HEADER IMMUNE SYSTEM 12-JAN-14 4OE8 OBSLTE 01-FEB-17 4OE8 5MJ3 TITLE INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-12 SUBUNIT BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-12B, CYTOTOXIC LYMPHOCYTE MATURATION FACTOR 40 KDA COMPND 5 SUBUNIT, CLMF P40, IL-12 SUBUNIT P40, NK CELL STIMULATORY FACTOR COMPND 6 CHAIN 2, NKSF2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: INTERLEUKIN-23 SUBUNIT ALPHA; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: IL-23 SUBUNIT ALPHA, IL-23-A, INTERLEUKIN-23 SUBUNIT P19, COMPND 12 IL-23P19; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: ALPHABODY MA12; COMPND 16 CHAIN: C; COMPND 17 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: IL12B, NKSF2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PHLSEC; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: IL23A, SGRF, UNQ2498/PRO5798; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PHLSEC; SOURCE 23 MOL_ID: 3; SOURCE 24 ORGANISM_SCIENTIFIC: IN-SILICO; SOURCE 25 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 27 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 28 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 29 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS DESIGNED ANTIPARALLEL TRIPLE-HELIX COILED-COIL, ALPHABODY, KEYWDS 2 IMMUNOGLOBULIN DOMAIN, 4-HELICAL BUNDLE CYTOKINE, ANTAGONIST, N- KEYWDS 3 LINKED GLYCOSYLATION, ALKYLATION, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.DESMET,K.VERSTRAETE,Y.BLOCH,E.LORENT,Y.WEN,B.DEVREESE, AUTHOR 2 K.VANDENBROUCKE,S.LOVERIX,T.HETTMANN,S.DEROO,K.SOMERS,P.HENDRIKX, AUTHOR 3 I.LASTERS,S.N.SAVVIDES REVDAT 4 01-FEB-17 4OE8 1 OBSLTE REVDAT 3 27-JAN-16 4OE8 1 COMPND TITLE REVDAT 2 12-NOV-14 4OE8 1 JRNL REVDAT 1 05-NOV-14 4OE8 0 JRNL AUTH J.DESMET,K.VERSTRAETE,Y.BLOCH,E.LORENT,Y.WEN,B.DEVREESE, JRNL AUTH 2 K.VANDENBROUCKE,S.LOVERIX,T.HETTMANN,S.DEROO,K.SOMERS, JRNL AUTH 3 P.HENDERIKX,I.LASTERS,S.N.SAVVIDES JRNL TITL STRUCTURAL BASIS OF IL-23 ANTAGONISM BY AN ALPHABODY PROTEIN JRNL TITL 2 SCAFFOLD. JRNL REF NAT COMMUN V. 5 5237 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 25354530 JRNL DOI 10.1038/NCOMMS6237 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.3_1479) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 63099 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3155 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 40.6217 - 4.9540 0.99 2761 145 0.1723 0.1967 REMARK 3 2 4.9540 - 3.9332 0.99 2694 142 0.1457 0.1769 REMARK 3 3 3.9332 - 3.4363 0.99 2660 140 0.1564 0.2145 REMARK 3 4 3.4363 - 3.1223 0.99 2672 140 0.1789 0.2209 REMARK 3 5 3.1223 - 2.8985 0.99 2649 140 0.1855 0.2298 REMARK 3 6 2.8985 - 2.7277 0.99 2632 138 0.1802 0.2181 REMARK 3 7 2.7277 - 2.5911 0.99 2626 138 0.1853 0.2402 REMARK 3 8 2.5911 - 2.4783 0.99 2634 139 0.1741 0.2322 REMARK 3 9 2.4783 - 2.3829 0.99 2630 139 0.1699 0.2136 