HEADER CYTOKINE 27-JAN-10 3LKJ TITLE SMALL MOLECULE INHIBITION OF THE TNF FAMILY CYOKINE CD40 LIGAND TITLE 2 THROUGH A SUBUNIT FRACTURE MECHANISM CAVEAT 3LKJ NAG C 2 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD40 LIGAND; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 121-261; COMPND 5 SYNONYM: CD40-L, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 5, COMPND 6 TNF-RELATED ACTIVATION PROTEIN, TRAP, T-CELL ANTIGEN GP39, CD40 COMPND 7 LIGAND, MEMBRANE FORM, CD40 LIGAND, SOLUBLE FORM; COMPND 8 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: CD40L, CD40LG, TNFSF5, TRAP; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_COMMON: YEAST; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS CD40L, CD154, TNF-FAMILY CYTOKINE, PROTEIN-PROTEIN INTERACTION, CELL KEYWDS 2 MEMBRANE, CYTOKINE, DISEASE MUTATION, DISULFIDE BOND, GLYCOPROTEIN, KEYWDS 3 MEMBRANE, PHOSPHOPROTEIN, SECRETED, SIGNAL-ANCHOR, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR L.F.SILVIAN,A.WHITTY REVDAT 5 20-NOV-24 3LKJ 1 REMARK REVDAT 4 06-SEP-23 3LKJ 1 HETSYN REVDAT 3 29-JUL-20 3LKJ 1 CAVEAT COMPND REMARK HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 13-JUL-11 3LKJ 1 JRNL REVDAT 1 02-FEB-11 3LKJ 0 JRNL AUTH L.F.SILVIAN,J.E.FRIEDMAN,K.STRAUCH,T.G.CACHERO,E.S.DAY, JRNL AUTH 2 F.QIAN,B.CUNNINGHAM,A.FUNG,L.SUN,L.SU,Z.ZHENG,G.KUMARAVEL, JRNL AUTH 3 A.WHITTY JRNL TITL SMALL MOLECULE INHIBITION OF THE TNF FAMILY CYTOKINE CD40 JRNL TITL 2 LIGAND THROUGH A SUBUNIT FRACTURE MECHANISM. JRNL REF ACS CHEM.BIOL. V. 6 636 2011 JRNL REFN ISSN 1554-8929 JRNL PMID 21417339 JRNL DOI 10.1021/CB2000346 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 15596 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 853 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1047 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3003 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 151 REMARK 3 SOLVENT ATOMS : 72 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.633 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.355 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.263 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.551 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3225 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4374 ; 1.972 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 385 ; 7.576 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;39.247 ;24.113 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;22.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;17.313 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 508 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2381 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1946 ; 0.985 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3118 ; 1.839 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1279 ; 2.215 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1256 ; 3.665 