HEADER LIPID BINDING PROTEIN 09-JUL-20 6ZPR TITLE SOLUTION 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,MIXED LINEAGE COMPND 3 KINASE DOMAIN-LIKE PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: HMLKL,HMLKL; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: LIG = CYS86 COVALENTLY LABELLED WITH COMPOUND,LIG = COMPND 8 CYS86 COVALENTLY LABELLED WITH COMPOUND 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 SOLUTION NMR NUMMDL 20 AUTHOR M.RUEBBELKE,M.BAUER,J.HAMILTON,F.BINDER,H.NAR,M.ZEEB REVDAT 3 06-JAN-21 6ZPR 1 JRNL REVDAT 2 30-DEC-20 6ZPR 1 JRNL REVDAT 1 16-DEC-20 6ZPR 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. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.9 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZPR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109777. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.5; 7.1 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE, 150 MM REMARK 210 SODIUM CHLORIDE; 20 MM SODIUM REMARK 210 PHOSPHATE, 150 MM SODIUM CHLORIDE REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 340 UM [U-13C; U-15N] MLKL, 1200 REMARK 210 UM COMPOUND, 93% H2O/7% D2O; 385 REMARK 210 UM [U-13C; U-15N] MLKL, 840 UM REMARK 210 COMPOUND, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCCH TOCSY; 3D REMARK 210 HNCC TOCSY; 3D 1H-15N NOESY; 2D REMARK 210 1H-13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D HCCH-TOCSY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D FILT. 1H- REMARK 210 13C NOESY ALIPHATIC; 3D FILT. 1H- REMARK 210 13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4.2, TOPSPIN REMARK 210 3.6, TOPSPIN 3.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 1 SER A -1 159.36 63.28 REMARK 500 1 LYS A 22 36.07 -95.28 REMARK 500 1 TYR A 23 -165.17 -120.32 REMARK 500 1 LYS A 50 143.51 -173.41 REMARK 500 1 ARG A 51 103.01 -52.37 REMARK 500 1 PRO A 54 89.21 -69.72 REMARK 500 1 SER A 55 172.39 -53.78 REMARK 500 1 PHE A 98 50.34 -112.14 REMARK 500 1 GLU A 119 -60.03 -102.71 REMARK 500 1 VAL A 124 71.18 34.96 REMARK 500 1 SER A 125 -63.47 178.93 REMARK 500 1 SER A 128 -70.58 -84.85 REMARK 500 1 ALA A 131 -40.48 -132.22 REMARK 500 1 TRP A 133 -65.89 -130.04 REMARK 500 2 LYS A 22 42.44 -92.80 REMARK 500 2 TYR A 23 -167.65 -129.11 REMARK 500 2 ARG A 51 106.11 -55.06 REMARK 500 2 SER A 52 -170.90 -67.50 REMARK 500 2 VAL A 53 74.83 -151.78 REMARK 500 2 GLU A 119 -60.40 -103.60 REMARK 500 2 PRO A 123 73.43 -69.76 REMARK 500 2 SER A 125 -61.58 178.48 REMARK 500 2 SER A 128 -73.45 -86.17 REMARK 500 2 GLN A 129 172.66 -52.58 REMARK 500 2 ALA A 131 -68.84 -141.82 REMARK 500 2 TRP A 133 -61.89 -172.05 REMARK 500 3 LYS A 22 34.84 -95.02 REMARK 500 3 TYR A 23 -163.32 -119.85 REMARK 500 3 GLN A 48 -71.04 -121.87 REMARK 500 3 LYS A 50 176.82 -57.53 REMARK 