HEADER SIGNALING PROTEIN 25-SEP-18 6MKB TITLE CRYSTAL STRUCTURE OF MURINE 4-1BB LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 139-309; COMPND 5 SYNONYM: 4-1BB LIGAND,4-1BBL; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TNFSF9, CD137L, CD157L, LY63L; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PACGP67A KEYWDS TNF, SIGNALING PROTEIN, DIMER EXPDTA X-RAY DIFFRACTION AUTHOR A.BITRA,D.M.ZAJONC,T.DOUKOV REVDAT 5 11-OCT-23 6MKB 1 HETSYN REVDAT 4 29-JUL-20 6MKB 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 20-FEB-19 6MKB 1 JRNL REVDAT 2 26-DEC-18 6MKB 1 JRNL REVDAT 1 19-DEC-18 6MKB 0 JRNL AUTH A.BITRA,T.DOUKOV,G.DESTITO,M.CROFT,D.M.ZAJONC JRNL TITL CRYSTAL STRUCTURE OF THE M4-1BB/4-1BBL COMPLEX REVEALS AN JRNL TITL 2 UNUSUAL DIMERIC LIGAND THAT UNDERGOES STRUCTURAL CHANGES JRNL TITL 3 UPON 4-1BB RECEPTOR BINDING. JRNL REF J. BIOL. CHEM. V. 294 1831 2019 JRNL REFN ESSN 1083-351X JRNL PMID 30545939 JRNL DOI 10.1074/JBC.RA118.006297 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 27146 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1306 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.26 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 543 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2012 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 535 REMARK 3 BIN R VALUE (WORKING SET) : 0.2018 REMARK 3 BIN FREE R VALUE : 0.1646 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.47 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 8 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5158 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 245 REMARK 3 SOLVENT ATOMS : 286 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52190 REMARK 3 B22 (A**2) : -0.52190 REMARK 3 B33 (A**2) : 1.04390 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.300 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.517 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.270 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.552 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.277 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5603 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7659 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2529 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 908 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5603 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 6 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 730 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5936 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.18 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.82 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 3.04 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 74.0581 -20.6013 28.6850 REMARK 3 T TENSOR REMARK 3 T11: -0.2110 T22: 0.0183 REMARK 3 T33: -0.0626 T12: 0.0956 REMARK 3 T13: 0.0458 T23: -0.1535 REMARK 3 L TENSOR REMARK 3 L11: 2.0679 L22: 1.9936 REMARK 3 L33: 3.8985 L12: 0.1699 REMARK 3 L13: -0.2697 L23: -1.2422 REMARK 3 S TENSOR REMARK 3 S11: 0.2056 S12: -0.1106 S13: 0.1755 REMARK 