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3LKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.990 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16300 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ID 1ALY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG3350, 50MM HEPES PH 7.5, 0.2M REMARK 280 SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 31.65150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.26700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.80350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.26700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.65150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.80350 REMARK 290 SMTRY3 4 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: 6750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 SER A 179 REMARK 465 ASN A 180 REMARK 465 ARG A 181 REMARK 465 GLU A 182 REMARK 465 HIS A 212 REMARK 465 SER A 213 REMARK 465 SER A 214 REMARK 465 ALA A 215 REMARK 465 SER B 132 REMARK 465 LYS B 133 REMARK 465 THR B 134 REMARK 465 ARG B 181 REMARK 465 GLU B 182 REMARK 465 ALA B 183 REMARK 465 SER B 184 REMARK 465 SER B 185 REMARK 465 GLN B 186 REMARK 465 ARG C 181 REMARK 465 GLU C 182 REMARK 465 ALA C 183 REMARK 465 SER C 184 REMARK 465 SER C 185 REMARK 465 GLN C 186 REMARK 465 ALA C 187 REMARK 465 HIS C 212 REMARK 465 SER C 213 REMARK 465 SER C 214 REMARK 465 ALA C 215 REMARK 465 LYS C 216 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 LYS A 143 CG CD CE NZ REMARK 470 LYS B 216 CG CD CE NZ REMARK 470 LYS C 159 CG CD 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 O ALA B 130 O HOH B 26 1.99 REMARK 500 NE2 HIS B 224 O HOH B 81 2.02 REMARK 500 O4 NAG C 2 C1 NAG C 3 2.12 REMARK 500 ND2 ASN B 240 O5 NAG B 2 2.19 REMARK 500 O4 LKJ C 1 O HOH C 79 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 TYR A 145 79.40 -110.25 REMARK 500 THR A 251 123.96 -25.09 REMARK 500 ALA B 130 99.64 -43.66 REMARK 500 ASN B 151 4.53 -68.98 REMARK 500 SER B 179 17.93 -66.97 REMARK 500 LYS B 216 -136.16 -167.86 REMARK 500 SER C 132 -41.70 74.94 REMARK 500 LYS C 133 -156.84 -83.48 REMARK 500 GLU C 142 46.26 -77.80 REMARK 500 ASN C 151 -9.70 77.79 REMARK 500 LYS C 159 -31.59 -132.87 REMARK 500 SER C 179 -157.54 -84.50 REMARK 500 CYS C 218 47.17 -140.77 REMARK 500 PHE C 253 -61.76 -101.67 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 NAG A 3 REMARK 610 NAG B 3 REMARK 610 NAG C 3 DBREF 3LKJ A 121 261 UNP P29965 CD40L_HUMAN 121 261 DBREF 3LKJ B 121 261 UNP P29965 CD40L_HUMAN 121 261 DBREF 3LKJ C 121 261 UNP P29965 CD40L_HUMAN 121 261 SEQRES 1 A 141 GLN ILE ALA ALA HIS VAL ILE SER GLU ALA SER SER LYS SEQRES 2 A 141 THR THR SER VAL LEU GLN TRP ALA GLU LYS GLY TYR TYR SEQRES 3 A 141 THR MET SER ASN ASN LEU VAL THR LEU GLU ASN GLY LYS SEQRES 4 A 141 GLN LEU THR VAL LYS ARG GLN GLY LEU TYR TYR ILE TYR SEQRES 5 A 141 ALA GLN VAL THR PHE CYS SER ASN ARG GLU ALA SER SER SEQRES 6 