HEADER LIPID BINDING PROTEIN 03-AUG-20 6ZZ1 TITLE CRYSTAL STRUCTURE OF MLKL EXECUTIONER DOMAIN IN COMPLEX WITH A TITLE 2 COVALENT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: MIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HMLKL; COMPND 5 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: MLKL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NECROPTOSIS, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.FIEGEN,M.BAUER,H.NAR REVDAT 3 31-JAN-24 6ZZ1 1 REMARK REVDAT 2 06-JAN-21 6ZZ1 1 JRNL REVDAT 1 23-DEC-20 6ZZ1 0 JRNL AUTH M.RUBBELKE,D.FIEGEN,M.BAUER,F.BINDER,J.HAMILTON,J.KING, JRNL AUTH 2 S.THAMM,H.NAR,M.ZEEB JRNL TITL LOCKING MIXED-LINEAGE KINASE DOMAIN-LIKE PROTEIN IN ITS JRNL TITL 2 AUTO-INHIBITED STATE PREVENTS NECROPTOSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 33272 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 33318170 JRNL DOI 10.1073/PNAS.2017406117 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 3 NUMBER OF REFLECTIONS : 28985 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1501 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 15.54 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2184 REMARK 3 BIN FREE R VALUE : 0.1848 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 36 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11090 REMARK 3 B22 (A**2) : -0.11090 REMARK 3 B33 (A**2) : 0.22190 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) : 0.240 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.126 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.118 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.125 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.119 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 : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2415 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3235 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 931 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 449 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2373 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 298 ; 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 : 2141 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.61 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.80 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZZ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1292110472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-18 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999940 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 : AUTOPROC, XDS JAN 31, 202 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.1.7, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28984 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 19.705 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : 0.02900 REMARK 200 FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 24.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.79700 REMARK 200 R SYM FOR SHELL (I) : 0.79700 REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIMPLE, MOLREP REMARK 200 STARTING MODEL: 4BTF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32 % POLYETHYLENE GLYCOL MONOMETHYL REMARK 280 ETHER 2,000, 0.15 M POTASSIUM BROMIDE, 0.1 M TRIS, PH 9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.25050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.87575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.62525 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 LYS A 50 REMARK 465 ARG A 51 REMARK 465 VAL A 124 REMARK 465 SER A 125 REMARK 465 PRO A 126 REMARK 465 ILE A 127 REMARK 465 SER A 128 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 GLN B 48 REMARK 465 GLY B 49 REMARK 465 LYS B 50 REMARK 465 ARG B 51 REMARK 465 VAL B 124 REMARK 465 SER B 125 REMARK 465 PRO B 126 REMARK 465 ILE B 127 REMARK 465 SER B 128 REMARK 465 GLN B 129 REMARK 465 MET B 150 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 ARG B 121 54.17 32.