> Summary

Summary for 1F42

Related1F45
DescriptorINTERLEUKIN-12 BETA CHAIN
Functional Keywordscytokine
Biological sourceHomo sapiens (human)
Total number of polymer chains2
Total molecular weight35725.12
Authors
Yoon, C.,Johnston, S.C.,Tang, J.,Tobin, J.F.,Somers, W.S. (deposition date: 2000-06-07, release date: 2001-06-13, modification date: 2011-07-13)
Primary citation
Yoon, C.,Johnston, S.C.,Tang, J.,Stahl, M.,Tobin, J.F.,Somers, W.S.
Charged residues dominate a unique interlocking topography in the heterodimeric cytokine interleukin-12.
EMBO J., 19:3530-3541, 2000
PubMed: 10899108
DOI: 10.1093/emboj/19.14.3530
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.5 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers31.0%5.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1f42
no rotation
Molmil generated image of 1f42
rotated about x axis by 90°
Molmil generated image of 1f42
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AINTERLEUKIN-12 BETA CHAINpolymer30634740.21
UniProt (P29460)
Pfam (PF10420)
Homo sapiens (human)@PDBj
SUGAR (3-MER)polymer586.51
5-MERCAPTO-2-NITRO-BENZOIC ACIDnon-polymer199.22
waterwater18.055

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight35326.8
Non-Polymers*Number of molecules2
Total molecular weight398.4
All*Total molecular weight35725.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.5 Å)
Cell axes34.00055.000189.200
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits15.00 - 2.50
the highest resolution shell value -
R-factor0.281 (0.227*)
R-work0.22700
R-free0.28100
RMSD bond length0.017
RMSD bond angle1.880

Data Collection Statistics

Resolution limits15.00 - 2.50
the highest resolution shell value - 2.50*
Number of reflections90266 (12537*)
Number of measurements90266*
Rmerge_l_obs0.054
the highest resolution shell value0.160
Completeness97.0
the highest resolution shell value79.*
Redundancy7.2
the highest resolution shell value3
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5 (8.0*)298 (18*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein4 (mg/ml)
21dropTris10 (mM)
31reservoirPEG800018 (%)
41reservoircalcium acetate0.2 (M)
51reservoirsodium cacodylate0.1 (M)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005615cellular_componentextracellular space
A0043514cellular_componentinterleukin-12 complex
A0070743cellular_componentinterleukin-23 complex
A0016020cellular_componentmembrane
A0004896molecular_functioncytokine receptor activity
A0042802molecular_functionidentical protein binding
A0042164molecular_functioninterleukin-12 alpha subunit binding
A0005143molecular_functioninterleukin-12 receptor binding
A0046982molecular_functionprotein heterodimerization activity
A0007050biological_processcell cycle arrest
A0016477biological_processcell migration
A0071346biological_processcellular response to interferon-gamma
A0071222biological_processcellular response to lipopolysaccharide
A0050829biological_processdefense response to Gram-negative bacterium
A0042832biological_processdefense response to protozoan
A0051607biological_processdefense response to virus
A0042095biological_processinterferon-gamma biosynthetic process
A0030101biological_processnatural killer cell activation
A0002323biological_processnatural killer cell activation involved in immune response
A0044130biological_processnegative regulation of growth of symbiont in host
A0002862biological_processnegative regulation of inflammatory response to antigenic stimulus
A0032693biological_processnegative regulation of interleukin-10 production
A0032700biological_processnegative regulation of interleukin-17 production
A0048662biological_processnegative regulation of smooth muscle cell proliferation
A0042104biological_processpositive regulation of activated T cell proliferation
A0010535biological_processpositive regulation of activation of JAK2 kinase activity
A0045785biological_processpositive regulation of cell adhesion
A0002230biological_processpositive regulation of defense response to virus by host
A0032725biological_processpositive regulation of granulocyte macrophage colony-stimulating factor production
A0050729biological_processpositive regulation of inflammatory response
A0045078biological_processpositive regulation of interferon-gamma biosynthetic process
A0032729biological_processpositive regulation of interferon-gamma production
A0032733biological_processpositive regulation of interleukin-10 production
A0032735biological_processpositive regulation of interleukin-12 production
A0032740biological_processpositive regulation of interleukin-17 production
A0050671biological_processpositive regulation of lymphocyte proliferation
A0043382biological_processpositive regulation of memory T cell differentiation
A0032946biological_processpositive regulation of mononuclear cell proliferation
A0032816biological_processpositive regulation of natural killer cell activation
A0002860biological_processpositive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
A0032819biological_processpositive regulation of natural killer cell proliferation
A0042346biological_processpositive regulation of NF-kappaB import into nucleus
A0051135biological_processpositive regulation of NK T cell activation
A0051142biological_processpositive regulation of NK T cell proliferation
A0045672biological_processpositive regulation of osteoclast differentiation
A0034393biological_processpositive regulation of smooth muscle cell apoptotic process
A0001916biological_processpositive regulation of T cell mediated cytotoxicity
A0042102biological_processpositive regulation of T cell proliferation
A0002827biological_processpositive regulation of T-helper 1 type immune response
A2000330biological_processpositive regulation of T-helper 17 cell lineage commitment
A2000318biological_processpositive regulation of T-helper 17 type immune response
A0034105biological_processpositive regulation of tissue remodeling
A0032760biological_processpositive regulation of tumor necrosis factor production
A0042517biological_processpositive regulation of tyrosine phosphorylation of Stat3 protein
A0042520biological_processpositive regulation of tyrosine phosphorylation of Stat4 protein
A0042523biological_processpositive regulation of tyrosine phosphorylation of Stat5 protein
A0042035biological_processregulation of cytokine biosynthetic process
A0042510biological_processregulation of tyrosine phosphorylation of Stat1 protein
A0010224biological_processresponse to UV-B
A0019233biological_processsensory perception of pain
A0019953biological_processsexual reproduction
A0042088biological_processT-helper 1 type immune response
A0042093biological_processT-helper cell differentiation
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC17BINDING SITE FOR RESIDUE NAG A 501
ChainResidue
ATRP2
AGLU12
AHIS83
AASP191
ATYR198
AASN200
ANAG