A 141 GLN ALA PRO PHE ILE ALA SER LEU CYS LEU LYS SER PRO SEQRES 7 A 141 GLY ARG PHE GLU ARG ILE LEU LEU ARG ALA ALA ASN THR SEQRES 8 A 141 HIS SER SER ALA LYS PRO CYS GLY GLN GLN SER ILE HIS SEQRES 9 A 141 LEU GLY GLY VAL PHE GLU LEU GLN PRO GLY ALA SER VAL SEQRES 10 A 141 PHE VAL ASN VAL THR ASP PRO SER GLN VAL SER HIS GLY SEQRES 11 A 141 THR GLY PHE THR SER PHE GLY LEU LEU LYS LEU SEQRES 1 B 141 GLN ILE ALA ALA HIS VAL ILE SER GLU ALA SER SER LYS SEQRES 2 B 141 THR THR SER VAL LEU GLN TRP ALA GLU LYS GLY TYR TYR SEQRES 3 B 141 THR MET SER ASN ASN LEU VAL THR LEU GLU ASN GLY LYS SEQRES 4 B 141 GLN LEU THR VAL LYS ARG GLN GLY LEU TYR TYR ILE TYR SEQRES 5 B 141 ALA GLN VAL THR PHE CYS SER ASN ARG GLU ALA SER SER SEQRES 6 B 141 GLN ALA PRO PHE ILE ALA SER LEU CYS LEU LYS SER PRO SEQRES 7 B 141 GLY ARG PHE GLU ARG ILE LEU LEU ARG ALA ALA ASN THR SEQRES 8 B 141 HIS SER SER ALA LYS PRO CYS GLY GLN GLN SER ILE HIS SEQRES 9 B 141 LEU GLY GLY VAL PHE GLU LEU GLN PRO GLY ALA SER VAL SEQRES 10 B 141 PHE VAL ASN VAL THR ASP PRO SER GLN VAL SER HIS GLY SEQRES 11 B 141 THR GLY PHE THR SER PHE GLY LEU LEU LYS LEU SEQRES 1 C 141 GLN ILE ALA ALA HIS VAL ILE SER GLU ALA SER SER LYS SEQRES 2 C 141 THR THR SER VAL LEU GLN TRP ALA GLU LYS GLY TYR TYR SEQRES 3 C 141 THR MET SER ASN ASN LEU VAL THR LEU GLU ASN GLY LYS SEQRES 4 C 141 GLN LEU THR VAL LYS ARG GLN GLY LEU TYR TYR ILE TYR SEQRES 5 C 141 ALA GLN VAL THR PHE CYS SER ASN ARG GLU ALA SER SER SEQRES 6 C 141 GLN ALA PRO PHE ILE ALA SER LEU CYS LEU LYS SER PRO SEQRES 7 C 141 GLY ARG PHE GLU ARG ILE LEU LEU ARG ALA ALA ASN THR SEQRES 8 C 141 HIS SER SER ALA LYS PRO CYS GLY GLN GLN SER ILE HIS SEQRES 9 C 141 LEU GLY GLY VAL PHE GLU LEU GLN PRO GLY ALA SER VAL SEQRES 10 C 141 PHE VAL ASN VAL THR ASP PRO SER GLN VAL SER HIS GLY SEQRES 11 C 141 THR GLY PHE THR SER PHE GLY LEU LEU LYS LEU MODRES 3LKJ ASN B 240 ASN GLYCOSYLATION SITE MODRES 3LKJ ASN A 240 ASN GLYCOSYLATION SITE MODRES 3LKJ ASN C 240 ASN GLYCOSYLATION SITE HET NAG A 2 14 HET NAG A 3 14 HET NAG B 2 14 HET NAG B 3 14 HET LKJ C 1 67 HET NAG C 2 14 HET NAG C 3 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM LKJ (2R)-{[(2'-[(BIPHENYL-3-YLMETHYL)CARBAMOYL]-6'-{[(2R)- HETNAM 2 LKJ 2-(PYRROLIDIN-1-YLMETHYL)PYRROLIDIN-1-YL]CARBONYL}-6- HETNAM 3 LKJ {[(2R)-2-(1H-PYRROL-1-YLMETHYL)PYRROLIDIN-1- HETNAM 4 LKJ YL]CARBONYL}-4,4'-BIPYRIDIN-2-YL) HETNAM 5 LKJ CARBONYL]AMINO}(CYCLOHEXYL)ETHANOIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG 6(C8 H15 N O6) FORMUL 8 LKJ C53 H60 N8 O6 FORMUL 11 HOH *72(H2 O) HELIX 1 1 ASP A 243 VAL A 247 5 5 HELIX 2 2 ASP B 243 VAL B 247 5 5 HELIX 3 3 ASP C 243 VAL C 247 5 5 SHEET 1 A 3 GLN A 139 ALA A 141 0 SHEET 2 A 3 ALA A 123 GLU A 129 -1 N ILE A 127 O ALA A 141 SHEET 3 A 3 THR A 147 MET A 148 -1 O THR A 147 N HIS A 125 SHEET 1 B 5 GLN A 139 ALA A 141 0 SHEET 2 B 5 ALA A 123 GLU A 129 -1 N ILE A 127 O ALA A 141 SHEET 3 B 5 SER A 255 LYS A 260 -1 