HEADER IMMUNE SYSTEM/DNA 21-DEC-16 5UC6 TITLE STRUCTURAL INSIGHTS INTO IL-1 ALPHA RECOGNITION BY A NAPHTHYL-MODIFIED TITLE 2 APTAMER THAT MIMICS IL-1RI DOMAIN III COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 113-271; COMPND 5 SYNONYM: IL-1 ALPHA,HEMATOPOIETIN-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))- COMPND 9 D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)- COMPND 10 R(P*(85Y))-D(P*CP*GP*(ATD))-3'); COMPND 11 CHAIN: B; COMPND 12 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: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS SOMAMER, IMMUNE SYSTEM-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.REN,A.PYLE REVDAT 6 04-OCT-23 5UC6 1 LINK REVDAT 5 20-NOV-19 5UC6 1 REMARK REVDAT 4 22-AUG-18 5UC6 1 LINK ATOM REVDAT 3 15-NOV-17 5UC6 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK ATOM REVDAT 2 18-OCT-17 5UC6 1 JRNL REVDAT 1 11-OCT-17 5UC6 0 JRNL AUTH X.REN,A.D.GELINAS,I.VON CARLOWITZ,N.JANJIC,A.M.PYLE JRNL TITL STRUCTURAL BASIS FOR IL-1 ALPHA RECOGNITION BY A MODIFIED JRNL TITL 2 DNA APTAMER THAT SPECIFICALLY INHIBITS IL-1 ALPHA SIGNALING. JRNL REF NAT COMMUN V. 8 810 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28993621 JRNL DOI 10.1038/S41467-017-00864-2 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 16627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 787 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 64.8006 - 3.8158 0.97 2732 118 0.1497 0.2009 REMARK 3 2 3.8158 - 3.0287 0.99 2658 123 0.1648 0.1853 REMARK 3 3 3.0287 - 2.6458 0.99 2601 164 0.2106 0.2314 REMARK 3 4 2.6458 - 2.4039 1.00 2598 132 0.2170 0.2707 REMARK 3 5 2.4039 - 2.2316 1.00 2625 120 0.2278 0.2762 REMARK 3 6 2.2316 - 2.1000 1.00 2626 130 0.2144 0.2648 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1863 REMARK 3 ANGLE : 1.344 2581 REMARK 3 CHIRALITY : 0.097 279 REMARK 3 PLANARITY : 0.006 244 REMARK 3 DIHEDRAL : 20.686 966 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5UC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16642 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 64.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2ILA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 0.1 M NA ACETATE, AND 22% REMARK 280 POLYETHYLENE GLYCOL 8,000, EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.78667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.57333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.57333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.78667 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 375 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 PHE A 4 REMARK 465 SER A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 SER A 8 REMARK 465 ATD B 23 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 360 O HOH A 385 2.02 REMARK 500 O HOH B 226 O HOH B 248 2.03 REMARK 500 O HOH A 328 O HOH B 218 2.03 REMARK 500 OD1 ASP A 49 O HOH A 301 2.07 REMARK 500 O HOH B 236 O HOH B 247 2.09 REMARK 500 O HOH A 348 O HOH A 377 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 346 O HOH B 243 3884 2.18 