AC24BINDING SITE FOR RESIDUE NAG A 502
ChainResidue
ATRP2
AGLU12
ANAG
AMAN

AC32BINDING SITE FOR RESIDUE MAN A 503
ChainResidue
ATRP2
ANAG

AC46BINDING SITE FOR RESIDUE MNB A 504
ChainResidue
ACYS177
APRO223
AVAL230
ACYS305
AHOH
AHOH

AC56BINDING SITE FOR RESIDUE MNB A 505
ChainResidue
ACYS252
AGLN254
AARG266
AARG287
ATRP297
ATRP300

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
MAN_1f42_A_5032ALPHA-D-MANNOSE binding site
ChainResidueligand
AILE1-TRP2MAN: ALPHA-D-MANNOSE

NAG_1f42_A_5023N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ATRP2NAG: N-ACETYL-D-GLUCOSAMINE
AGLU12NAG: N-ACETYL-D-GLUCOSAMINE
ATRP90NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1f42_A_50110N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ATRP2NAG: N-ACETYL-D-GLUCOSAMINE
ALEU4NAG: N-ACETYL-D-GLUCOSAMINE
AVAL10NAG: N-ACETYL-D-GLUCOSAMINE
AGLU12NAG: N-ACETYL-D-GLUCOSAMINE
AHIS83NAG: N-ACETYL-D-GLUCOSAMINE
ATRP90NAG: N-ACETYL-D-GLUCOSAMINE
AMET189NAG: N-ACETYL-D-GLUCOSAMINE
AASP191NAG: N-ACETYL-D-GLUCOSAMINE
ATYR198NAG: N-ACETYL-D-GLUCOSAMINE
AASN200NAG: N-ACETYL-D-GLUCOSAMINE

MNB_1f42_A_50445-MERCAPTO-2-NITRO-BENZOIC ACID binding site
ChainResidueligand
ASER175-PRO178MNB: 5-MERCAPTO-2-NITRO-BENZOIC ACID

MNB_1f42_A_50585-MERCAPTO-2-NITRO-BENZOIC ACID binding site
ChainResidueligand
ACYS252-GLN254MNB: 5-MERCAPTO-2-NITRO-BENZOIC ACID
AARG266MNB: 5-MERCAPTO-2-NITRO-BENZOIC ACID
APHE268MNB: 5-MERCAPTO-2-NITRO-BENZOIC ACID
AARG287MNB: 5-MERCAPTO-2-NITRO-BENZOIC ACID
ATRP297MNB: 5-MERCAPTO-2-NITRO-BENZOIC ACID
ATRP300MNB: 5-MERCAPTO-2-NITRO-BENZOIC ACID

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS013541Long hematopoietin receptor, soluble alpha chains family signature. [LIV]-x-P-D-P(2)-x(2)-[LIV]-x(8,11)-[LVAM]-x(3)-W-x(2)-P-x-[ST]-W-x(4,6)
ChainResidueDetails
ANA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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