O PHE A 256 N VAL A 126 SHEET 4 B 5 GLY A 167 PHE A 177 -1 N TYR A 170 O LEU A 259 SHEET 5 B 5 GLN A 221 LEU A 231 -1 O GLY A 227 N ILE A 171 SHEET 1 C 5 VAL A 153 GLU A 156 0 SHEET 2 C 5 GLN A 160 VAL A 163 -1 O GLN A 160 N GLU A 156 SHEET 3 C 5 SER A 236 VAL A 241 -1 O VAL A 237 N LEU A 161 SHEET 4 C 5 PHE A 189 LYS A 196 -1 N CYS A 194 O PHE A 238 SHEET 5 C 5 ARG A 203 ASN A 210 -1 O LEU A 205 N LEU A 193 SHEET 1 D 3 TRP B 140 ALA B 141 0 SHEET 2 D 3 ALA B 123 SER B 128 -1 N ILE B 127 O ALA B 141 SHEET 3 D 3 THR B 147 MET B 148 -1 O THR B 147 N HIS B 125 SHEET 1 E 5 TRP B 140 ALA B 141 0 SHEET 2 E 5 ALA B 123 SER B 128 -1 N ILE B 127 O ALA B 141 SHEET 3 E 5 SER B 255 LYS B 260 -1 O PHE B 256 N VAL B 126 SHEET 4 E 5 GLY B 167 CYS B 178 -1 N GLN B 174 O SER B 255 SHEET 5 E 5 GLN B 220 LEU B 231 -1 O ILE B 223 N VAL B 175 SHEET 1 F 5 VAL B 153 GLU B 156 0 SHEET 2 F 5 GLN B 160 VAL B 163 -1 O GLN B 160 N GLU B 156 SHEET 3 F 5 SER B 236 VAL B 241 -1 O VAL B 237 N LEU B 161 SHEET 4 F 5 PHE B 189 LYS B 196 -1 N SER B 192 O ASN B 240 SHEET 5 F 5 ARG B 203 ASN B 210 -1 O LEU B 205 N LEU B 193 SHEET 1 G 5 GLN C 139 ALA C 141 0 SHEET 2 G 5 ALA C 123 GLU C 129 -1 N ILE C 127 O ALA C 141 SHEET 3 G 5 SER C 255 LYS C 260 -1 O PHE C 256 N VAL C 126 SHEET 4 G 5 GLY C 167 PHE C 177 -1 N TYR C 172 O GLY C 257 SHEET 5 G 5 GLN C 221 LEU C 231 -1 O LEU C 231 N GLY C 167 SHEET 1 H 5 VAL C 153 GLU C 156 0 SHEET 2 H 5 GLN C 160 VAL C 163 -1 O THR C 162 N THR C 154 SHEET 3 H 5 SER C 236 VAL C 241 -1 O VAL C 237 N LEU C 161 SHEET 4 H 5 PHE C 189 SER C 197 -1 N CYS C 194 O PHE C 238 SHEET 5 H 5 ARG C 200 ASN C 210 -1 O LEU C 205 N LEU C 193 SSBOND 1 CYS A 178 CYS A 218 1555 1555 2.05 SSBOND 2 CYS B 178 CYS B 218 1555 1555 2.07 LINK C1 NAG A 2 ND2 ASN A 240 1555 1555 1.43 LINK C1 NAG B 2 ND2 ASN B 240 1555 1555 1.43 LINK C1 NAG C 2 ND2 ASN C 240 1555 1555 1.45 CISPEP 1 LYS A 216 PRO A 217 0 1.00 CISPEP 2 PRO A 217 CYS A 218 0 -6.84 CISPEP 3 SER B 213 SER B 214 0 -5.54 CISPEP 4 SER B 214 ALA B 215 0 -8.79 CRYST1 63.303 67.607 108.534 90.00 90.00 90.00 P 21 21 21 12 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 0.015797 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014791 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009214 0.00000 CONECT 456 696 CONECT 696 456 CONECT 857 3007 CONECT 1451 1702 CONECT 1702 1451 CONECT 1863 3035 CONECT 2850 3130 CONECT 3007 857 3008 3018 CONECT 3008 3007 3009 3015 CONECT 3009 3008 3010 3016 CONECT 3010 3009 3011 3017 CONECT 3011 3010 3012 3018 CONECT 3012 3011 3019 CONECT 3013 3014 3015 3020 CONECT 3014 3013 CONECT 3015 3008 3013 CONECT 3016 3009 CONECT 3017 3010 CONECT 3018 3007 3011 CONECT 3019 3012 CONECT 3020 3013 CONECT 3021 3022 3032 CONECT 3022 3021 3023 3029 CONECT 3023 3022 3024 3030 CONECT 3024 3023 3025 3031 CONECT 3025 3024 3026 3032 CONECT 3026 3025 3033 CONECT 3027 3028 3029 3034 CONECT 3028 3027 CONECT 3029 3022 3027 CONECT 