3 S21: 0.1860 S22: -0.1189 S23: 0.3019 REMARK 3 S31: -0.4876 S32: -0.2493 S33: -0.0866 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 68.8443 -35.9393 12.0938 REMARK 3 T TENSOR REMARK 3 T11: -0.1844 T22: 0.0025 REMARK 3 T33: -0.0591 T12: 0.0120 REMARK 3 T13: 0.0127 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 1.5868 L22: 1.7722 REMARK 3 L33: 2.8882 L12: 1.0238 REMARK 3 L13: -0.9341 L23: -0.9326 REMARK 3 S TENSOR REMARK 3 S11: -0.0689 S12: 0.0128 S13: -0.1047 REMARK 3 S21: -0.2340 S22: 0.0969 S23: -0.1533 REMARK 3 S31: 0.1503 S32: -0.2490 S33: -0.0280 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 35.4610 -10.9877 -1.1610 REMARK 3 T TENSOR REMARK 3 T11: -0.0335 T22: -0.1569 REMARK 3 T33: -0.0533 T12: -0.0725 REMARK 3 T13: -0.0020 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 2.5005 L22: 0.7430 REMARK 3 L33: 2.4376 L12: 0.8579 REMARK 3 L13: -0.7625 L23: -0.5505 REMARK 3 S TENSOR REMARK 3 S11: -0.0318 S12: -0.2409 S13: -0.1621 REMARK 3 S21: -0.0162 S22: 0.0834 S23: 0.0019 REMARK 3 S31: -0.1282 S32: 0.2690 S33: -0.0516 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): 19.4840 -7.6745 -17.6005 REMARK 3 T TENSOR REMARK 3 T11: 0.0471 T22: -0.2420 REMARK 3 T33: -0.0677 T12: -0.0476 REMARK 3 T13: -0.1108 T23: 0.1103 REMARK 3 L TENSOR REMARK 3 L11: 2.2811 L22: 1.8679 REMARK 3 L33: 3.8431 L12: -0.0893 REMARK 3 L13: -1.2664 L23: 0.4990 REMARK 3 S TENSOR REMARK 3 S11: -0.0026 S12: 0.2883 S13: 0.3554 REMARK 3 S21: 0.0080 S22: 0.0897 S23: -0.0158 REMARK 3 S31: -0.4879 S32: -0.2587 S33: -0.0871 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MKB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000237095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-17 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27191 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.79100 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: 6D3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULFATE, 0.1M MES PH REMARK 280 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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 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 39.41200 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 78.82400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 350 REMARK 350 BIOMOLECULE: 2 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: 4820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, G, H 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 ASN A 139 REMARK 465 THR A 140 REMARK 465 THR A 141 REMARK 465 GLN A 142 REMARK 465 GLN A 143 REMARK 465 GLY A 144 REMARK 465 SER A 247 REMARK 465 MET A 248 REMARK 465 GLU A 249 REMARK 465 TRP A 308 REMARK 465 GLU A 309 REMARK 465 ASN B 139 REMARK 465 THR B 140 REMARK 465 THR B 141 REMARK 465 GLN B 142 REMARK 465 GLN B 143 REMARK 465 GLY B 144 REMARK 465 ASN C 139 REMARK 465 THR C 140 REMARK 465 THR C 141 REMARK 465 GLN C 142 REMARK 465 GLN C 143 REMARK 465 GLY C 144 REMARK 465 ASN D 139 REMARK 465 THR D 140 REMARK 465 THR D 141 REMARK 465 GLN D 142 REMARK 465 GLN D 143 REMARK 465 GLY D 144 REMARK 465 ASP D 