REMARK 3 10 2.3829 - 2.3007 0.99 2635 138 0.1641 0.2160 REMARK 3 11 2.3007 - 2.2288 0.98 2588 137 0.1696 0.2234 REMARK 3 12 2.2288 - 2.1651 0.99 2622 138 0.1731 0.1836 REMARK 3 13 2.1651 - 2.1081 0.99 2612 137 0.1738 0.2199 REMARK 3 14 2.1081 - 2.0567 0.98 2611 137 0.1850 0.2168 REMARK 3 15 2.0567 - 2.0099 0.98 2591 137 0.1790 0.1943 REMARK 3 16 2.0099 - 1.9671 0.99 2593 136 0.1855 0.2171 REMARK 3 17 1.9671 - 1.9278 0.98 2620 138 0.1874 0.2259 REMARK 3 18 1.9278 - 1.8914 0.99 2591 136 0.2022 0.2365 REMARK 3 19 1.8914 - 1.8576 0.97 2590 137 0.2232 0.2584 REMARK 3 20 1.8576 - 1.8261 0.99 2562 135 0.2408 0.3055 REMARK 3 21 1.8261 - 1.7967 0.97 2619 138 0.2504 0.3078 REMARK 3 22 1.7967 - 1.7690 0.98 2596 136 0.2715 0.3187 REMARK 3 23 1.7690 - 1.7430 0.82 2156 114 0.2745 0.3519 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.740 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 4516 REMARK 3 ANGLE : 1.051 6161 REMARK 3 CHIRALITY : 0.042 713 REMARK 3 PLANARITY : 0.005 775 REMARK 3 DIHEDRAL : 12.614 1686 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 4OE8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-FEB-14. REMARK 100 THE RCSB ID CODE IS RCSB084381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000020 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.75% PEG 3350, 200MM SODIUM REMARK 280 SULPHATE, PH 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.37000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 MET A 1 REMARK 465 CYS A 2 REMARK 465 HIS A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 LEU A 6 REMARK 465 VAL A 7 REMARK 465 ILE A 8 REMARK 465 SER A 9 REMARK 465 TRP A 10 REMARK 465 PHE A 11 REMARK 465 SER A 12 REMARK 465 LEU A 13 REMARK 465 VAL A 14 REMARK 465 PHE A 15 REMARK 465 LEU A 16 REMARK 465 ALA A 17 REMARK 465 SER A 18 REMARK 465 PRO A 19 REMARK 465 LEU A 20 REMARK 465 VAL A 21 REMARK 465 ALA A 22 REMARK 465 LYS A 280 REMARK 465 SER A 281 REMARK 465 LYS A 282 REMARK 465 ARG A 283 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 ARG B 5 REMARK 465 ALA B 6 REMARK 465 VAL B 7 REMARK 465 MET B 8 REMARK 465 LEU B 9 REMARK 465 LEU B 10 REMARK 465 LEU B 11 REMARK 465 LEU B 12 REMARK 465 LEU B 13 REMARK 465 PRO B 14 REMARK 465 TRP B 15 REMARK 465 THR B 16 REMARK 465 ALA B 17 REMARK 465 GLN B 18 REMARK 465 GLY B 19 REMARK 465 ARG B 20 REMARK 465 ALA B 21 REMARK 465 VAL B 22 REMARK 465 PRO B 23 REMARK 465 GLY B 24 REMARK 465 GLY B 25 REMARK 465 SER B 26 REMARK 465 SER B 27 REMARK 465 TRP B 142 REMARK 465 GLU B 143 REMARK 465 THR B 144 REMARK 465 GLN B 145 REMARK 465 GLN B 146 REMARK 465 ILE B 147 REMARK 465 PRO B 148 REMARK 465 SER B 149 REMARK 465 GLY B 190 REMARK 465 THR B 191 REMARK 465 LYS B 192 REMARK 465 HIS B 193 REMARK 465 HIS B 194 REMARK 465 HIS B 195 REMARK 465 HIS B 196 REMARK 465 HIS B 197 REMARK 465 HIS B 198 REMARK 465 HIS C 1 REMARK 465 THR