500 3 PRO A 54 89.72 -69.69 REMARK 500 3 SER A 55 -178.45 -63.79 REMARK 500 3 PRO A 123 73.30 -69.79 REMARK 500 3 SER A 125 -62.07 178.89 REMARK 500 3 ILE A 127 -71.23 -66.16 REMARK 500 3 SER A 128 -72.41 -82.69 REMARK 500 3 GLN A 129 179.95 -55.81 REMARK 500 3 ALA A 131 -56.68 -162.74 REMARK 500 3 TRP A 133 -65.68 -167.36 REMARK 500 4 LYS A 22 34.76 -95.06 REMARK 500 4 TYR A 23 -162.81 -118.72 REMARK 500 4 ARG A 51 96.05 -61.60 REMARK 500 4 PRO A 54 86.85 -69.77 REMARK 500 4 PRO A 123 71.72 -69.77 REMARK 500 4 SER A 125 -61.96 179.32 REMARK 500 4 ILE A 127 -70.35 -65.83 REMARK 500 4 SER A 128 -70.75 -84.97 REMARK 500 4 GLN A 129 178.75 -55.44 REMARK 500 4 ALA A 131 -169.50 -60.86 REMARK 500 4 TRP A 133 -65.57 -123.73 REMARK 500 REMARK 500 THIS ENTRY HAS 209 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QOK A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6ZLE RELATED DB: PDB REMARK 900 UNLIGANDED STRUCTURE REMARK 900 RELATED ID: 34528 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF MLKL EXECUTIONER DOMAIN IN COMPLEX WITH A REMARK 900 COVALENT INHBIBITOR DBREF 6ZPR A 2 85 UNP Q8NB16 MLKL_HUMAN 2 85 DBREF 6ZPR A 86 154 UNP Q8NB16 MLKL_HUMAN 86 154 SEQADV 6ZPR GLY A -2 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZPR SER A -1 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZPR PRO A 0 UNP Q8NB16 EXPRESSION TAG SEQADV 6ZPR GLY A 1 UNP Q8NB16 EXPRESSION TAG SEQRES 1 A 157 GLY SER PRO GLY GLU ASN LEU LYS HIS ILE ILE THR LEU SEQRES 2 A 157 GLY GLN VAL ILE HIS LYS ARG CYS GLU GLU MET LYS TYR SEQRES 3 A 157 CYS LYS LYS GLN CYS ARG ARG LEU GLY HIS ARG VAL LEU SEQRES 4 A 157 GLY LEU ILE LYS PRO LEU GLU MET LEU GLN ASP GLN GLY SEQRES 5 A 157 LYS ARG SER VAL PRO SER GLU LYS LEU THR THR ALA MET SEQRES 6 A 157 ASN ARG PHE LYS ALA ALA LEU GLU GLU ALA ASN GLY GLU SEQRES 7 A 157 ILE GLU LYS PHE SER ASN ARG SER ASN ILE CYS ARG PHE SEQRES 8 A 157 LEU THR ALA SER GLN ASP LYS ILE LEU PHE LYS ASP VAL SEQRES 9 A 157 ASN ARG LYS LEU SER ASP VAL TRP LYS GLU LEU SER LEU SEQRES 10 A 157 LEU LEU GLN VAL GLU GLN ARG MET PRO VAL SER PRO ILE SEQRES 11 A 157 SER GLN GLY ALA SER TRP ALA GLN GLU ASP GLN GLN ASP SEQRES 12 A 157 ALA ASP GLU ASP ARG ARG ALA PHE GLN MET LEU ARG ARG SEQRES 13 A 157 ASP HET QOK A 201 34 HETNAM QOK 7-(2-METHOXYETHOXYMETHYL)-1,3-DIMETHYL-PURINE-2,6-DIONE FORMUL 2 QOK C11 H16 N4 O4 HELIX 1 AA1 GLY A 1 MET A 21 1 21 HELIX 2 AA2 TYR A 23 GLN A 27 5 5 HELIX 3 AA3 CYS A 28 ASP A 47 1 20 HELIX 4 AA4 SER A 55 PHE A 79 1 25 HELIX 5 AA5 ASN A 81 ALA A 91 1 11 HELIX 6 AA6 ASP A 100 GLU A 119 1 20 HELIX 7 AA7 TRP A 133 LEU A 151 1 19 LINK SG CYS A 86 C7 QOK A 201 1555 1555 1.76 SITE 1 AC1 8 CYS A 24 ARG A 82 ILE A 85 CYS A 86 SITE 2 AC1 8 LEU A 89 ASP A 144 PHE A 148 LEU A 151 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1