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6ZVO RELATED DB: PDB REMARK 900 RELATED ID: 6ZLE RELATED DB: PDB REMARK 900 RELATED ID: 6ZPR RELATED DB: PDB DBREF 6ZZ1 A 2 150 UNP Q8NB16 MLKL_HUMAN 2 150 DBREF 6ZZ1 B 2 150 UNP Q8NB16 MLKL_HUMAN 2 150 SEQADV 6ZZ1 GLY A -2 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZZ1 SER A -1 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZZ1 PRO A 0 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZZ1 GLY A 1 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZZ1 GLY B -2 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZZ1 SER B -1 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZZ1 PRO B 0 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZZ1 GLY B 1 UNP Q8NB16 EXPRESSION TAG SEQRES 1 A 153 GLY SER PRO GLY GLU ASN LEU LYS HIS ILE ILE THR LEU SEQRES 2 A 153 GLY GLN VAL ILE HIS LYS ARG CYS GLU GLU MET LYS TYR SEQRES 3 A 153 CYS LYS LYS GLN CYS ARG ARG LEU GLY HIS ARG VAL LEU SEQRES 4 A 153 GLY LEU ILE LYS PRO LEU GLU MET LEU GLN ASP GLN GLY SEQRES 5 A 153 LYS ARG SER VAL PRO SER GLU LYS LEU THR THR ALA MET SEQRES 6 A 153 ASN ARG PHE LYS ALA ALA LEU GLU GLU ALA ASN GLY GLU SEQRES 7 A 153 ILE GLU LYS PHE SER ASN ARG SER ASN ILE CYS ARG PHE SEQRES 8 A 153 LEU THR ALA SER GLN ASP LYS ILE LEU PHE LYS ASP VAL SEQRES 9 A 153 ASN ARG LYS LEU SER ASP VAL TRP LYS GLU LEU SER LEU SEQRES 10 A 153 LEU LEU GLN VAL GLU GLN ARG MET PRO VAL SER PRO ILE SEQRES 11 A 153 SER GLN GLY ALA SER TRP ALA GLN GLU ASP GLN GLN ASP SEQRES 12 A 153 ALA ASP GLU ASP ARG ARG ALA PHE GLN MET SEQRES 1 B 153 GLY SER PRO GLY GLU ASN LEU LYS HIS ILE ILE THR LEU SEQRES 2 B 153 GLY GLN VAL ILE HIS LYS ARG CYS GLU GLU MET LYS TYR SEQRES 3 B 153 CYS LYS LYS GLN CYS ARG ARG LEU GLY HIS ARG VAL LEU SEQRES 4 B 153 GLY LEU ILE LYS PRO LEU GLU MET LEU GLN ASP GLN GLY SEQRES 5 B 153 LYS ARG SER VAL PRO SER GLU LYS LEU THR THR ALA MET SEQRES 6 B 153 ASN ARG PHE LYS ALA ALA LEU GLU GLU ALA ASN GLY GLU SEQRES 7 B 153 ILE GLU LYS PHE SER ASN ARG SER ASN ILE CYS ARG PHE SEQRES 8 B 153 LEU THR ALA SER GLN ASP LYS ILE LEU PHE LYS ASP VAL SEQRES 9 B 153 ASN ARG LYS LEU SER ASP VAL TRP LYS GLU LEU SER LEU SEQRES 10 B 153 LEU LEU GLN VAL GLU GLN ARG MET PRO VAL SER PRO ILE SEQRES 11 B 153 SER GLN GLY ALA SER TRP ALA GLN GLU ASP GLN GLN ASP SEQRES 12 B 153 ALA ASP GLU ASP ARG ARG ALA PHE GLN MET HET QOK A 201 19 HET QOK B 201 19 HETNAM QOK 7-(2-METHOXYETHOXYMETHYL)-1,3-DIMETHYL-PURINE-2,6-DIONE FORMUL 3 QOK 2(C11 H16 N4 O4) FORMUL 5 HOH *154(H2 O) HELIX 1 AA1 PRO A 0 MET A 21 1 22 HELIX 2 AA2 CYS A 24 ASP A 47 1 24 HELIX 3 AA3 SER A 55 SER A 80 1 26 HELIX 4 AA4 ASN A 81 SER A 92 1 12 HELIX 5 AA5 PHE A 98 ARG A 121 1 24 HELIX 6 AA6 SER A 132 MET A 150 1 19 HELIX 7 AA7 GLY B 1 MET B 21 1 21 HELIX 8 AA8 CYS B 24 ASP B 47 1 24 HELIX 9 AA9 SER B 55 SER B 80 1 26 HELIX 10 AB1 ASN B 81 SER B 92 1 12 HELIX 11 AB2 PHE B 98 ARG B 121 1 24 HELIX 12 AB3 SER B 132 GLN B 149 1 18 LINK SG CYS A 86 C7 QOK A 201 1555 1555 1.75 LINK SG CYS B 86 C7 QOK B 201 1555 1555 1.74 CRYST1 56.709 56.709 90.501 90.00 90.00 90.00 P 43 8 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 0.017634 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011050 0.00000