HEADER TRANSCRIPTION/INHIBITOR 01-DEC-12 4I80 TITLE CRYSTAL STRUCTURE OF HUMAN MENIN IN COMPLEX WITH A HIGH-AFFINITY TITLE 2 MACROCYCLIC PEPTIDOMIMETICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MENIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MACROCYCLIC PEPTIDOMIMETIC; COMPND 7 CHAIN: B; COMPND 8 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: MEN1, SCG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: CHEMICALLY SYNTHESIZED COMPOUND KEYWDS MENIN, MEN1, MLL, MACROCYCLIC PEPTIDOMIMETIC, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.HUANG,M.LEI REVDAT 4 15-NOV-17 4I80 1 REMARK REVDAT 3 21-JUN-17 4I80 1 DBREF REVDAT 2 19-JUN-13 4I80 1 LINK REVDAT 1 06-MAR-13 4I80 0 JRNL AUTH H.ZHOU,L.LIU,J.HUANG,D.BERNARD,H.KARATAS,A.NAVARRO,M.LEI, JRNL AUTH 2 S.WANG JRNL TITL STRUCTURE-BASED DESIGN OF HIGH-AFFINITY MACROCYCLIC JRNL TITL 2 PEPTIDOMIMETICS TO BLOCK THE MENIN-MIXED LINEAGE LEUKEMIA 1 JRNL TITL 3 (MLL1) PROTEIN-PROTEIN INTERACTION. JRNL REF J.MED.CHEM. V. 56 1113 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23244744 JRNL DOI 10.1021/JM3015298 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 16307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1622 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.7126 - 7.0797 1.00 1453 148 0.2003 0.2083 REMARK 3 2 7.0797 - 5.6229 1.00 1370 141 0.2035 0.2569 REMARK 3 3 5.6229 - 4.9131 1.00 1322 166 0.1958 0.2067 REMARK 3 4 4.9131 - 4.4644 1.00 1314 156 0.1944 0.2416 REMARK 3 5 4.4644 - 4.1446 1.00 1336 134 0.1911 0.2220 REMARK 3 6 4.1446 - 3.9004 1.00 1303 141 0.1960 0.2658 REMARK 3 7 3.9004 - 3.7052 0.99 1274 170 0.2120 0.2464 REMARK 3 8 3.7052 - 3.5440 0.93 1202 134 0.2367 0.2688 REMARK 3 9 3.5440 - 3.4076 0.87 1160 119 0.2698 0.2517 REMARK 3 10 3.4076 - 3.2900 0.81 1042 109 0.2830 0.3198 REMARK 3 11 3.2900 - 3.1872 0.75 997 96 0.3034 0.3880 REMARK 3 12 3.1872 - 3.0960 0.71 912 108 0.3024 0.3570 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 79.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 107.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -46.32870 REMARK 3 B22 (A**2) : -46.32870 REMARK 3 B33 (A**2) : 92.65740 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 3983 REMARK 3 ANGLE : 1.246 5403 REMARK 3 CHIRALITY : 0.067 600 REMARK 3 PLANARITY : 0.005 694 REMARK 3 DIHEDRAL : 15.717 1455 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I80 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076419. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97941 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 : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16363 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.096 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 25.50 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.1 REMARK 200 DATA REDUNDANCY IN SHELL : 20.