HEADER CYTOKINE 24-JUN-09 2KKI TITLE SOLUTION STRUCTURE OF HUMAN INTERLEUKIN 1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 121-271; COMPND 5 SYNONYM: IL-1 ALPHA, HEMATOPOIETIN-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IL1A, IL1F1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET(20B)+ KEYWDS PROTEIN, CYTOKINE, GLYCOPROTEIN, INFLAMMATORY RESPONSE, LIPOPROTEIN, KEYWDS 2 MITOGEN, MYRISTATE, POLYMORPHISM, PYROGEN, SECRETED EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR S.K.MOHAN,H.-K.CHANG,C.YU REVDAT 2 16-MAR-22 2KKI 1 REMARK REVDAT 1 30-JUN-10 2KKI 0 JRNL AUTH H.-K.CHANG,S.K.MOHAN,Y.CHIN JRNL TITL 1H, 13C AND 15N BACKBONE AND SIDE CHAIN RESONANCE JRNL TITL 2 ASSIGNMENTS OF HUMAN INTERLEUKIN 1ALPHA JRNL REF BIOMOL.NMR ASSIGN. V. 4 59 2010 JRNL REFN ISSN 1874-2718 JRNL PMID 20108067 JRNL DOI 10.1007/S12104-010-9207-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.1, CNS REMARK 3 AUTHORS : DR. MICHAEL NILGES, INSTITUT PASTEUR (ARIA), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101233. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM TRIS, 100MM SODIUM REMARK 210 CHLORIDE, 1.4MM PROTEIN, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HNCO; 3D HN(CO)CA; REMARK 210 3D CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY; 3D C(CO) REMARK 210 NH; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 1.1, SPARKY, TALOS, VNMRJ REMARK 210 VNMRJ_2.2C REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HB VAL A 81 HZ PHE A 111 1.11 REMARK 500 HZ2 LYS A 93 HB2 LEU A 109 1.18 REMARK 500 HB2 SER A 31 HB2 ALA A 51 1.28 REMARK 500 HG22 ILE A 71 HD23 LEU A 109 1.31 REMARK 500 HG22 ILE A 102 HB2 GLU A 106 1.33 REMARK 500 HD13 LEU A 45 HA LEU A 48 1.34 REMARK 500 HG2 GLU A 86 H ASP A 87 1.34 REMARK 500 OD2 ASP A 55 HE ARG A 73 1.55 REMARK 500 OD1 ASP A 65 HZ3 LYS A 67 1.58 REMARK 500 OD1 ASP A 26 H GLN A 30 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 59 CE1 TYR A 59 CZ 0.095 REMARK 500 2 TYR A 59 CZ TYR A 59 CE2 -0.085 REMARK 500 11 TYR A 80 CE1 TYR A 80 CZ 0.108 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3 PRO A 147 C - N - CA ANGL. DEV. = 10.6 DEGREES REMARK 500 6 PRO A 147 C - N - CA ANGL. DEV. = 11.5 DEGREES REMARK 500 7 PRO A 147 C - N - CA ANGL. DEV. = 11.1 DEGREES REMARK 500 8 PRO A 147 C - N - CA ANGL. DEV. = 11.3 DEGREES REMARK 500 10 PRO A 147 C - N - CA ANGL. DEV. = 11.2 DEGREES REMARK 500 11 PRO A 147 C - N - CA ANGL. DEV. = 11.4 DEGREES REMARK 500 14 PRO A 147 C - N - CA ANGL. DEV. = 11.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 MET A 15 -63.09 -94.90 REMARK 500 1 ILE A 18 -132.57 -89.03 REMARK 500 1 ASN A 29 74.83 56.29 REMARK 500 1 HIS A 46 -18.51 -140.43 REMARK 500 1 LEU A 48 -66.12 67.12 REMARK 500 1 GLU A 50 -28.11 -142.02 REMARK 500 1 SER A 62 43.30 -91.22 REMARK 500 1 ASP A 64 -129.31 -78.80 REMARK 500 1 ASP A 65 -80.82 -129.66 REMARK 500 1 GLN A 78 69.96 -100.90 REMARK 500 1 GLN A 84 -118.63 -90.00 REMARK 500 1 GLU A 86 -135.32 50.47 REMARK 500 1 GLU A 97 146.77 68.53 REMARK 500 1 LEU A 109 35.12 -91.65 REMARK 500 1 CYS A 141 -159.59 -104.86 REMARK 500 1 THR A 150 37.32 -89.11 REMARK 500 2 MET A 15 -64.77 -95.57 REMARK 500 2 ILE A 18 -131.85 -88.38 REMARK 500 2 ASN A 29 73.51 62.08 REMARK 500 2 HIS A 46 -17.19 -140.37 REMARK 500 2 LEU A 48 -66.95 67.33 REMARK 500 2 GLU A 50 -32.03 -143.43 REMARK 500 2 SER A 62 42.01 -92.79 REMARK 500 2 ASP A 