233 REMARK 465 MET D 248 REMARK 465 GLU D 249 REMARK 465 TRP D 308 REMARK 465 GLU D 309 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 ASP A 235 CG OD1 OD2 REMARK 470 ASP B 235 CG OD1 OD2 REMARK 470 ASP C 235 CG OD1 OD2 REMARK 470 ASP D 235 CG OD1 OD2 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 ASP A 233 -73.00 -113.29 REMARK 500 ASN A 236 66.03 -117.40 REMARK 500 ASP A 282 62.52 -118.61 REMARK 500 ASP B 170 -159.12 -72.95 REMARK 500 ASP B 232 -29.36 -38.60 REMARK 500 ASP C 232 -85.32 3.72 REMARK 500 ASP C 282 61.34 -115.76 REMARK 500 ASP D 282 61.26 -118.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 558 DISTANCE = 8.47 ANGSTROMS REMARK 525 HOH B 588 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH B 589 DISTANCE = 7.25 ANGSTROMS 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 SO4 C 403 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 164 O REMARK 620 2 LYS A 188 O 114.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 205 O REMARK 620 2 SER A 207 OG 113.6 REMARK 620 3 ASN A 293 O 96.9 109.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 408 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 205 O REMARK 620 2 SER B 207 OG 113.6 REMARK 620 3 ASN B 293 O 94.0 117.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS C 205 O REMARK 620 2 SER C 207 OG 113.7 REMARK 620 3 ASN C 293 O 96.5 112.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN C 293 O REMARK 620 2 THR C 295 OG1 98.7 REMARK 620 3 HOH C 540 O 124.6 130.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS D 205 O REMARK 620 2 SER D 207 OG 112.4 REMARK 620 3 ASN D 293 O 97.8 103.1 REMARK 620 N 1 2 DBREF 6MKB A 139 309 UNP P41274 TNFL9_MOUSE 139 309 DBREF 6MKB B 139 309 UNP P41274 TNFL9_MOUSE 139 309 DBREF 6MKB C 139 309 UNP P41274 TNFL9_MOUSE 139 309 DBREF 6MKB D 139 309 UNP P41274 TNFL9_MOUSE 139 309 SEQRES 1 A 171 ASN THR THR GLN GLN GLY SER PRO VAL PHE ALA LYS LEU SEQRES 2 A 171 LEU ALA LYS ASN GLN ALA SER LEU CYS ASN THR THR LEU SEQRES 3 A 171 ASN TRP HIS SER GLN ASP GLY ALA GLY SER SER TYR LEU SEQRES 4 A 171 SER GLN GLY LEU ARG TYR GLU GLU ASP LYS LYS GLU LEU SEQRES 5 A 171 VAL VAL ASP SER PRO GLY LEU TYR TYR VAL PHE LEU GLU SEQRES 6 A 171 LEU LYS LEU SER PRO THR PHE THR ASN THR GLY HIS LYS SEQRES 7 A 171 VAL GLN GLY TRP VAL SER LEU VAL LEU GLN ALA LYS PRO SEQRES 8 A 171 GLN VAL ASP ASP PHE ASP ASN LEU ALA LEU THR VAL GLU SEQRES 9 A 171 LEU PHE PRO CYS SER MET GLU ASN LYS LEU VAL ASP ARG SEQRES 10 A 171 SER TRP SER GLN LEU LEU LEU LEU LYS ALA GLY HIS ARG SEQRES 11 A 171 LEU SER VAL GLY LEU ARG ALA TYR LEU HIS GLY ALA GLN SEQRES 12 A 171 ASP ALA TYR ARG ASP TRP GLU LEU SER TYR PRO ASN THR SEQRES 13 A 171 THR SER PHE GLY LEU PHE LEU VAL LYS PRO ASP ASN PRO SEQRES 14 A 171 TRP GLU SEQRES 1 B 171 ASN THR THR GLN GLN GLY SER PRO VAL PHE ALA LYS LEU SEQRES 2 B 171 LEU ALA LYS ASN GLN ALA SER LEU CYS ASN THR THR LEU SEQRES 3 B 171 ASN TRP HIS SER GLN ASP GLY ALA GLY SER SER TYR LEU SEQRES 4 B 171 SER GLN GLY LEU ARG TYR GLU GLU ASP LYS LYS GLU LEU SEQRES 5 B 171 VAL VAL ASP SER PRO GLY LEU TYR TYR VAL PHE LEU GLU