C 29 REMARK 465 GLY C 30 REMARK 465 GLY C 31 REMARK 465 SER C 32 REMARK 465 GLY C 33 REMARK 465 GLY C 34 REMARK 465 SER C 35 REMARK 465 GLY C 36 REMARK 465 GLY C 37 REMARK 465 GLY C 38 REMARK 465 GLY C 39 REMARK 465 SER C 40 REMARK 465 GLY C 41 REMARK 465 GLY C 42 REMARK 465 SER C 43 REMARK 465 GLY C 44 REMARK 465 GLY C 45 REMARK 465 THR C 73 REMARK 465 GLY C 74 REMARK 465 SER C 75 REMARK 465 GLY C 76 REMARK 465 GLY C 77 REMARK 465 GLY C 78 REMARK 465 GLY C 79 REMARK 465 SER C 80 REMARK 465 GLY C 81 REMARK 465 GLY C 82 REMARK 465 SER C 83 REMARK 465 GLY C 84 REMARK 465 GLY C 85 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 130 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 157 CE NZ REMARK 470 ASP A 183 CG OD1 OD2 REMARK 470 ASN A 184 CG OD1 ND2 REMARK 470 LYS A 185 NZ REMARK 470 GLU A 253 CG CD OE1 OE2 REMARK 470 GLN A 278 CG CD OE1 NE2 REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 ASP A 287 CG OD1 OD2 REMARK 470 LYS A 293 NZ REMARK 470 GLN B 35 CD OE1 NE2 REMARK 470 LYS B 39 CD CE NZ REMARK 470 GLU B 59 CG CD OE1 OE2 REMARK 470 ASP B 61 CG OD1 OD2 REMARK 470 GLN B 80 CD OE1 NE2 REMARK 470 ARG B 83 CD NE CZ NH1 NH2 REMARK 470 GLN B 87 CD OE1 NE2 REMARK 470 GLU B 101 CD OE1 OE2 REMARK 470 LYS B 102 CG CD CE NZ REMARK 470 LEU B 150 CG CD1 CD2 REMARK 470 SER B 188 OG REMARK 470 GLN C 5 CD OE1 NE2 REMARK 470 LYS C 9 CE NZ REMARK 470 LYS C 23 CE NZ REMARK 470 MET C 46 SD CE REMARK 470 GLU C 49 CG CD OE1 OE2 REMARK 470 GLU C 50 CG CD OE1 OE2 REMARK 470 GLN C 52 CG CD OE1 NE2 REMARK 470 LYS C 53 CE NZ REMARK 470 GLU C 93 CG CD OE1 OE2 REMARK 470 LYS C 97 CE NZ 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 OE1 GLN C 13 O HOH C 233 2.05 REMARK 500 O HOH A 742 O HOH A 745 2.13 REMARK 500 O HOH A 755 O HOH B 302 2.13 REMARK 500 O HOH A 665 O HOH A 727 2.17 REMARK 500 OE1 GLU A 257 O HOH A 727 2.19 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 GLU A 55 -33.23 -149.79 REMARK 500 ASP A 63 -128.44 54.85 REMARK 500 LYS A 80 -5.90 -143.22 REMARK 500 ASN A 135 -174.68 -170.75 REMARK 500 ASP A 183 18.73 58.42 REMARK 500 LYS A 217 -110.46 58.74 REMARK 500 ASN A 303 -9.79 66.47 REMARK 500 SER A 317 -160.21 -108.27 REMARK 500 ALA B 29 61.53 61.43 REMARK 500 THR B 65 9.38 -68.55 REMARK 500 ASN B 85 101.53 -166.99 REMARK 500 SER B 151 104.39 74.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 406 REMARK 610 PG4 A 408 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 410 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 249 O REMARK 620 2 LEU A 246 O 78.3 REMARK 620 3 HOH A 599 O 80.7 97.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 409 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 114 O REMARK 620 2 LEU A 117 O 95.0 REMARK 620 3 HOH A 617 O 103.9 98.9 REMARK 620 4 HOH A 653 O 77.3 132.2 128.9 REMARK 620 5 HOH A 748 O 163.6 95.5 86.9 86.