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.3 M NACL, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 46.43950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 70.68950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 70.68950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.21975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 70.68950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 70.68950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.65925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 70.68950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.68950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.21975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 70.68950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.68950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.65925 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 46.43950 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.43950 REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE MACROCYCLIC PEPTIDOMIMETIC IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: MACROCYCLIC PEPTIDOMIMETIC REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 SER A 1 REMARK 465 GLY A 386 REMARK 465 GLU A 387 REMARK 465 GLU A 388 REMARK 465 ARG A 389 REMARK 465 PRO A 390 REMARK 465 GLY A 391 REMARK 465 GLU A 392 REMARK 465 GLN A 393 REMARK 465 SER A 394 REMARK 465 GLN A 395 REMARK 465 GLY A 396 REMARK 465 THR A 397 REMARK 465 GLN A 398 REMARK 465 SER A 399 REMARK 465 GLN A 400 REMARK 465 GLY A 401 REMARK 465 GLY A 528 REMARK 465 PRO A 529 REMARK 465 GLU A 530 REMARK 465 GLY A 531 REMARK 465 GLY A 532 REMARK 465 SER A 533 REMARK 465 THR A 534 REMARK 465 ALA A 535 REMARK 465 GLN A 536 REMARK 465 VAL A 537 REMARK 465 PRO A 538 REMARK 465 ALA A 539 REMARK 465 PRO A 540 REMARK 465 THR 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 GLN A 582 REMARK 465 SER A 583 REMARK 465 GLN A 584 REMARK 465 VAL A 585 REMARK 465 GLN A 586 REMARK 465 MET A 587 REMARK 465 LYS A 588 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 THR A 594 REMARK 465 PRO A 595 REMARK 465 SER A 596 REMARK 465 ASP A 597 REMARK 465 TYR A 598 REMARK 465 THR A 599 REMARK 465 LEU A 600 REMARK 465 SER A 601 REMARK 465 PHE A 602 REMARK 465 LEU A 603 REMARK 465 LYS A 604 REMARK 465 ARG A 605 REMARK 465 GLN A 606 REMARK 465 ARG A 607 REMARK 465 LYS A 608 REMARK 465 GLY A 609 REMARK 465 LEU A 610 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NAA 1E3 B 8 O PRO B 13 2.13 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 PRO A 69 C - N - CA ANGL. DEV. = 10.5 DEGREES REMARK 500 TRP B 7 O - C - N ANGL. DEV. = -14.1 DEGREES REMARK 500 1E3 B 8 C - N - CA ANGL. DEV. = 24.9 DEGREES REMARK 500 ARG B 12 CA - C - N ANGL. DEV. = -20.8 DEGREES REMARK 500 ARG B 12 O - C - N ANGL. DEV. = 22.1 DEGREES REMARK 500 PRO B 13 C - N - CA ANGL. DEV. = -20.3 DEGREES REMARK 500 PRO B 13 C - N - CD ANGL. DEV. = 15.2 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 LEU A 103 5.84 -62.82 REMARK 