64 -123.07 -77.65 REMARK 500 2 ASP A 65 -82.58 -124.68 REMARK 500 2 GLN A 78 69.56 -100.47 REMARK 500 2 GLN A 84 -116.73 -92.98 REMARK 500 2 GLU A 86 -139.40 53.53 REMARK 500 2 GLU A 97 143.95 62.65 REMARK 500 2 LEU A 109 37.44 -91.27 REMARK 500 2 CYS A 141 -159.46 -104.58 REMARK 500 2 THR A 150 37.36 -88.76 REMARK 500 3 MET A 15 -69.09 -103.78 REMARK 500 3 ILE A 18 -131.38 -89.71 REMARK 500 3 ASN A 29 72.48 53.70 REMARK 500 3 LEU A 48 -68.41 65.86 REMARK 500 3 GLU A 50 -25.29 -148.40 REMARK 500 3 SER A 62 42.55 -89.69 REMARK 500 3 ASP A 64 -128.09 -77.72 REMARK 500 3 ASP A 65 -83.80 -129.63 REMARK 500 3 GLN A 78 68.79 -100.85 REMARK 500 3 GLN A 84 -112.92 -93.55 REMARK 500 3 GLU A 86 -131.41 50.09 REMARK 500 3 GLU A 97 141.73 68.54 REMARK 500 3 LEU A 109 38.04 -91.71 REMARK 500 3 CYS A 141 -158.28 -97.04 REMARK 500 3 PRO A 146 146.89 -13.22 REMARK 500 3 PRO A 147 10.23 -3.65 REMARK 500 3 THR A 150 36.81 -89.50 REMARK 500 4 MET A 15 -62.00 -94.79 REMARK 500 REMARK 500 THIS ENTRY HAS 228 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 146 PRO A 147 1 136.37 REMARK 500 PRO A 146 PRO A 147 2 138.00 REMARK 500 PRO A 146 PRO A 147 4 127.33 REMARK 500 PRO A 146 PRO A 147 5 133.04 REMARK 500 PRO A 146 PRO A 147 9 132.37 REMARK 500 PRO A 146 PRO A 147 12 135.02 REMARK 500 PRO A 146 PRO A 147 13 135.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 TYR A 59 0.07 SIDE CHAIN REMARK 500 2 PHE A 112 0.07 SIDE CHAIN REMARK 500 4 TYR A 121 0.07 SIDE CHAIN REMARK 500 5 TYR A 80 0.09 SIDE CHAIN REMARK 500 7 TYR A 59 0.12 SIDE CHAIN REMARK 500 8 TYR A 59 0.07 SIDE CHAIN REMARK 500 9 TYR A 59 0.07 SIDE CHAIN REMARK 500 9 PHE A 111 0.07 SIDE CHAIN REMARK 500 9 PHE A 131 0.12 SIDE CHAIN REMARK 500 10 PHE A 112 0.06 SIDE CHAIN REMARK 500 11 TYR A 80 0.10 SIDE CHAIN REMARK 500 14 TYR A 59 0.07 SIDE CHAIN REMARK 500 14 TYR A 80 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16379 RELATED DB: BMRB DBREF 2KKI A 9 159 UNP P01583 IL1A_HUMAN 121 271 SEQRES 1 A 151 ASN VAL LYS TYR ASN PHE MET ARG ILE ILE LYS TYR GLU SEQRES 2 A 151 PHE ILE LEU ASN ASP ALA LEU ASN GLN SER ILE ILE ARG SEQRES 3 A 151 ALA ASN ASP GLN TYR LEU THR ALA ALA ALA LEU HIS ASN SEQRES 4 A 151 LEU ASP GLU ALA VAL LYS PHE ASP MET GLY ALA TYR LYS SEQRES 5 A 151 SER SER LYS ASP ASP ALA LYS ILE THR VAL ILE LEU ARG SEQRES 6 A 151 ILE SER LYS THR GLN LEU TYR VAL THR ALA GLN ASP GLU SEQRES 7 A 151 ASP GLN PRO VAL LEU LEU LYS GLU MET PRO GLU ILE PRO SEQRES 8 A 151 LYS THR ILE THR GLY SER GLU THR ASN LEU LEU PHE PHE SEQRES 9 A 151 TRP GLU THR HIS GLY THR LYS ASN TYR PHE THR SER VAL SEQRES 10 A 151 ALA HIS PRO ASN LEU PHE ILE ALA THR LYS GLN ASP TYR SEQRES 11 A 151 TRP VAL CYS LEU ALA GLY GLY PRO PRO SER ILE THR ASP SEQRES 12 A 151 PHE GLN ILE LEU GLU ASN GLN ALA HELIX 1 1 THR A 103 LEU A 110 5 8 SHEET 1 A 7 ASN A 13 ASN A 25 0 SHEET 2 A 7 LYS A 53 LYS A 60 -1 O MET A 56 N LYS A 19 SHEET 3 A 7 THR A 69 ILE A 74 -1 O THR A 69 N TYR A 59 SHEET 4 A 7 PHE A 111 HIS A 116 -1 O PHE A 111 N VAL A 70 SHEET 5 A 7 LYS A 119 THR A 123 -1 O THR A 123 N PHE A 112 SHEET 6 A 7 PHE A 152 LEU A 155 -1 O PHE A 152 N ASN A 120 SHEET 7 A 7 ASN A 13 ASN A 25 -1 N ILE A 23 O LEU A 155 SHEET 1 B 2 SER A 31 ARG A 34 0 SHEET 2 B 2 LEU A 40 ALA A 43 -1 O ALA A 43 N SER A 31 SHEET 1 C 2 TYR A 80 THR A 82 0 SHEET 2 C 2 LEU A 91 LYS A 93 -1 O LYS A 93 N TYR A 80 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1