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A REMARK 800 222 RESIDUES 401 TO 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OG9 RELATED DB: PDB DBREF 4OE8 A 1 328 UNP P29460 IL12B_HUMAN 1 328 DBREF 4OE8 B 1 189 UNP Q9NPF7 IL23A_HUMAN 1 189 DBREF 4OE8 C 1 118 PDB 4OE8 4OE8 1 118 SEQADV 4OE8 GLY B 190 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 THR B 191 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 LYS B 192 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 HIS B 193 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 HIS B 194 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 HIS B 195 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 HIS B 196 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 HIS B 197 UNP Q9NPF7 EXPRESSION TAG SEQADV 4OE8 HIS B 198 UNP Q9NPF7 EXPRESSION TAG SEQRES 1 A 328 MET CYS HIS GLN GLN LEU VAL ILE SER TRP PHE SER LEU SEQRES 2 A 328 VAL PHE LEU ALA SER PRO LEU VAL ALA ILE TRP GLU LEU SEQRES 3 A 328 LYS LYS ASP VAL TYR VAL VAL GLU LEU ASP TRP TYR PRO SEQRES 4 A 328 ASP ALA PRO GLY GLU MET VAL VAL LEU THR CYS ASP THR SEQRES 5 A 328 PRO GLU GLU ASP GLY ILE THR TRP THR LEU ASP GLN SER SEQRES 6 A 328 SER GLU VAL LEU GLY SER GLY LYS THR LEU THR ILE GLN SEQRES 7 A 328 VAL LYS GLU PHE GLY ASP ALA GLY GLN TYR THR CYS HIS SEQRES 8 A 328 LYS GLY GLY GLU VAL LEU SER HIS SER LEU LEU LEU LEU SEQRES 9 A 328 HIS LYS LYS GLU ASP GLY ILE TRP SER THR ASP ILE LEU SEQRES 10 A 328 LYS ASP GLN LYS GLU PRO LYS ASN LYS THR PHE LEU ARG SEQRES 11 A 328 CYS GLU ALA LYS ASN TYR SER GLY ARG PHE THR CYS TRP SEQRES 12 A 328 TRP LEU THR THR ILE SER THR ASP LEU THR PHE SER VAL SEQRES 13 A 328 LYS SER SER ARG GLY SER SER ASP PRO GLN GLY VAL THR SEQRES 14 A 328 CYS GLY ALA ALA THR LEU SER ALA GLU ARG VAL ARG GLY SEQRES 15 A 328 ASP ASN LYS GLU TYR GLU TYR SER VAL GLU CYS GLN GLU SEQRES 16 A 328 ASP SER ALA CYS PRO ALA ALA GLU GLU SER LEU PRO ILE SEQRES 17 A 328 GLU VAL MET VAL ASP ALA VAL HIS LYS LEU LYS TYR GLU SEQRES 18 A 328 ASN TYR THR SER SER PHE PHE ILE ARG ASP ILE ILE LYS SEQRES 19 A 328 PRO ASP PRO PRO LYS ASN LEU GLN LEU LYS PRO LEU LYS SEQRES 20 A 328 ASN SER ARG GLN VAL GLU VAL SER TRP GLU TYR PRO ASP SEQRES 21 A 328 THR TRP SER THR PRO HIS SER TYR PHE SER LEU THR PHE SEQRES 22 A 328 CYS VAL GLN VAL GLN GLY LYS SER LYS ARG GLU LYS LYS SEQRES 23 A 328 ASP ARG VAL PHE THR ASP LYS THR SER ALA THR VAL ILE SEQRES 24 A 328 CYS ARG LYS ASN ALA SER ILE SER VAL ARG ALA GLN ASP SEQRES 25 A 328 ARG TYR TYR SER SER SER TRP SER GLU TRP ALA SER VAL SEQRES 26 A 328 PRO CYS SER SEQRES 1 B 198 MET LEU GLY SER ARG ALA VAL MET LEU LEU LEU LEU LEU SEQRES 2 B 198 PRO TRP THR ALA GLN GLY ARG ALA VAL PRO GLY GLY SER SEQRES 3 B 198 SER PRO ALA TRP THR GLN CYS GLN GLN LEU SER GLN LYS SEQRES 4 B 198 LEU CYS THR LEU ALA TRP SER ALA HIS PRO LEU VAL GLY SEQRES 5 B 198 HIS MET ASP LEU ARG GLU GLU GLY ASP GLU GLU