SEQRES 6 B 171 LEU LYS LEU SER PRO THR PHE THR ASN THR GLY HIS LYS SEQRES 7 B 171 VAL GLN GLY TRP VAL SER LEU VAL LEU GLN ALA LYS PRO SEQRES 8 B 171 GLN VAL ASP ASP PHE ASP ASN LEU ALA LEU THR VAL GLU SEQRES 9 B 171 LEU PHE PRO CYS SER MET GLU ASN LYS LEU VAL ASP ARG SEQRES 10 B 171 SER TRP SER GLN LEU LEU LEU LEU LYS ALA GLY HIS ARG SEQRES 11 B 171 LEU SER VAL GLY LEU ARG ALA TYR LEU HIS GLY ALA GLN SEQRES 12 B 171 ASP ALA TYR ARG ASP TRP GLU LEU SER TYR PRO ASN THR SEQRES 13 B 171 THR SER PHE GLY LEU PHE LEU VAL LYS PRO ASP ASN PRO SEQRES 14 B 171 TRP GLU SEQRES 1 C 171 ASN THR THR GLN GLN GLY SER PRO VAL PHE ALA LYS LEU SEQRES 2 C 171 LEU ALA LYS ASN GLN ALA SER LEU CYS ASN THR THR LEU SEQRES 3 C 171 ASN TRP HIS SER GLN ASP GLY ALA GLY SER SER TYR LEU SEQRES 4 C 171 SER GLN GLY LEU ARG TYR GLU GLU ASP LYS LYS GLU LEU SEQRES 5 C 171 VAL VAL ASP SER PRO GLY LEU TYR TYR VAL PHE LEU GLU SEQRES 6 C 171 LEU LYS LEU SER PRO THR PHE THR ASN THR GLY HIS LYS SEQRES 7 C 171 VAL GLN GLY TRP VAL SER LEU VAL LEU GLN ALA LYS PRO SEQRES 8 C 171 GLN VAL ASP ASP PHE ASP ASN LEU ALA LEU THR VAL GLU SEQRES 9 C 171 LEU PHE PRO CYS SER MET GLU ASN LYS LEU VAL ASP ARG SEQRES 10 C 171 SER TRP SER GLN LEU LEU LEU LEU LYS ALA GLY HIS ARG SEQRES 11 C 171 LEU SER VAL GLY LEU ARG ALA TYR LEU HIS GLY ALA GLN SEQRES 12 C 171 ASP ALA TYR ARG ASP TRP GLU LEU SER TYR PRO ASN THR SEQRES 13 C 171 THR SER PHE GLY LEU PHE LEU VAL LYS PRO ASP ASN PRO SEQRES 14 C 171 TRP GLU SEQRES 1 D 171 ASN THR THR GLN GLN GLY SER PRO VAL PHE ALA LYS LEU SEQRES 2 D 171 LEU ALA LYS ASN GLN ALA SER LEU CYS ASN THR THR LEU SEQRES 3 D 171 ASN TRP HIS SER GLN ASP GLY ALA GLY SER SER TYR LEU SEQRES 4 D 171 SER GLN GLY LEU ARG TYR GLU GLU ASP LYS LYS GLU LEU SEQRES 5 D 171 VAL VAL ASP SER PRO GLY LEU TYR TYR VAL PHE LEU GLU SEQRES 6 D 171 LEU LYS LEU SER PRO THR PHE THR ASN THR GLY HIS LYS SEQRES 7 D 171 VAL GLN GLY TRP VAL SER LEU VAL LEU GLN ALA LYS PRO SEQRES 8 D 171 GLN VAL ASP ASP PHE ASP ASN LEU ALA LEU THR VAL GLU SEQRES 9 D 171 LEU PHE PRO CYS SER MET GLU ASN LYS LEU VAL ASP ARG SEQRES 10 D 171 SER TRP SER GLN LEU LEU LEU LEU LYS ALA GLY HIS ARG SEQRES 11 D 171 LEU SER VAL GLY LEU ARG ALA TYR LEU HIS GLY ALA GLN SEQRES 12 D 171 ASP ALA TYR ARG ASP TRP GLU LEU SER TYR PRO ASN THR SEQRES 13 D 171 THR SER PHE GLY LEU PHE LEU VAL LYS PRO ASP ASN PRO SEQRES 14 D 171 TRP GLU HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET NAG G 1 14 HET NAG G 2 14 HET BMA G 3 11 HET MAN G 4 11 HET NAG H 1 14 HET NAG H 2 14 HET BMA H 3 11 HET MAN H 4 11 HET MAN H 5 11 HET NA A 401 1 HET NA A 402 1 HET SO4 B 401 5 HET SO4 B 402 5 HET SO4 B 403 5 HET SO4 B 404 5 HET NA B 408 1 HET SO4 C 401 5 HET SO4 C 402 5 HET SO4 C 403 4 HET NA C 404 1 HET NA C 405 1 HET SO4 D 401 5 HET NA D 402 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 5 NAG 8(C8 H15 N O6) FORMUL 5 BMA 4(C6 H12 O6) FORMUL 5 MAN 4(C6 H12 O6) FORMUL 9 NA 6(NA 1+) FORMUL 11 SO4 8(O4 S 2-) FORMUL 23 HOH *286(H2 O) HELIX 1 AA1 ASP A 282 ARG A 285 5 4 HELIX 2 AA2 ASP B 282 ARG B 285 5 4 HELIX 3 AA3 ASP C 282 ARG C 285 5 4 HELIX 4 AA4 ASP