HEADER LIPID BINDING PROTEIN 23-FEB-21 7NM4 TITLE SOLUTION STRUCTURE OF MLKL EXECUTIONER DOMAIN IN COMPLEX WITH A TITLE 2 FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN; COMPND 3 CHAIN: A; 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 SOLUTION NMR NUMMDL 20 AUTHOR M.RUEBBELKE,M.BAUER,J.HAMILTON,F.BINDER,H.NAR,M.ZEEB REVDAT 4 14-JUN-23 7NM4 1 REMARK REVDAT 3 24-NOV-21 7NM4 1 JRNL REVDAT 2 17-NOV-21 7NM4 1 JRNL REVDAT 1 22-SEP-21 7NM4 0 JRNL AUTH M.RUBBELKE,J.HAMILTON,F.BINDER,M.BAUER,J.KING,H.NAR,M.ZEEB JRNL TITL DISCOVERY AND STRUCTURE-BASED OPTIMIZATION OF FRAGMENTS JRNL TITL 2 BINDING THE MIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN JRNL TITL 3 EXECUTIONER DOMAIN. JRNL REF J.MED.CHEM. V. 64 15629 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34672548 JRNL DOI 10.1021/ACS.JMEDCHEM.1C00686 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 7NM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292114157. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.1; 7.5 REMARK 210 IONIC STRENGTH : 170; 170 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 385 UM [U-13C; U-15N] MLKL REMARK 210 EXECUTIONER DOMAIN, 2000 UM CPD REMARK 210 3, 100% D2O; 315 UM [U-13C; U- REMARK 210 15N] MLKL EXECUTIONER DOMAIN, REMARK 210 1600 UM CPD 3, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HNCCH TOCSY; 3D HNCC TOCSY; 3D REMARK 210 1H-15N NOESY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HCCH-TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D FILT. 1H-13C REMARK 210 NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4.2, TOPSPIN REMARK 210 3.5, TOPSPIN 3.6 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 : TARGET FUNCTION 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: 9990 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: CLOSE CONTACTS 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 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 1 LYS A 50 -65.29 -101.32 REMARK 500 1 SER A 92 -169.31 -119.56 REMARK 500 1 ASP A 94 97.96 59.32 REMARK 500 1 PRO A 123 -175.51 -69.78 REMARK 500 1 VAL A 124 -52.86 -127.12 REMARK 500 1 PRO A 126 85.56 -69.69 REMARK 500 1 SER A 128 -74.50 -67.86 REMARK 500 2 PRO A 0 -168.76 -69.71 REMARK 500 2 LYS A 50 -70.19 -88.91 REMARK 500 2 ARG A 51 103.74 -57.76 REMARK 500 2 SER A 52 -75.67 -51.02 REMARK 500 2 GLN A 120 112.48 -160.80 REMARK 500 2 ARG A 121 103.08 -55.82 REMARK 500 2 PRO A 126 76.69 -69.76 REMARK 500 2 ARG A 152 140.39 -172.07 REMARK 500 2 ARG A 153 -174.06 -60.89 REMARK 500 3 SER A -1 -61.11 179.43 REMARK 500 3 LYS A 22 -45.32 -139.64 REMARK 500 3 TYR A 23 -60.19 -90.50 REMARK 500 3 ARG A 51 103.30 -56.79 REMARK 500 3 VAL A 53 134.26 -173.70 REMARK 500 3 PRO A 126 82.47 -69.72 REMARK 500 3 GLN A 129 -74.44 -56.66 REMARK 500 3 ALA A 131 35.67 -142.55 REMARK 500 4 LYS A 22 -40.78 -136.49 REMARK 500 4 ASN A 81 171.47 -54.79 REMARK 500 4 PRO A 126 78.97 -69.85 REMARK 500 4 ALA A 131 45.49 -92.43 REMARK 500 4 LEU A 151 154.65 -48.14 REMARK 500 5 SER A -1 78.87 64.26 REMARK 500 5 ASP A 94 -177.49 -66.52 REMARK 500 5 ARG A 121 -169.66 -60.33 REMARK 500 5 MET A 122 -61.61 -177.39 REMARK 500 5 VAL A 124 -62.49 -96.92 REMARK 500 5 PRO A 126 76.88 -69.75 REMARK 500 5 SER A 128 -71.87 -97.91 REMARK 500 5 ARG A 152 35.71 -148.02 REMARK 500 6 SER A -1 68.44 -167.94 REMARK 500 6 SER A 52 -66.76 -90.89 REMARK 500 6 VAL A 53 134.75 -176.48 REMARK 500 6 GLN A 93 -75.32 -50.67 REMARK 500 6 GLN A 120 109.27 -162.04 REMARK 500 6 ARG A 121 102.99 -52.58 REMARK 500 6 PRO A 126 77.52 -69.66 REMARK 500 7 VAL A 53 133.11 65.18 REMARK 500 7 ASN A 81 -174.61 -62.31 REMARK 500 7 GLN A 93 -71.82 -87.61 REMARK 500 7 ASP A 94 177.48 -56.19 REMARK 500 7 PRO A 126 82.01 -69.78 REMARK 500 7 ALA A 131 33.72 -142.28 REMARK 500 REMARK 500 THIS ENTRY HAS 177 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 UJ8 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34604 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF MLKL EXECUTIONER DOMAIN IN COMPLEX WITH A REMARK 900 FRAGMENT DBREF 7NM4 A 2 154 UNP Q8NB16 MLKL_HUMAN 2 154 SEQADV 7NM4 GLY A -2 UNP Q8NB16 EXPRESSION TAG SEQADV 7NM4 SER A -1 UNP Q8NB16 EXPRESSION TAG SEQADV 7NM4 PRO A 0 UNP Q8NB16 EXPRESSION TAG SEQADV 7NM4 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 UJ8 A 201 38 HETNAM UJ8 (~{S})-1~{H}-BENZIMIDAZOL-2-YL-(4-PROPAN-2-YLPHENYL) HETNAM 2 UJ8 METHANOL FORMUL 2 UJ8 C17 H18 N2 O HELIX 1 AA1 GLY A 1 CYS A 18 1 18 HELIX 2 AA2 GLU A 19 MET A 21 5 3 HELIX 3 AA3 CYS A 24 GLY A 49 1 26 HELIX 4 AA4 SER A 55 SER A 80 1 26 HELIX 5 AA5 ASN A 81 SER A 92 1 12 HELIX 6 AA6 PHE A 98 VAL A 118 1 21 HELIX 7 AA7 ALA A 131 ARG A 152 1 22 SITE 1 AC1 9 SER A -1 ASN A 3 LEU A 4 LEU A 42 SITE 2 AC1 9 LEU A 45 PRO A 54 SER A 55 THR A 59 SITE 3 AC1 9 MET A 62 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