THR THR SEQRES 6 B 198 ASN ASP VAL PRO HIS ILE GLN CYS GLY ASP GLY CYS ASP SEQRES 7 B 198 PRO GLN GLY LEU ARG ASP ASN SER GLN PHE CYS LEU GLN SEQRES 8 B 198 ARG ILE HIS GLN GLY LEU ILE PHE TYR GLU LYS LEU LEU SEQRES 9 B 198 GLY SER ASP ILE PHE THR GLY GLU PRO SER LEU LEU PRO SEQRES 10 B 198 ASP SER PRO VAL GLY GLN LEU HIS ALA SER LEU LEU GLY SEQRES 11 B 198 LEU SER GLN LEU LEU GLN PRO GLU GLY HIS HIS TRP GLU SEQRES 12 B 198 THR GLN GLN ILE PRO SER LEU SER PRO SER GLN PRO TRP SEQRES 13 B 198 GLN ARG LEU LEU LEU ARG PHE LYS ILE LEU ARG SER LEU SEQRES 14 B 198 GLN ALA PHE VAL ALA VAL ALA ALA ARG VAL PHE ALA HIS SEQRES 15 B 198 GLY ALA ALA THR LEU SER PRO GLY THR LYS HIS HIS HIS SEQRES 16 B 198 HIS HIS HIS SEQRES 1 C 118 HIS MET SER ILE GLN GLU ILE GLN LYS GLU ILE ALA GLN SEQRES 2 C 118 ILE GLN ALA VAL ILE ALA GLY ILE GLN LYS TYR ILE TYR SEQRES 3 C 118 THR MET THR GLY GLY SER GLY GLY SER GLY GLY GLY GLY SEQRES 4 C 118 SER GLY GLY SER GLY GLY MET SER ILE GLU GLU ILE GLN SEQRES 5 C 118 LYS GLN ILE ALA ALA ILE GLN YCM GLN ILE ALA ALA ILE SEQRES 6 C 118 GLN LYS GLN ILE TYR ALA MET THR GLY SER GLY GLY GLY SEQRES 7 C 118 GLY SER GLY GLY SER GLY GLY GLY GLY SER GLY MET SER SEQRES 8 C 118 ILE GLU GLU ILE GLN LYS GLN ILE ALA ALA ILE GLN GLU SEQRES 9 C 118 GLN ILE LEU ALA ILE TYR LYS GLN ILE MET ALA MET VAL SEQRES 10 C 118 THR MODRES 4OE8 ASN A 222 ASN GLYCOSYLATION SITE MODRES 4OE8 YCM C 60 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HET YCM C 60 10 HET NAG A 401 14 HET NAG A 402 14 HET BMA A 403 11 HET MAN A 404 11 HET MAN A 405 11 HET PG4 A 406 11 HET PG4 A 407 13 HET PG4 A 408 11 HET NA A 409 1 HET NA A 410 1 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM BMA BETA-D-MANNOSE HETNAM MAN ALPHA-D-MANNOSE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM NA SODIUM ION HETSYN YCM CYSTEINE-S-ACETAMIDE FORMUL 3 YCM C5 H10 N2 O3 S FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 4 MAN 2(C6 H12 O6) FORMUL 5 PG4 3(C8 H18 O5) FORMUL 8 NA 2(NA 1+) FORMUL 10 HOH *410(H2 O) HELIX 1 1 GLU A 81 ALA A 85 5 5 HELIX 2 2 PHE A 228 ILE A 233 1 6 HELIX 3 3 ALA B 29 ALA B 47 1 19 HELIX 4 4 GLY B 60 THR B 64 5 5 HELIX 5 5 ASP B 78 SER B 86 1 9 HELIX 6 6 SER B 86 GLY B 105 1 20 HELIX 7 7 SER B 106 GLY B 111 1 6 HELIX 8 8 SER B 119 GLN B 136 1 18 HELIX 9 9 GLN B 154 LEU B 187 1 34 HELIX 10 10 SER C 3 MET C 28 1 26 HELIX 11 11 SER C 47 TYR C 70 1 24 HELIX 12 12 SER C 91 THR C 118 1 28 SHEET 1 A 6 TRP A 24 LYS A 27 0 SHEET 2 A 6 VAL A 30 ASP A 36 -1 O VAL A 32 N TRP A 24 SHEET 3 A 6 GLU A 95 GLU A 108 1 O LEU A 101 N TYR A 31 SHEET 4 A 6 GLY A 86 LYS A 92 -1 N TYR A 88 O SER A 100 SHEET 5 A 6 THR A 59 LEU A 62 -1 N THR A 61 O THR A 89 SHEET 6 A 6 GLY A 70 SER A 71 -1 O GLY A 70 N TRP A 60 SHEET 1 B 4 TRP A 24 LYS A 27 0 SHEET 2 B 4 VAL A 30 ASP A 36 -1 O VAL A 32 N TRP A 24 SHEET 3 B 4 GLU A 95 GLU A 108 1 O LEU A 101 N