HEADER IMMUNE SYSTEM 15-SEP-21 7S79 TITLE STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC PHOSPHONO-MLL TITLE 2 PEPTIDE ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-7 ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-299; COMPND 5 SYNONYM: MHC CLASS I ANTIGEN B*7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 21-119; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: MLL CLEAVAGE PRODUCT N320; COMPND 14 CHAIN: E; COMPND 15 FRAGMENT: PHOSPHONO-MLL(747-755) PEPTIDE; COMPND 16 SYNONYM: N-TERMINAL CLEAVAGE PRODUCT OF 320 KDA,P320; COMPND 17 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: HLA-B, HLAB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET30A; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606 KEYWDS HLA, MLL PEPTIDE, MHC-I, HLA-B*07:02, HLA-B7, IMMUNITY, IMMUNE KEYWDS 2 SYSTEM, PHOSPHOPEPTIDE, PHOSPHONO ANALOG, CANCER EXPDTA X-RAY DIFFRACTION AUTHOR L.PATSKOVSKA,Y.PATSKOVSKY,S.NYOVANIE,A.NATARAJAN,B.JOSHI,B.MORIN, AUTHOR 2 C.BRITTSAN,O.HUBER,S.GORDON,X.MICHELET,F.SCHMITZBERGER,R.STEIN, AUTHOR 3 M.FINDEIS,A.HURWITZ,M.VAN DIJK,J.BUELL,D.UNDERWOOD,M.KROGSGAARD REVDAT 5 06-NOV-24 7S79 1 REMARK REVDAT 4 15-NOV-23 7S79 1 LINK ATOM REVDAT 3 18-OCT-23 7S79 1 REMARK REVDAT 2 20-SEP-23 7S79 1 JRNL REVDAT 1 02-NOV-22 7S79 0 JRNL AUTH Y.PATSKOVSKY,A.NATARAJAN,L.PATSKOVSKA,S.NYOVANIE,B.JOSHI, JRNL AUTH 2 B.MORIN,C.BRITTSAN,O.HUBER,S.GORDON,X.MICHELET, JRNL AUTH 3 F.SCHMITZBERGER,R.B.STEIN,M.A.FINDEIS,A.HURWITZ,M.VAN DIJK, JRNL AUTH 4 E.CHANTZOURA,A.S.YAGUE,D.POLLACK SMITH,J.S.BUELL, JRNL AUTH 5 D.UNDERWOOD,M.KROGSGAARD JRNL TITL MOLECULAR MECHANISM OF PHOSPHOPEPTIDE NEOANTIGEN JRNL TITL 2 IMMUNOGENICITY. JRNL REF NAT COMMUN V. 14 3763 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37353482 JRNL DOI 10.1038/S41467-023-39425-1 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 77832 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2491 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5516 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 193 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3155 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 567 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75000 REMARK 3 B22 (A**2) : 0.75000 REMARK 3 B33 (A**2) : -1.51000 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.345 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3448 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3005 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4704 ; 1.571 ; 1.664 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6993 ; 1.408 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 424 ; 6.446 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 236 ;28.794 ;20.932 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 565 ;12.600 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;17.143 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3987 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 818 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7S79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100.000 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97953 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SI(111) MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80429 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 29.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: 7RZD REMARK 200 REMARK 200 REMARK: RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-24% PEG4000, 0.1 SODIUM CITRATE, REMARK 280 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE, PH REMARK 280 8.00, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 119.42850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.93000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.93000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.71425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.93000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.93000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 179.14275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.93000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.93000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.71425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.93000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.93000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 179.14275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 119.42850 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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 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 ARG A 44 CD NE CZ NH1 NH2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 58 CG CD CE NZ 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 ARG E 3 C E7P E 4 N 0.195 REMARK 500 E7P E 4 C PRO E 5 N 0.120 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 ARG A 14 65.36 -152.82 REMARK 500 ASP A 29 -124.02 46.71 REMARK 500 LYS A 176 -118.59 49.26 REMARK 500 GLN A 224 53.27 -103.62 REMARK 500 ARG A 239 -8.13 83.91 REMARK 500 TRP B 60 -2.44 76.