500 GLU A 109 86.67 -67.60 REMARK 500 HIS A 139 47.31 71.63 REMARK 500 ASP A 180 11.16 -146.73 REMARK 500 ASN A 189 -2.08 68.46 REMARK 500 ASN A 203 10.32 -61.05 REMARK 500 ASN A 212 -39.48 -38.23 REMARK 500 THR A 311 -73.03 -39.65 REMARK 500 ARG A 332 66.86 33.91 REMARK 500 ASP A 370 -63.18 -136.80 REMARK 500 PRO A 373 -4.86 -56.49 REMARK 500 ARG A 452 1.75 -57.50 REMARK 500 THR A 521 -142.13 -75.74 REMARK 500 SER A 572 -76.01 -46.30 REMARK 500 SER A 573 -36.38 -38.85 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 TRP B 7 1E3 B 8 146.54 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 1E3 B 8 -14.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3U84 RELATED DB: PDB REMARK 900 RELATED ID: 3U85 RELATED DB: PDB REMARK 900 RELATED ID: 3U88 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 MENIN SEQUENCE (CHAIN A) IS MENIN ISOFORM 2 (UNP IDENTIFIER: O00255- REMARK 999 2). THE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE CANONICAL REMARK 999 SEQUENCE AS FOLLOWS: RESIDUES 149-153 ARE MISSING DBREF 4I80 A 2 459 UNP O00255 MEN1_HUMAN 2 459 DBREF 4I80 A 520 610 UNP O00255 MEN1_HUMAN 520 610 DBREF 4I80 B 5 13 PDB 4I80 4I80 5 13 SEQADV 4I80 SER A 1 UNP O00255 EXPRESSION TAG SEQRES 1 A 550 SER GLY LEU LYS ALA ALA GLN LYS THR LEU PHE PRO LEU SEQRES 2 A 550 ARG SER ILE ASP ASP VAL VAL ARG LEU PHE ALA ALA GLU SEQRES 3 A 550 LEU GLY ARG GLU GLU PRO ASP LEU VAL LEU LEU SER LEU SEQRES 4 A 550 VAL LEU GLY PHE VAL GLU HIS PHE LEU ALA VAL ASN ARG SEQRES 5 A 550 VAL ILE PRO THR ASN VAL PRO GLU LEU THR PHE GLN PRO SEQRES 6 A 550 SER PRO ALA PRO ASP PRO PRO GLY GLY LEU THR TYR PHE SEQRES 7 A 550 PRO VAL ALA ASP LEU SER ILE ILE ALA ALA LEU TYR ALA SEQRES 8 A 550 ARG PHE THR ALA GLN ILE ARG GLY ALA VAL ASP LEU SER SEQRES 9 A 550 LEU TYR PRO ARG GLU GLY GLY VAL SER SER ARG GLU LEU SEQRES 10 A 550 VAL LYS LYS VAL SER ASP VAL ILE TRP ASN SER LEU SER SEQRES 11 A 550 ARG SER TYR PHE LYS ASP ARG ALA HIS ILE GLN SER LEU SEQRES 12 A 550 PHE SER PHE ILE THR GLY THR LYS LEU ASP SER SER GLY SEQRES 13 A 550 VAL ALA PHE ALA VAL VAL GLY ALA CYS GLN ALA LEU GLY SEQRES 14 A 550 LEU ARG ASP VAL HIS LEU ALA LEU SER GLU ASP HIS ALA SEQRES 15 A 550 TRP VAL VAL PHE GLY PRO ASN GLY GLU GLN THR ALA GLU SEQRES 16 A 550 VAL THR TRP HIS GLY LYS GLY ASN GLU ASP ARG ARG GLY SEQRES 17 A 550 GLN THR VAL ASN ALA GLY VAL ALA GLU ARG SER TRP LEU SEQRES 18 A 550 TYR LEU LYS GLY SER TYR MET ARG CYS ASP ARG LYS MET SEQRES 19 A 550 GLU VAL ALA PHE MET VAL CYS ALA ILE ASN PRO SER ILE SEQRES 20 A 550 ASP LEU HIS THR ASP SER LEU GLU LEU LEU GLN LEU GLN SEQRES 21 A 550 GLN LYS LEU LEU TRP LEU LEU TYR ASP LEU GLY HIS LEU SEQRES 22 A 550 GLU ARG TYR PRO MET ALA LEU GLY ASN LEU ALA ASP LEU SEQRES 23 A 550 GLU GLU LEU GLU PRO THR PRO GLY ARG PRO ASP PRO LEU SEQRES 24 A 550 THR LEU TYR HIS LYS GLY ILE ALA SER ALA LYS THR TYR SEQRES 25 A 550 TYR ARG ASP GLU HIS ILE TYR PRO TYR MET TYR LEU ALA SEQRES 26 A 550 GLY TYR HIS