TYR A 31 SHEET 4 B 4 ILE A 111 TRP A 112 -1 O ILE A 111 N GLU A 108 SHEET 1 C 2 GLU A 44 THR A 49 0 SHEET 2 C 2 THR A 74 VAL A 79 -1 O LEU A 75 N LEU A 48 SHEET 1 D 4 ARG A 130 GLU A 132 0 SHEET 2 D 4 ARG A 139 THR A 146 -1 O TRP A 143 N ARG A 130 SHEET 3 D 4 LYS A 185 GLU A 195 -1 O TYR A 187 N THR A 146 SHEET 4 D 4 THR A 174 VAL A 180 -1 N ARG A 179 O GLU A 186 SHEET 1 E 7 ARG A 130 GLU A 132 0 SHEET 2 E 7 ARG A 139 THR A 146 -1 O TRP A 143 N ARG A 130 SHEET 3 E 7 LYS A 185 GLU A 195 -1 O TYR A 187 N THR A 146 SHEET 4 E 7 GLN A 166 CYS A 170 -1 N THR A 169 O GLN A 194 SHEET 5 E 7 LEU A 152 ARG A 160 -1 N ARG A 160 O GLN A 166 SHEET 6 E 7 ILE A 208 HIS A 216 -1 O MET A 211 N LYS A 157 SHEET 7 E 7 LYS A 219 PHE A 227 -1 O PHE A 227 N ILE A 208 SHEET 1 F 3 LYS A 239 PRO A 245 0 SHEET 2 F 3 GLN A 251 GLU A 257 -1 O GLU A 257 N LYS A 239 SHEET 3 F 3 SER A 295 ILE A 299 -1 O ALA A 296 N VAL A 254 SHEET 1 G 4 ASP A 287 THR A 291 0 SHEET 2 G 4 LEU A 271 GLN A 278 -1 N VAL A 275 O VAL A 289 SHEET 3 G 4 SER A 305 ASP A 312 -1 O SER A 307 N GLN A 276 SHEET 4 G 4 ALA A 323 PRO A 326 -1 O VAL A 325 N ILE A 306 SSBOND 1 CYS A 50 CYS A 90 1555 1555 2.04 SSBOND 2 CYS A 131 CYS A 142 1555 1555 2.07 SSBOND 3 CYS A 170 CYS A 193 1555 1555 2.02 SSBOND 4 CYS A 199 CYS B 73 1555 1555 2.05 SSBOND 5 CYS A 300 CYS A 327 1555 1555 2.04 SSBOND 6 CYS B 77 CYS B 89 1555 1555 2.03 LINK C GLN C 59 N YCM C 60 1555 1555 1.33 LINK C YCM C 60 N GLN C 61 1555 1555 1.33 LINK ND2 ASN A 222 C1 NAG A 401 1555 1555 1.43 LINK O4 NAG A 402 C1 BMA A 403 1555 1555 1.44 LINK O4 NAG A 401 C1 NAG A 402 1555 1555 1.44 LINK O6 BMA A 403 C1 MAN A 405 1555 1555 1.44 LINK O3 BMA A 403 C1 MAN A 404 1555 1555 1.44 LINK O SER A 249 NA NA A 410 1555 1555 2.16 LINK O THR A 114 NA NA A 409 1555 1555 2.21 LINK O LEU A 117 NA NA A 409 1555 1555 2.32 LINK O LEU A 246 NA NA A 410 1555 1555 2.61 LINK NA NA A 409 O HOH A 617 1555 1555 2.31 LINK NA NA A 410 O HOH A 599 1555 1555 2.45 LINK NA NA A 409 O HOH A 653 1555 1555 2.50 LINK NA NA A 409 O HOH A 748 1555 1555 2.58 CISPEP 1 GLU A 122 PRO A 123 0 5.92 CISPEP 2 THR A 264 PRO A 265 0 0.02 CISPEP 3 GLU B 59 GLY B 60 0 1.13 CISPEP 4 GLU B 112 PRO B 113 0 -4.87 SITE 1 AC1 3 ASP A 36 LYS A 107 GLY A 110 SITE 1 AC2 5 LYS A 27 SER A 155 HOH A 716 SER B 153 SITE 2 AC2 5 GLN B 154 SITE 1 AC3 6 THR A 169 GLY A 171 GLU A 192 GLN A 194 SITE 2 AC3 6 HOH A 512 HOH B 273 SITE 1 AC4 5 THR A 114 LEU A 117 HOH A 617 HOH A 653 SITE 2 AC4 5 HOH A 748 SITE 1 AC5 4 LEU A 246 SER A 249 HOH A 599 HOH B 228 SITE 1 AC6 8 TRP A 24 GLU A 34 HIS A 105 TRP A 112 SITE 2 AC6 8 TYR A 220 ASN A 222 HOH A 601 HOH A 717 CRYST1 56.960 56.740 100.070 90.00 99.73 90.00 P 1 21 1 2 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 0.017556 0.000000 0.003012 0.00000 SCALE2 0.000000 0.017624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010139 0.00000