HEADER PROTEIN BINDING 05-JUN-24 9C4V TITLE MENIN MUTANT G331D IN COMPLEX WITH MLL PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MENIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE 2A; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: C-TERMINAL CLEAVAGE PRODUCT OF 180 KDA,P180; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MEN1, SCG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.D.CLEGG,T.CIERPICKI,J.GREMBECKA REVDAT 2 24-DEC-25 9C4V 1 JRNL REVDAT 1 14-MAY-25 9C4V 0 JRNL AUTH J.RAY,B.CLEGG,J.GREMBECKA,T.CIERPICKI JRNL TITL DRUG-RESISTANT MENIN VARIANTS RETAIN HIGH BINDING AFFINITY JRNL TITL 2 AND INTERACTIONS WITH MLL1. JRNL REF J.BIOL.CHEM. V. 300 07777 2024 JRNL REFN ESSN 1083-351X JRNL PMID 39276940 JRNL DOI 10.1016/J.JBC.2024.107777 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 84536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.826 REMARK 3 FREE R VALUE TEST SET COUNT : 4080 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5660 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 302 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3741 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 529 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27900 REMARK 3 B22 (A**2) : -0.05900 REMARK 3 B33 (A**2) : -0.21900 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): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.198 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3963 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3714 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5386 ; 1.914 ; 1.824 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8534 ; 0.669 ; 1.749 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 497 ; 5.903 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 27 ; 9.823 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 646 ;11.999 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 596 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4744 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 938 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 810 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 71 ; 0.145 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1976 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 333 ; 0.154 ; 0.200 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): 1965 ; 2.109 ; 1.809 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1965 ; 2.110 ; 1.809 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2469 ; 3.037 ; 3.237 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2470 ; 3.036 ; 3.239 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1998 ; 3.246 ; 2.107 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1999 ; 3.247 ; 2.108 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2917 ; 4.847 ; 3.716 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2918 ; 4.846 ; 3.717 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 BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9C4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000282805. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-23 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 : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 722 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 722 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.469 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.0830 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.92300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.090 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.0 / 22.07.2010 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M