3030 3023 CONECT 3031 3024 CONECT 3032 3021 3025 CONECT 3033 3026 CONECT 3034 3027 CONECT 3035 1863 3036 3046 CONECT 3036 3035 3037 3043 CONECT 3037 3036 3038 3044 CONECT 3038 3037 3039 3045 CONECT 3039 3038 3040 3046 CONECT 3040 3039 3047 CONECT 3041 3042 3043 3048 CONECT 3042 3041 CONECT 3043 3036 3041 CONECT 3044 3037 CONECT 3045 3038 CONECT 3046 3035 3039 CONECT 3047 3040 CONECT 3048 3041 CONECT 3049 3050 3060 CONECT 3050 3049 3051 3057 CONECT 3051 3050 3052 3058 CONECT 3052 3051 3053 3059 CONECT 3053 3052 3054 3060 CONECT 3054 3053 3061 CONECT 3055 3056 3057 3062 CONECT 3056 3055 CONECT 3057 3050 3055 CONECT 3058 3051 CONECT 3059 3052 CONECT 3060 3049 3053 CONECT 3061 3054 CONECT 3062 3055 CONECT 3063 3064 3065 3087 CONECT 3064 3063 3066 3075 CONECT 3065 3063 CONECT 3066 3064 3069 3078 CONECT 3067 3078 3081 3086 CONECT 3068 3093 CONECT 3069 3066 3072 CONECT 3070 3093 3094 CONECT 3071 3108 CONECT 3072 3069 3075 CONECT 3073 3092 3107 CONECT 3074 3129 CONECT 3075 3064 3072 CONECT 3076 3108 3109 3112 CONECT 3077 3129 CONECT 3078 3066 3067 CONECT 3079 3113 3114 3117 CONECT 3080 3121 CONECT 3081 3067 3083 CONECT 3082 3121 3122 CONECT 3083 3081 3085 CONECT 3084 3087 3120 CONECT 3085 3083 3086 CONECT 3086 3067 3085 CONECT 3087 3063 3084 3088 CONECT 3088 3087 3089 CONECT 3089 3088 3090 3119 CONECT 3090 3089 3091 3118 CONECT 3091 3090 3092 CONECT 3092 3073 3091 3093 CONECT 3093 3068 3070 3092 CONECT 3094 3070 3095 CONECT 3095 3094 3096 3106 CONECT 3096 3095 3097 CONECT 3097 3096 3098 CONECT 3098 3097 3099 CONECT 3099 3098 3100 3106 CONECT 3100 3099 3101 3105 CONECT 3101 3100 3102 CONECT 3102 3101 3103 CONECT 3103 3102 3104 CONECT 3104 3103 3105 CONECT 3105 3100 3104 CONECT 3106 3095 3099 CONECT 3107 3073 3108 3118 CONECT 3108 3071 3076 3107 CONECT 3109 3076 3110 3113 CONECT 3110 3109 3111 CONECT 3111 3110 3112 CONECT 3112 3076 3111 CONECT 3113 3079 3109 CONECT 3114 3079 3115 CONECT 3115 3114 3116 CONECT 3116 3115 3117 CONECT 3117 3079 3116 CONECT 3118 3090 3107 CONECT 3119 3089 3120 CONECT 3120 3084 3119 3121 CONECT 3121 3080 3082 3120 CONECT 3122 3082 3123 3129 CONECT 3123 3122 3124 3128 CONECT 3124 3123 3125 CONECT 3125 3124 3126 CONECT 3126 3125 3127 CONECT 3127 3126 3128 CONECT 3128 3123 3127 CONECT 3129 3074 3077 3122 CONECT 3130 2850 3131 3141 CONECT 3131 3130 3132 3138 CONECT 3132 3131 3133 3139 CONECT 3133 3132 3134 3140 CONECT 3134 3133 3135 3141 CONECT 3135 3134 3142 CONECT 3136 3137 3138 3143 CONECT 3137 3136 CONECT 3138 3131 3136 CONECT 3139 3132 CONECT 3140 3133 CONECT 3141 3130 3134 CONECT 3142 3135 CONECT 3143 3136 CONECT 3144 3145 3155 CONECT 3145 3144 3146 3152 CONECT 3146 3145 3147 3153 CONECT 3147 3146 3148 3154 CONECT 3148 3147 3149 3155 CONECT 3149 3148 3156 CONECT 3150 3151 3152 3157 CONECT 3151 3150 CONECT 3152 3145 3150 CONECT 3153 3146 CONECT 3154 3147 CONECT 3155 3144 3148 CONECT 3156 3149 CONECT 3157 3150 MASTER 338 0 7 3 36 0 0 6 3226 3 158 33 END