D 282 ARG D 285 5 4 SHEET 1 AA1 5 TRP A 166 HIS A 167 0 SHEET 2 AA1 5 PHE A 148 ALA A 153 -1 N LEU A 152 O HIS A 167 SHEET 3 AA1 5 SER A 296 PRO A 304 -1 O PHE A 297 N LEU A 151 SHEET 4 AA1 5 GLY A 196 PRO A 208 -1 N TYR A 199 O PHE A 300 SHEET 5 AA1 5 VAL A 253 LEU A 263 -1 O LEU A 261 N TYR A 198 SHEET 1 AA2 5 TRP A 166 HIS A 167 0 SHEET 2 AA2 5 PHE A 148 ALA A 153 -1 N LEU A 152 O HIS A 167 SHEET 3 AA2 5 SER A 296 PRO A 304 -1 O PHE A 297 N LEU A 151 SHEET 4 AA2 5 GLY A 196 PRO A 208 -1 N TYR A 199 O PHE A 300 SHEET 5 AA2 5 TRP A 287 GLU A 288 -1 O GLU A 288 N SER A 207 SHEET 1 AA3 4 THR A 162 THR A 163 0 SHEET 2 AA3 4 HIS A 267 HIS A 278 -1 O LEU A 273 N THR A 162 SHEET 3 AA3 4 GLU A 189 VAL A 192 -1 N VAL A 192 O HIS A 267 SHEET 4 AA3 4 LEU A 181 GLU A 184 -1 N ARG A 182 O VAL A 191 SHEET 1 AA4 4 THR A 162 THR A 163 0 SHEET 2 AA4 4 HIS A 267 HIS A 278 -1 O LEU A 273 N THR A 162 SHEET 3 AA4 4 GLN A 218 LYS A 228 -1 N SER A 222 O ARG A 274 SHEET 4 AA4 4 ALA A 238 LEU A 243 -1 O VAL A 241 N VAL A 221 SHEET 1 AA5 5 TRP B 166 HIS B 167 0 SHEET 2 AA5 5 PHE B 148 ALA B 153 -1 N LEU B 152 O HIS B 167 SHEET 3 AA5 5 SER B 296 PRO B 304 -1 O PHE B 297 N LEU B 151 SHEET 4 AA5 5 GLY B 196 PRO B 208 -1 N LEU B 197 O VAL B 302 SHEET 5 AA5 5 VAL B 253 LEU B 263 -1 O LEU B 261 N TYR B 198 SHEET 1 AA6 5 TRP B 166 HIS B 167 0 SHEET 2 AA6 5 PHE B 148 ALA B 153 -1 N LEU B 152 O HIS B 167 SHEET 3 AA6 5 SER B 296 PRO B 304 -1 O PHE B 297 N LEU B 151 SHEET 4 AA6 5 GLY B 196 PRO B 208 -1 N LEU B 197 O VAL B 302 SHEET 5 AA6 5 TRP B 287 GLU B 288 -1 O GLU B 288 N SER B 207 SHEET 1 AA7 4 THR B 162 THR B 163 0 SHEET 2 AA7 4 HIS B 267 HIS B 278 -1 O LEU B 273 N THR B 162 SHEET 3 AA7 4 GLU B 189 VAL B 192 -1 N VAL B 192 O HIS B 267 SHEET 4 AA7 4 LEU B 181 GLU B 184 -1 N ARG B 182 O VAL B 191 SHEET 1 AA8 4 THR B 162 THR B 163 0 SHEET 2 AA8 4 HIS B 267 HIS B 278 -1 O LEU B 273 N THR B 162 SHEET 3 AA8 4 GLN B 218 LYS B 228 -1 N SER B 222 O ARG B 274 SHEET 4 AA8 4 ALA B 238 LEU B 243 -1 O LEU B 243 N GLY B 219 SHEET 1 AA9 5 TRP C 166 HIS C 167 0 SHEET 2 AA9 5 PHE C 148 ALA C 153 -1 N LEU C 152 O HIS C 167 SHEET 3 AA9 5 SER C 296 PRO C 304 -1 O PHE C 297 N LEU C 151 SHEET 4 AA9 5 GLY C 196 PRO C 208 -1 N LEU C 197 O VAL C 302 SHEET 5 AA9 5 VAL C 253 LEU C 263 -1 O LEU C 261 N TYR C 198 SHEET 1 AB1 5 TYR C 176 LEU C 177 0 SHEET 2 AB1 5 PHE C 148 ALA C 153 -1 N LYS C 150 O TYR C 176 SHEET 3 AB1 5 SER C 296 PRO C 304 -1 O PHE C 297 N LEU C 151 SHEET 4 AB1 5 GLY C 196 PRO C 208 -1 N LEU C 197 O VAL C 302 SHEET 5 AB1 5 TRP C 287 GLU C 288 -1 O GLU C 288 N SER C 207 SHEET 1 AB2 4 THR C 162 THR C 163 0 SHEET 2 AB2 4 HIS C 267 HIS C 278 -1 O LEU C 273 N THR C 162 SHEET 3 AB2 4 GLU C 189 VAL C 192 -1 N VAL C 192 O HIS C 267 SHEET 4 AB2 4 LEU C 181 GLU C 184 -1 N ARG C 182 O VAL C 191 SHEET 1 AB3 4 THR C 162 THR C 163 0 SHEET 2 AB3 4 HIS C 267 HIS C 278 -1 O LEU C 273 N THR C 162 SHEET 3 AB3 4 GLN C 218 LYS C 228 -1 N GLN C 226 O SER C 270 SHEET 4 AB3 4 ALA C 238 LEU C 243 -1 O LEU C 243 N GLY C 219 SHEET 1 AB4 5 TRP D 166 HIS D 167 0 SHEET 2 AB4 5 PHE D 148 ALA D 153 -1 N LEU D 152 O HIS D 167 SHEET 3 AB4 5 SER D 296 PRO D 304 -1 O PHE D 297 N LEU D 151 SHEET 4 AB4 5 GLY D 196 PRO D 208 -1 N LEU D 197 O VAL D 302 SHEET 5 AB4 5 VAL D 253 LEU D 263 -1 O LEU D 261 N TYR D 198 SHEET 1 AB5 5 TRP D 166 HIS D 167 0 SHEET 2 AB5 5 PHE D 148 ALA D 153 -1 N LEU D 152 O HIS D 167 SHEET 3 AB5 5 SER D 296 PRO D 304 -1 O PHE D 297 N LEU D 151 SHEET 4 AB5 5 GLY D 196 PRO D 208 -1 N LEU D 197 O VAL D 302 SHEET 5 AB5 5 TRP D 287 GLU D 288 -1 O GLU D 288 N SER D 207 SHEET 1 AB6 4 THR D 162 THR D 163 0 SHEET 2 AB6 4 HIS D 267 HIS D 278 -1 O LEU D 273 N THR D 162 SHEET 3 AB6 4 GLU D 189 VAL D 192 -1 N VAL D 192 O HIS D 267 SHEET 4 AB6 4 LEU D 181 GLU D 184 -1 N GLU D 184 O GLU D 189 SHEET 1 AB7 4 THR D 162 THR D 163 0 SHEET 2 AB7 4 HIS D 267 HIS D 278 -1 O LEU D 273 N THR D 162 SHEET 3 AB7 4 GLN D 218 LYS D 228 -1 N SER D 222 O ARG D 274 SHEET 4 AB7 4 ALA D 238 LEU D 243 -1 O LEU D 243 N GLY D 219 SSBOND 1 CYS A 246 CYS B 246 1555 1555 2.04 SSBOND 2 CYS C 246 CYS D 246 1555 1555 2.03 LINK ND2 ASN A 161 C1 NAG E 1 1555 1555 1.43 LINK ND2 ASN B 161 C1 NAG F 1 1555 1555 1.43 LINK ND2 ASN C 161 C1 NAG G 1 1555 1555 1.43 LINK ND2 ASN D 161 C1 NAG H 1 1555 1555 1.43 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.40 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.42 LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.44 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.42 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.43 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.44 LINK O4 NAG G 2 C1 BMA G 3 1555 1555 1.44 LINK O6 BMA G 3 C1 MAN G 4 1555 1555 1.44 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.41 LINK O4 NAG H 2 C1 BMA H 3 1555 1555 1.42 LINK O3 BMA H 3 C1 MAN H 4 1555 1555 1.44 LINK O6 BMA H 3 C1 MAN H 5 1555 1555 1.40 LINK O LEU A 164 NA NA A 401 1555 1555 2.47 LINK O LYS A 188 NA NA A 401 1555 1555 2.74 LINK O LYS A 205 NA NA A 402 1555 1555 2.64 LINK OG SER A 207 NA NA A 402 1555 1555 2.80 LINK O ASN A 293 NA NA A 402 1555 1555 2.59 LINK O LYS B 205 NA NA B 408 1555 1555 2.77 LINK OG SER B 207 NA NA B 408 1555 1555 2.69 LINK O ASN B 293 NA NA B 408 1555 1555 2.57 LINK O LYS C 205 NA NA C 404 1555 1555 2.67 LINK OG SER C 207 NA NA C 404 1555 1555 2.77 LINK O ASN C 293 NA NA C 404 1555 1555 2.60 LINK O ASN C 293 NA NA C 405 1555 1555 3.13 LINK OG1 THR C 295 NA NA C 405 1555 1555 3.19 LINK NA NA C 405 O HOH C 540 1555 1555 2.50 LINK O LYS D 205 NA NA D 402 1555 1555 2.55 LINK OG SER D 207 NA NA D 402 1555 1555 2.96 LINK O ASN D 293 NA NA D 402 1555 1555 2.68 CISPEP 1 LYS A 228 PRO A 229 0 0.52 CISPEP 2 TYR A 291 PRO A 292 0 9.63 CISPEP 3 LYS B 228 PRO B 229 0 1.03 CISPEP 4 TYR B 291 PRO B 292 0 9.86 CISPEP 5 LYS C 228 PRO C 229 0 0.76 CISPEP 6 TYR C 291 PRO C 292 0 10.11 CISPEP 7 LYS D 228 PRO D 229 0 -0.93 CISPEP 8 TYR D 291 PRO D 292 0 9.22 CRYST1 77.362 77.362 118.236 90.00 90.00 120.00 P 31 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 0.012926 0.007463 0.000000 0.00000 SCALE2 0.000000 0.014926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008458 0.00000