CYS ARG ASN ARG ASN VAL ARG GLU ALA LEU SEQRES 27 A 550 GLN ALA TRP ALA ASP THR ALA THR VAL ILE GLN ASP TYR SEQRES 28 A 550 ASN TYR CYS ARG GLU ASP GLU GLU ILE TYR LYS GLU PHE SEQRES 29 A 550 PHE GLU VAL ALA ASN ASP VAL ILE PRO ASN LEU LEU LYS SEQRES 30 A 550 GLU ALA ALA SER LEU LEU GLU ALA GLY GLU GLU ARG PRO SEQRES 31 A 550 GLY GLU GLN SER GLN GLY THR GLN SER GLN GLY SER ALA SEQRES 32 A 550 LEU GLN ASP PRO GLU CYS PHE ALA HIS LEU LEU ARG PHE SEQRES 33 A 550 TYR ASP GLY ILE CYS LYS TRP GLU GLU GLY SER PRO THR SEQRES 34 A 550 PRO VAL LEU HIS VAL GLY TRP ALA THR PHE LEU VAL GLN SEQRES 35 A 550 SER LEU GLY ARG PHE GLU GLY GLN VAL ARG GLN LYS VAL SEQRES 36 A 550 ARG ILE VAL SER GLY THR VAL ALA GLY THR ALA ARG GLY SEQRES 37 A 550 PRO GLU GLY GLY SER THR ALA GLN VAL PRO ALA PRO THR SEQRES 38 A 550 ALA SER PRO PRO PRO GLU GLY PRO VAL LEU THR PHE GLN SEQRES 39 A 550 SER GLU LYS MET LYS GLY MET LYS GLU LEU LEU VAL ALA SEQRES 40 A 550 THR LYS ILE ASN SER SER ALA ILE LYS LEU GLN LEU THR SEQRES 41 A 550 ALA GLN SER GLN VAL GLN MET LYS LYS GLN LYS VAL SER SEQRES 42 A 550 THR PRO SER ASP TYR THR LEU SER PHE LEU LYS ARG GLN SEQRES 43 A 550 ARG LYS GLY LEU SEQRES 1 B 9 ACE ARG TRP 1E3 PHE PRO ALA ARG PRO HET ACE B 5 3 HET 1E3 B 8 12 HETNAM ACE ACETYL GROUP HETNAM 1E3 (2S)-2,9-DIAMINONONANOIC ACID FORMUL 2 ACE C2 H4 O FORMUL 2 1E3 C9 H20 N2 O2 HELIX 1 1 LYS A 4 THR A 9 1 6 HELIX 2 2 SER A 15 LEU A 27 1 13 HELIX 3 3 ASP A 33 VAL A 50 1 18 HELIX 4 4 ASP A 82 GLY A 99 1 18 HELIX 5 5 ASP A 102 TYR A 106 5 5 HELIX 6 6 SER A 114 SER A 128 1 15 HELIX 7 7 SER A 142 THR A 150 1 9 HELIX 8 8 ASP A 153 GLY A 169 1 17 HELIX 9 9 GLY A 187 GLU A 191 5 5 HELIX 10 10 VAL A 211 GLU A 217 1 7 HELIX 11 11 TYR A 222 SER A 226 5 5 HELIX 12 12 ASP A 231 ALA A 242 1 12 HELIX 13 13 SER A 253 LEU A 270 1 18 HELIX 14 14 TYR A 276 GLU A 290 1 15 HELIX 15 15 ASP A 297 ARG A 314 1 18 HELIX 16 16 ILE A 318 ASN A 331 1 14 HELIX 17 17 ASN A 333 GLN A 349 1 17 HELIX 18 18 CYS A 354 GLU A 356 5 3 HELIX 19 19 ASP A 357 ASP A 370 1 14 HELIX 20 20 ASP A 370 LEU A 383 1 14 HELIX 21 21 ASP A 406 GLU A 425 1 20 HELIX 22 22 HIS A 433 GLY A 445 1 13 HELIX 23 23 SER A 555 GLY A 560 1 6 HELIX 24 24 MET A 561 LYS A 562 5 2 HELIX 25 25 GLU A 563 ALA A 567 5 5 HELIX 26 26 ASN A 571 THR A 580 1 10 SHEET 1 A 2 PHE A 63 PRO A 67 0 SHEET 2 A 2 LEU A 75 PRO A 79 -1 O THR A 76 N SER A 66 SHEET 1 B 4 GLN A 192 ALA A 194 0 SHEET 2 B 4 ALA A 182 PHE A 186 -1 N PHE A 186 O GLN A 192 SHEET 3 B 4 HIS A 174 LEU A 177 -1 N ALA A 176 O TRP A 183 SHEET 4 B 4 MET A 228 ARG A 229 -1 O MET A 228 N LEU A 177 LINK C ACE B 5 N ARG B 6 1555 1555 1.27 LINK C 1E3 B 8 N PHE B 9 1555 1555 1.26 LINK NAA 1E3 B 8 C PRO B 13 1555 1555 1.38 LINK C TRP B 7 N 1E3 B 8 1555 1555 1.34 CISPEP 1 PHE A 11 PRO A 12 0 -4.14 CRYST1 141.379 141.379 92.879 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 0.007073 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010767 0.00000