HEPES, PH REMARK 280 7.5, 25% (W/V) PEG-3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285K 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 24.54100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.46300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.10850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.46300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.54100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.10850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 PRO A 538 REMARK 465 ALA A 539 REMARK 465 PRO A 540 REMARK 465 ALA A 541 REMARK 465 ALA A 542 REMARK 465 SER A 543 REMARK 465 PRO A 544 REMARK 465 PRO A 545 REMARK 465 PRO A 546 REMARK 465 GLU A 547 REMARK 465 GLY A 548 REMARK 465 LYS A 589 REMARK 465 GLN A 590 REMARK 465 LYS A 591 REMARK 465 VAL A 592 REMARK 465 SER A 593 REMARK 465 SER B 4 REMARK 465 ALA B 5 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 GLU A 30 CG CD OE1 OE2 REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 ARG A 131 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 LEU A 249 CG CD1 CD2 REMARK 470 ARG A 355 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 460 CG1 CG2 REMARK 470 LYS A 569 CG CD CE NZ REMARK 470 GLN A 586 CG CD OE1 NE2 REMARK 470 MET A 587 CG SD CE REMARK 470 LYS A 588 CG CD CE NZ REMARK 470 ARG B 6 CB CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 217 CD GLU A 217 OE1 -0.072 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 31 CB - CA - C ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 207 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 295 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 335 CD - NE - CZ ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG A 335 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 452 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 456 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 456 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 12 CG - CD - NE ANGL. DEV. = -18.6 DEGREES REMARK 500 GLY B 14 O - C - N ANGL. DEV. = 10.3 DEGREES 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 77 -60.72 -155.15 REMARK 500 SER A 178 -158.60 -96.27 REMARK 500 ASP A 180 10.61 -144.12 REMARK 500 SER A 226 48.33 -87.27 REMARK 500 ASP A 370 -58.76 -140.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 109 GLY A 110 147.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 21 0.12 SIDE CHAIN REMARK 500 ARG A 207 0.08 SIDE CHAIN REMARK 500 ARG A 332 0.08 SIDE CHAIN REMARK 500 ARG B 8 0.11 SIDE CHAIN 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 A1223 DISTANCE = 6.02 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 1PE A 604 DBREF 9C4V A 1 459 UNP O00255 MEN1_HUMAN 1 459 DBREF 9C4V A 460 593 UNP O00255 MEN1_HUMAN 537 593 DBREF 9C4V B 4 15 UNP Q03164 KMT2A_HUMAN 4 15 SEQADV 9C4V GLY A -4 UNP O00255 EXPRESSION TAG SEQADV 9C4V GLY A -3 UNP O00255 EXPRESSION TAG SEQADV 9C4V SER A -2 UNP O00255 EXPRESSION TAG SEQADV 9C4V SER A -1 UNP O00255 EXPRESSION TAG SEQADV 9C4V SER A 0 UNP O00255 EXPRESSION TAG SEQADV 9C4V A UNP O00255 ILE 54 DELETION SEQADV 9C4V A UNP O00255 PRO 55 DELETION SEQADV 9C4V A UNP O00255 THR 56 DELETION SEQADV 9C4V A UNP O00255 ASN 57 DELETION SEQADV 9C4V A UNP O00255 VAL 58 DELETION SEQADV 9C4V A UNP O00255 PRO 59 DELETION SEQADV 9C4V A UNP O00255 GLU 60 DELETION SEQADV 9C4V A UNP O00255 LEU 61 DELETION SEQADV 9C4V A UNP O00255 THR 62 DELETION SEQADV 9C4V A UNP O00255 PHE 63 DELETION SEQADV 9C4V A UNP O00255 GLN 64 DELETION SEQADV 9C4V A UNP O00255 PRO 65 DELETION SEQADV 9C4V A UNP O00255 SER 66 DELETION SEQADV 9C4V A UNP O00255 PRO 67 DELETION SEQADV 9C4V A