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 E7P E 4 12.44 REMARK 500 REMARK 500 REMARK: NULL 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 B 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 577 O REMARK 620 2 HIS B 84 O 94.9 REMARK 620 3 LEU B 87 O 177.9 86.2 REMARK 620 4 HOH B 206 O 83.4 84.1 94.9 REMARK 620 5 HOH B 287 O 105.6 159.2 73.4 101.2 REMARK 620 6 HOH B 321 O 100.0 95.7 81.7 176.6 77.8 REMARK 620 N 1 2 3 4 5 DBREF 7S79 A 1 275 UNP P01889 1B07_HUMAN 25 299 DBREF 7S79 B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 7S79 E 1 9 UNP Q03164 KMT2A_HUMAN 747 755 SEQADV 7S79 MET B 0 UNP P61769 INITIATING METHIONINE SEQADV 7S79 E7P E 4 UNP Q03164 SER 750 CONFLICT SEQRES 1 A 275 GLY SER HIS SER MET ARG TYR PHE TYR THR SER VAL SER SEQRES 2 A 275 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE SER VAL GLY SEQRES 3 A 275 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 275 ALA ALA SER PRO ARG GLU GLU PRO ARG ALA PRO TRP ILE SEQRES 5 A 275 GLU GLN GLU GLY PRO GLU TYR TRP ASP ARG ASN THR GLN SEQRES 6 A 275 ILE TYR LYS ALA GLN ALA GLN THR ASP ARG GLU SER LEU SEQRES 7 A 275 ARG ASN LEU ARG GLY TYR TYR ASN GLN SER GLU ALA GLY SEQRES 8 A 275 SER HIS THR LEU GLN SER MET TYR GLY CYS ASP VAL GLY SEQRES 9 A 275 PRO ASP GLY ARG LEU LEU ARG GLY HIS ASP GLN TYR ALA SEQRES 10 A 275 TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 275 ARG SER TRP THR ALA ALA ASP THR ALA ALA GLN ILE THR SEQRES 12 A 275 GLN ARG LYS TRP GLU ALA ALA ARG GLU ALA GLU GLN ARG SEQRES 13 A 275 ARG ALA TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU ARG SEQRES 14 A 275 ARG TYR LEU GLU ASN GLY LYS ASP LYS LEU GLU ARG ALA SEQRES 15 A 275 ASP PRO PRO LYS THR HIS VAL THR HIS HIS PRO ILE SER SEQRES 16 A 275 ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 275 TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY SEQRES 18 A 275 GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG SEQRES 19 A 275 PRO ALA GLY ASP ARG THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 A 275 VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS SEQRES 21 A 275 VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG SEQRES 22 A 275 TRP GLU SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 B 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 E 9 GLU PRO ARG E7P PRO SER HIS SER MET HET E7P E 4 10 HET GOL A 301 6 HET GOL A 302 6 HET GOL B 101 6 HET GOL B 102 6 HET NA B 103 1 HETNAM E7P (2S)-2-AMINO-4-PHOSPHONOBUTANOIC ACID HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 E7P C4 H10 N O5 P FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 NA NA 1+ FORMUL 9 HOH *567(H2 O) HELIX 1 AA1 ALA A 49 GLU A 53 5 5 HELIX 2 AA2 GLY A 56 TYR A 85 1 30 HELIX 3 AA3 ASP A 137 ALA A 150 1 14 HELIX 4 AA4 ARG A 151 GLY A 162 1 12 HELIX 5 AA5 GLY A 162 LYS A 176 1 15 HELIX 6 AA6 LYS A 176 ARG A 181 1 6 HELIX 7 AA7 THR A 225 THR A 228 5 4 HELIX 8 AA8 GLU A 253 GLN A 255 5 3 SHEET 1 AA1 8 GLU A 46 PRO A 47 0 SHEET 2 AA1 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 AA1 8 ARG A 21 VAL A 28 -1 N GLY A 26 O PHE A 33 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O VAL A 103 N HIS A 3 SHEET 6 AA1 8 LEU A 109 TYR A 118 -1 O LEU A 110 N ASP A 102 SHEET 7 AA1 8 LYS A 121 LEU A 126 -1 O LEU A 126 N ASP A 114 SHEET 8 AA1 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 AA2 4 LYS A 186 PRO A 193 0 SHEET 2 AA2 4 GLU A 198 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 AA2 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 AA2 4 GLU A 229 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 AA3 4 LYS A 186 PRO A 193 0 SHEET 2 AA3 4 GLU A 198 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 AA3 4 PHE A 241 PRO A 250 -1 O ALA A 245 N CYS A 203 SHEET 4 AA3 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 AA4 4 GLU A 222 ASP A 223 0 SHEET 2 AA4 4 THR A 214 ARG A 219 -1 N ARG A 219 O GLU A 222 SHEET 3 AA4 4 TYR A 257 GLN A 262 -1 O HIS A 260 N THR A 216 SHEET 4 AA4 4 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 AA5 4 LYS B 6 SER B 11 0 SHEET 2 AA5 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA5 4 PHE B 62 PHE B 70 -1 O THR B 68 N LEU B 23 SHEET 4 AA5 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 AA6 4 LYS B 6 SER B 11 0 SHEET 2 AA6 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA6 4 PHE B 62 PHE B 70 -1 O THR B 68 N LEU B 23 SHEET 4 AA6 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 AA7 4 GLU B 44 ARG B 45 0 SHEET 2 AA7 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 AA7 4 TYR B 78 ASN B 83 -1 O ALA B 79 N LEU B 40 SHEET 4 AA7 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.13 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.04 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.01 LINK C ARG E 3 N E7P E 4 1555 1555 1.53 LINK C E7P E 4 N PRO E 5 1555 1555 1.46 LINK O HOH A 577 NA NA B 103 5545 1555 2.36 LINK O HIS B 84 NA NA B 103 1555 1555 2.59 LINK O LEU B 87 NA NA B 103 1555 1555 2.54 LINK NA NA B 103 O HOH B 206 1555 1555 2.30 LINK NA NA B 103 O HOH B 287 1555 1555 2.26 LINK NA NA B 103 O HOH B 321 1555 1555 2.34 CISPEP 1 TYR A 209 PRO A 210 0 1.61 CISPEP 2 HIS B 31 PRO B 32 0 -0.73 CRYST1 65.860 65.860 238.857 90.00 90.00 90.00 P 41 21 2 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 0.015184 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004187 0.00000