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 DA B 5 O3' DA B 5 C3' -0.041 REMARK 500 DG B 17 O3' DG B 17 C3' -0.038 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 DG B 2 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 85Y B 3 O3' - P - O5' ANGL. DEV. = -21.5 DEGREES REMARK 500 85Y B 3 O3' - P - OP1 ANGL. DEV. = 6.8 DEGREES REMARK 500 85Y B 3 C3' - O3' - P ANGL. DEV. = -8.2 DEGREES REMARK 500 DG B 4 O3' - P - OP2 ANGL. DEV. = 12.6 DEGREES REMARK 500 85Y B 7 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 85Y B 7 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 DA B 9 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 85Y B 10 O3' - P - OP2 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 13 C3' - O3' - P ANGL. DEV. = 19.6 DEGREES REMARK 500 85Y B 15 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES REMARK 500 DA B 16 O3' - P - OP2 ANGL. DEV. = 6.9 DEGREES REMARK 500 85Y B 20 O3' - P - O5' ANGL. DEV. = 17.9 DEGREES REMARK 500 85Y B 20 O3' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 85Y B 20 O3' - P - OP1 ANGL. DEV. = -26.9 DEGREES REMARK 500 DC B 21 O3' - P - O5' ANGL. DEV. = 46.9 DEGREES REMARK 500 DC B 21 O3' - P - OP1 ANGL. DEV. = -34.3 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 MET A 15 -75.37 -96.55 REMARK 500 ASN A 36 -126.60 -132.46 REMARK 500 GLN A 84 -131.05 -109.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 64 OD1 REMARK 620 2 ASP A 65 O 106.0 REMARK 620 3 HOH A 333 O 80.9 79.1 REMARK 620 4 85Y B 7 O21 91.8 86.9 161.6 REMARK 620 5 HOH B 222 O 160.5 93.1 99.0 93.5 REMARK 620 6 HOH B 245 O 89.3 163.3 97.0 99.8 71.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 90 O REMARK 620 2 VAL A 140 O 103.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 108 O REMARK 620 2 LEU A 110 O 106.0 REMARK 620 3 SER A 124 OG 138.0 113.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 132 O REMARK 620 2 THR A 150 O 92.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 101 DBREF 5UC6 A 1 159 UNP P01583 IL1A_HUMAN 113 271 DBREF 5UC6 B 1 23 PDB 5UC6 5UC6 1 23 SEQRES 1 A 159 SER ALA PRO PHE SER PHE LEU SER ASN VAL LYS TYR ASN SEQRES 2 A 159 PHE MET ARG ILE ILE LYS TYR GLU PHE ILE LEU ASN ASP SEQRES 3 A 159 ALA LEU ASN GLN SER ILE ILE ARG ALA ASN ASP GLN TYR SEQRES 4 A 159 LEU THR ALA ALA ALA LEU HIS ASN LEU ASP GLU ALA VAL SEQRES 5 A 159 LYS PHE ASP MET GLY ALA TYR LYS SER SER LYS ASP ASP SEQRES 6 A 159 ALA LYS ILE THR VAL ILE LEU ARG ILE SER LYS THR GLN SEQRES 7 A 159 LEU TYR VAL THR ALA GLN ASP GLU ASP GLN PRO VAL LEU SEQRES 8 A 159 LEU LYS GLU MET PRO GLU ILE PRO LYS THR ILE THR GLY SEQRES 9 A 159 SER GLU THR ASN LEU LEU PHE PHE TRP GLU THR HIS GLY SEQRES 10 A 159 THR LYS ASN TYR PHE THR SER VAL ALA HIS PRO ASN LEU SEQRES 11 A 159 PHE ILE ALA THR LYS GLN ASP TYR TRP VAL CYS LEU ALA SEQRES 12 A 159 GLY GLY PRO PRO SER ILE THR ASP PHE GLN ILE LEU GLU SEQRES 13 A 159 ASN GLN ALA SEQRES 1 B 23 DC DG 85Y DG DA DG 85Y 85Y DA 85Y DG DG DG SEQRES 2 B 23 85Y 85Y DA DG DA DG 85Y DC DG ATD HET 85Y B 3 33 HET 85Y B 7 33 HET 85Y B 8 33 HET 85Y B 10 33 HET 