UNP O00255 ALA 68 DELETION SEQADV 9C4V A UNP O00255 PRO 69 DELETION SEQADV 9C4V A UNP O00255 ASP 70 DELETION SEQADV 9C4V A UNP O00255 PRO 71 DELETION SEQADV 9C4V A UNP O00255 PRO 72 DELETION SEQADV 9C4V A UNP O00255 GLY 73 DELETION SEQADV 9C4V ASP A 326 UNP O00255 GLY 326 ENGINEERED MUTATION SEQADV 9C4V A UNP O00255 GLU 387 DELETION SEQADV 9C4V A UNP O00255 GLU 388 DELETION SEQADV 9C4V A UNP O00255 ARG 389 DELETION SEQADV 9C4V A UNP O00255 PRO 390 DELETION SEQADV 9C4V A UNP O00255 GLY 391 DELETION SEQADV 9C4V A UNP O00255 GLU 392 DELETION SEQADV 9C4V A UNP O00255 GLN 393 DELETION SEQADV 9C4V A UNP O00255 SER 394 DELETION SEQADV 9C4V A UNP O00255 GLN 395 DELETION SEQADV 9C4V A UNP O00255 GLY 396 DELETION SEQADV 9C4V A UNP O00255 THR 397 DELETION SEQADV 9C4V A UNP O00255 GLN 398 DELETION SEQADV 9C4V ALA A 541 UNP O00255 THR 541 VARIANT SEQADV 9C4V ALA B 5 UNP Q03164 CYS 5 ENGINEERED MUTATION SEQADV 9C4V NH2 B 16 UNP Q03164 AMIDATION SEQRES 1 A 489 GLY GLY SER SER SER MET GLY LEU LYS ALA ALA GLN LYS SEQRES 2 A 489 THR LEU PHE PRO LEU ARG SER ILE ASP ASP VAL VAL ARG SEQRES 3 A 489 LEU PHE ALA ALA GLU LEU GLY ARG GLU GLU PRO ASP LEU SEQRES 4 A 489 VAL LEU LEU SER LEU VAL LEU GLY PHE VAL GLU HIS PHE SEQRES 5 A 489 LEU ALA VAL ASN ARG VAL GLY LEU THR TYR PHE PRO VAL SEQRES 6 A 489 ALA ASP LEU SER ILE ILE ALA ALA LEU TYR ALA ARG PHE SEQRES 7 A 489 THR ALA GLN ILE ARG GLY ALA VAL ASP LEU SER LEU TYR SEQRES 8 A 489 PRO ARG GLU GLY GLY VAL SER SER ARG GLU LEU VAL LYS SEQRES 9 A 489 LYS VAL SER ASP VAL ILE TRP ASN SER LEU SER ARG SER SEQRES 10 A 489 TYR PHE LYS ASP ARG ALA HIS ILE GLN SER LEU PHE SER SEQRES 11 A 489 PHE ILE THR GLY THR LYS LEU ASP SER SER GLY VAL ALA SEQRES 12 A 489 PHE ALA VAL VAL GLY ALA CYS GLN ALA LEU GLY LEU ARG SEQRES 13 A 489 ASP VAL HIS LEU ALA LEU SER GLU ASP HIS ALA TRP VAL SEQRES 14 A 489 VAL PHE GLY PRO ASN GLY GLU GLN THR ALA GLU VAL THR SEQRES 15 A 489 TRP HIS GLY LYS GLY ASN GLU ASP ARG ARG GLY GLN THR SEQRES 16 A 489 VAL ASN ALA GLY VAL ALA GLU ARG SER TRP LEU TYR LEU SEQRES 17 A 489 LYS GLY SER TYR MET ARG CYS ASP ARG LYS MET GLU VAL SEQRES 18 A 489 ALA PHE MET VAL CYS ALA ILE ASN PRO SER ILE ASP LEU SEQRES 19 A 489 HIS THR ASP SER LEU GLU LEU LEU GLN LEU GLN GLN LYS SEQRES 20 A 489 LEU LEU TRP LEU LEU TYR ASP LEU GLY HIS LEU GLU ARG SEQRES 21 A 489 TYR PRO MET ALA LEU GLY ASN LEU ALA ASP LEU GLU GLU SEQRES 22 A 489 LEU GLU PRO THR PRO GLY ARG PRO ASP PRO LEU THR LEU SEQRES 23 A 489 TYR HIS LYS GLY ILE ALA SER ALA LYS THR TYR TYR ARG SEQRES 24 A 489 ASP GLU HIS ILE TYR PRO TYR MET TYR LEU ALA ASP TYR SEQRES 25 A 489 HIS CYS ARG ASN ARG ASN VAL ARG GLU ALA LEU GLN ALA SEQRES 26 A 489 TRP ALA ASP THR ALA THR VAL ILE GLN ASP TYR ASN TYR SEQRES 27 A 489 CYS ARG GLU ASP GLU GLU ILE TYR LYS GLU PHE PHE GLU SEQRES 28 A 489 VAL ALA ASN ASP VAL ILE PRO ASN LEU LEU LYS GLU ALA SEQRES 29 A 489 ALA SER LEU LEU GLU ALA GLY SER GLN GLY SER ALA LEU SEQRES 30 A 489 GLN ASP PRO GLU CYS PHE ALA HIS LEU LEU ARG PHE TYR SEQRES 31 A 489 ASP GLY ILE CYS LYS TRP GLU GLU GLY SER PRO THR PRO SEQRES 32 A 489 VAL LEU HIS VAL GLY TRP ALA THR PHE LEU VAL GLN SER SEQRES 33 A 489 LEU GLY ARG PHE GLU GLY GLN VAL ARG GLN LYS VAL ARG SEQRES 34 A 489 ILE VAL SER VAL PRO ALA PRO ALA ALA SER PRO PRO PRO SEQRES 35 A 489 GLU GLY PRO VAL LEU THR PHE GLN SER GLU LYS MET LYS SEQRES 36 A 489 GLY MET LYS GLU LEU LEU VAL ALA THR LYS ILE ASN SER SEQRES 37 A 489 SER ALA ILE LYS LEU GLN LEU THR ALA GLN SER GLN VAL SEQRES 38 A 489 GLN MET LYS LYS GLN LYS VAL SER SEQRES 1 B 13 SER ALA ARG TRP ARG PHE PRO ALA ARG PRO GLY THR NH2 HET NH2 B 16 3 HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HET 