85Y B 14 33 HET 85Y B 15 33 HET 85Y B 20 33 HET MG A 201 1 HET NA A 202 1 HET MG A 203 1 HET MG A 204 1 HET MG A 205 1 HET PO4 B 101 4 HETNAM 85Y 2'-DEOXY-5-{[(NAPHTHALEN-2-YL)METHYL]CARBAMOYL}URIDINE HETNAM 2 85Y 5'-(DIHYDROGEN PHOSPHATE) HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 2 85Y 7(C21 H22 N3 O9 P) FORMUL 3 MG 4(MG 2+) FORMUL 4 NA NA 1+ FORMUL 8 PO4 O4 P 3- FORMUL 9 HOH *145(H2 O) HELIX 1 AA1 ASN A 47 ALA A 51 5 5 HELIX 2 AA2 SER A 105 LEU A 109 5 5 SHEET 1 AA1 8 THR A 101 THR A 103 0 SHEET 2 AA1 8 LYS A 11 ASP A 26 -1 N TYR A 12 O ILE A 102 SHEET 3 AA1 8 PHE A 152 LEU A 155 -1 O GLN A 153 N ASN A 25 SHEET 4 AA1 8 LYS A 119 SER A 124 -1 N ASN A 120 O PHE A 152 SHEET 5 AA1 8 PHE A 111 HIS A 116 -1 N PHE A 112 O THR A 123 SHEET 6 AA1 8 THR A 69 ILE A 74 -1 N VAL A 70 O PHE A 111 SHEET 7 AA1 8 PHE A 54 SER A 61 -1 N ASP A 55 O ARG A 73 SHEET 8 AA1 8 LYS A 11 ASP A 26 -1 N MET A 15 O ALA A 58 SHEET 1 AA2 2 SER A 31 ARG A 34 0 SHEET 2 AA2 2 LEU A 40 ALA A 43 -1 O ALA A 43 N SER A 31 SHEET 1 AA3 2 LEU A 79 THR A 82 0 SHEET 2 AA3 2 LEU A 91 GLU A 94 -1 O LYS A 93 N TYR A 80 SHEET 1 AA4 2 PHE A 131 ALA A 133 0 SHEET 2 AA4 2 CYS A 141 ALA A 143 -1 O ALA A 143 N PHE A 131 LINK O3' DG B 2 P 85Y B 3 1555 1555 1.56 LINK O3' 85Y B 3 P DG B 4 1555 1555 1.56 LINK O3' DG B 6 P 85Y B 7 1555 1555 1.56 LINK O3' 85Y B 7 P 85Y B 8 1555 1555 1.56 LINK O3' 85Y B 8 P DA B 9 1555 1555 1.56 LINK O3' DA B 9 P 85Y B 10 1555 1555 1.56 LINK O3' 85Y B 10 P DG B 11 1555 1555 1.56 LINK O3' DG B 13 P 85Y B 14 1555 1555 1.56 LINK O3' 85Y B 14 P 85Y B 15 1555 1555 1.56 LINK O3' 85Y B 15 P DA B 16 1555 1555 1.56 LINK O3' DG B 19 P 85Y B 20 1555 1555 1.56 LINK O3' 85Y B 20 P DC B 21 1555 1555 1.56 LINK O3' DG B 22 P PO4 B 101 1555 1555 1.56 LINK O LYS A 11 MG MG A 201 1555 1555 2.86 LINK OD1 ASP A 64 NA NA A 202 1555 1555 2.40 LINK O ASP A 65 NA NA A 202 1555 1555 2.34 LINK O VAL A 90 MG MG A 204 1555 1555 2.80 LINK O ASN A 108 MG MG A 205 1555 1555 2.89 LINK O LEU A 110 MG MG A 205 1555 1555 2.78 LINK OG SER A 124 MG MG A 205 1555 1555 2.62 LINK O ILE A 132 MG MG A 203 1555 1555 2.96 LINK O VAL A 140 MG MG A 204 1555 1555 2.94 LINK O THR A 150 MG MG A 203 1555 1555 2.55 LINK NA NA A 202 O HOH A 333 1555 1555 2.42 LINK NA NA A 202 O21 85Y B 7 1555 1555 2.53 LINK NA NA A 202 O HOH B 222 1555 1555 2.20 LINK NA NA A 202 O HOH B 245 1555 1555 2.63 CISPEP 1 PRO A 146 PRO A 147 0 3.92 SITE 1 AC1 5 LYS A 11 ASN A 13 LYS A 60 SER A 61 SITE 2 AC1 5 SER A 62 SITE 1 AC2 6 ASP A 64 ASP A 65 HOH A 333 85Y B 7 SITE 2 AC2 6 HOH B 222 HOH B 245 SITE 1 AC3 5 TYR A 121 PHE A 122 ILE A 132 THR A 150 SITE 2 AC3 5 PHE A 152 SITE 1 AC4 6 TYR A 39 LEU A 40 PRO A 89 VAL A 90 SITE 2 AC4 6 TRP A 139 VAL A 140 SITE 1 AC5 6 ALA A 83 THR A 107 ASN A 108 LEU A 110 SITE 2 AC5 6 SER A 124 VAL A 125 SITE 1 AC6 2 DG B 22 HOH B 229 CRYST1 74.790 74.790 86.360 90.00 90.00 120.00 P 31 2 1 6 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 0.013371 0.007720 0.000000 0.00000 SCALE2 0.000000 0.015439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011579 0.00000