1PE A 604 26 HET PG0 A 605 19 HET EDO A 606 10 HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM PG0 2-(2-METHOXYETHOXY)ETHANOL HETNAM EDO 1,2-ETHANEDIOL HETSYN 1PE PEG400 HETSYN PG0 PEG 6000 HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NH2 H2 N FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 1PE C10 H22 O6 FORMUL 7 PG0 C5 H12 O3 FORMUL 8 EDO C2 H6 O2 FORMUL 9 HOH *529(H2 O) HELIX 1 AA1 LYS A 4 THR A 9 1 6 HELIX 2 AA2 SER A 15 GLY A 28 1 14 HELIX 3 AA3 ASP A 33 VAL A 50 1 18 HELIX 4 AA4 ASP A 82 VAL A 101 1 20 HELIX 5 AA5 ASP A 102 TYR A 106 5 5 HELIX 6 AA6 SER A 114 LEU A 129 1 16 HELIX 7 AA7 SER A 142 THR A 150 1 9 HELIX 8 AA8 ASP A 153 LEU A 168 1 16 HELIX 9 AA9 GLY A 187 GLU A 191 5 5 HELIX 10 AB1 VAL A 211 GLU A 217 1 7 HELIX 11 AB2 SER A 219 SER A 226 5 8 HELIX 12 AB3 ASP A 231 ALA A 242 1 12 HELIX 13 AB4 SER A 253 LEU A 270 1 18 HELIX 14 AB5 TYR A 276 GLU A 290 1 15 HELIX 15 AB6 ASP A 297 TYR A 313 1 17 HELIX 16 AB7 ILE A 318 ASN A 331 1 14 HELIX 17 AB8 ASN A 333 GLN A 349 1 17 HELIX 18 AB9 ASP A 357 ASP A 370 1 14 HELIX 19 AC1 ASP A 370 ALA A 385 1 16 HELIX 20 AC2 SER A 402 GLN A 405 5 4 HELIX 21 AC3 ASP A 406 GLU A 425 1 20 HELIX 22 AC4 HIS A 433 ARG A 446 1 14 HELIX 23 AC5 GLU A 448 GLN A 453 1 6 HELIX 24 AC6 SER A 555 LYS A 562 1 8 HELIX 25 AC7 GLU A 563 ALA A 567 5 5 HELIX 26 AC8 ASN A 571 THR A 580 1 10 SHEET 1 AA1 4 GLN A 192 ALA A 194 0 SHEET 2 AA1 4 ALA A 182 PHE A 186 -1 N VAL A 184 O ALA A 194 SHEET 3 AA1 4 HIS A 174 LEU A 177 -1 N ALA A 176 O TRP A 183 SHEET 4 AA1 4 MET A 228 ARG A 229 -1 O MET A 228 N LEU A 177 SHEET 1 AA2 2 SER A 246 ASP A 248 0 SHEET 2 AA2 2 THR A 251 ASP A 252 -1 O THR A 251 N ILE A 247 SHEET 1 AA3 2 ARG A 456 ILE A 457 0 SHEET 2 AA3 2 VAL A 550 LEU A 551 1 O LEU A 551 N ARG A 456 LINK C THR B 15 N NH2 B 16 1555 1555 1.32 CISPEP 1 PHE A 11 PRO A 12 0 -1.78 CRYST1 49.082 80.217 124.926 90.00 90.00 90.00 P 21 21 21 4 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 0.020374 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008005 0.00000 CONECT 7633 7644 CONECT 7644 7633 7645 7646 CONECT 7645 7644 CONECT 7646 7644 CONECT 7648 7649 7650 7651 7652 CONECT 7649 7648 CONECT 7650 7648 CONECT 7651 7648 CONECT 7652 7648 CONECT 7653 7654 7655 7656 7657 CONECT 7654 7653 CONECT 7655 7653 CONECT 7656 7653 CONECT 7657 7653 CONECT 7658 7659 7660 7661 7662 CONECT 7659 7658 CONECT 7660 7658 CONECT 7661 7658 CONECT 7662 7658 CONECT 7663 7664 7674 7675 CONECT 7664 7663 7666 CONECT 7665 7666 7667 7676 7677 CONECT 7666 7664 7665 7678 7679 CONECT 7667 7665 7669 CONECT 7668 7669 7670 7680 7681 CONECT 7669 7667 7668 7682 7683 CONECT 7670 7668 7672 CONECT 7671 7672 7673 7684 7685 CONECT 7672 7670 7671 7686 7687 CONECT 7673 7671 7688 CONECT 7674 7663 CONECT 7675 7663 CONECT 7676 7665 CONECT 7677 7665 CONECT 7678 7666 CONECT 7679 7666 CONECT 7680 7668 CONECT 7681 7668 CONECT 7682 7669 CONECT 7683 7669 CONECT 7684 7671 CONECT 7685 7671 CONECT 7686 7672 CONECT 7687 7672 CONECT 7688 7673 CONECT 7689 7690 7697 7698 CONECT 7690 7689 7691 CONECT 7691 7690 7692 7699 7700 CONECT 7692 7691 7693 7701 7702 CONECT 7693 7692 7694 CONECT 7694 7693 7695 7703 7704 CONECT 7695 7694 7696 7705 7706 CONECT 7696 7695 7707 CONECT 7697 7689 CONECT 7698 7689 CONECT 7699 7691 CONECT 7700 7691 CONECT 7701 7692 CONECT 7702 7692 CONECT 7703 7694 CONECT 7704 7694 CONECT 7705 7695 CONECT 7706 7695 CONECT 7707 7696 CONECT 7708 7709 7710 7712 7713 CONECT 7709 7708 7714 CONECT 7710 7708 7711 7715 7716 CONECT 7711 7710 7717 CONECT 7712 7708 CONECT 7713 7708 CONECT 7714 7709 CONECT 7715 7710 CONECT 7716 7710 CONECT 7717 7711 MASTER 410 0 7 26 8 0 0 6 4308 2 74 39 END