HEADER TRANSFERASE 07-APR-20 6WH8 TITLE THE STRUCTURE OF NTMT1 IN COMPLEX WITH COMPOUND BM-30 COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-TERMINAL XAA-PRO-LYS N-METHYLTRANSFERASE 1; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: ALPHA N-TERMINAL PROTEIN METHYLTRANSFERASE 1A, COMPND 5 METHYLTRANSFERASE-LIKE PROTEIN 11A,N-TERMINAL RCC1 METHYLTRANSFERASE, COMPND 6 X-PRO-LYS N-TERMINAL PROTEIN METHYLTRANSFERASE 1A,NTM1A; COMPND 7 EC: 2.1.1.244; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 4HP-PRO-LYS-ARG-NH2, BM-30; COMPND 11 CHAIN: C, D; COMPND 12 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: NTMT1, C9ORF32, METTL11A, NRMT, NRMT1, AD-003; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS METHYLTRANSFERASE, ENZYME, INHIBITOR COMPLEX, TRANSFERASE, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.NOINAJ,D.CHEN,R.HUANG REVDAT 3 18-OCT-23 6WH8 1 REMARK REVDAT 2 10-MAR-21 6WH8 1 JRNL REVDAT 1 26-AUG-20 6WH8 0 JRNL AUTH B.D.MACKIE,D.CHEN,G.DONG,C.DONG,H.PARKER,C.E.SCHANER TOOLEY, JRNL AUTH 2 N.NOINAJ,J.MIN,R.HUANG JRNL TITL SELECTIVE PEPTIDOMIMETIC INHIBITORS OF NTMT1/2: RATIONAL JRNL TITL 2 DESIGN, SYNTHESIS, CHARACTERIZATION, AND CRYSTALLOGRAPHIC JRNL TITL 3 STUDIES. JRNL REF J.MED.CHEM. V. 63 9512 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32689795 JRNL DOI 10.1021/ACS.JMEDCHEM.0C00689 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 72828 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.750 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 29.5500 - 4.1628 1.00 5479 154 0.1682 0.1782 REMARK 3 2 4.1628 - 3.3055 1.00 5183 147 0.1532 0.1693 REMARK 3 3 3.3055 - 2.8881 1.00 5118 144 0.1702 0.1829 REMARK 3 4 2.8881 - 2.6242 1.00 5106 145 0.1624 0.2039 REMARK 3 5 2.6242 - 2.4362 1.00 5039 141 0.1639 0.1721 REMARK 3 6 2.4362 - 2.2926 1.00 5070 144 0.1628 0.2077 REMARK 3 7 2.2926 - 2.1779 1.00 5002 141 0.1883 0.2072 REMARK 3 8 2.1779 - 2.0831 1.00 5036 142 0.1760 0.1993 REMARK 3 9 2.0831 - 2.0029 1.00 5001 141 0.1962 0.2258 REMARK 3 10 2.0029 - 1.9338 1.00 4997 142 0.2354 0.2778 REMARK 3 11 1.9338 - 1.8734 1.00 4983 140 0.2945 0.3174 REMARK 3 12 1.8734 - 1.8198 1.00 4988 140 0.2804 0.2693 REMARK 3 13 1.8198 - 1.7719 1.00 4970 141 0.2887 0.3243 REMARK 3 14 1.7719 - 1.7290 0.98 4856 138 0.3172 0.3698 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.008 3784 REMARK 3 ANGLE : 0.879 5126 REMARK 3 CHIRALITY : 0.054 565 REMARK 3 PLANARITY : 0.005 661 REMARK 3 DIHEDRAL : 16.992 2254 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 6WH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-18 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 : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72963 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.729 REMARK 200 RESOLUTION RANGE LOW (A) : 29.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.21300 REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 18.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 4.57500 REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER WITHIN PHENIX REMARK 200 STARTING MODEL: 5E1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-HEPES, PH 7.5, 1.6 M AMMONIUM REMARK 280 SULFATE, AND 2% PEG 1000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 136.95400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.47700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.71550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.23850 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 171.19250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 136.95400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 68.47700 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.23850 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 102.71550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 171.19250 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 APPLY THE FOLLOWING TO CHAINS: B, A, C, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 922 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 997 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE 4HP-PRO-LYS-ARG-NH2, BM-30 IS OLIGOPEPTIDE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: 4HP-PRO-LYS-ARG-NH2, BM-30 REMARK 400 CHAIN: C, D 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 MET B -17 REMARK 465 GLY B -16 REMARK 465 SER B -15 REMARK 465 SER B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 SER B -7 REMARK 465 SER B -6 REMARK 465 GLY B -5 REMARK 465 LEU B -4 REMARK 465 MET A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 SER A -7 REMARK 465 SER A -6 REMARK 465 GLY A -5 REMARK 465 LEU A -4 REMARK 465 VAL A -3 REMARK 465 PRO A -2 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 VAL B -3 CG1 CG2 REMARK 470 LYS B 10 CD CE NZ REMARK 470 LYS B 15 NZ REMARK 470 LYS B 21 NZ REMARK 470 LYS B 101 CD CE NZ REMARK 470 ARG B 158 NH1 NH2 REMARK 470 ARG A -1 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 LYS A 10 CD CE NZ REMARK 470 LYS A 21 NZ REMARK 470 LYS A 77 NZ REMARK 470 ARG A 85 CD NE CZ NH1 NH2 REMARK 470 LYS A 101 CD CE NZ REMARK 470 ARG A 158 NH1 NH2 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 HH TYR B 19 O HOH B 803 1.50 REMARK 500 O HOH A 974 O HOH A 979 1.58 REMARK 500 OE1 GLU B 9 O HOH B 801 1.86 REMARK 500 O HOH A 971 O HOH A 979 1.87 REMARK 500 O HOH B 1051 O HOH B 1084 1.88 REMARK 500 O HOH B 1055 O HOH B 1068 1.91 REMARK 500 O HOH B 1007 O HOH C 104 1.92 REMARK 500 O HOH B 1018 O HOH B 1029 1.96 REMARK 500 O HOH A 901 O HOH A 996 2.00 REMARK 500 O HOH B 1096 O HOH A 1022 2.03 REMARK 500 O HOH A 943 O HOH A 1010 2.06 REMARK 500 O HOH B 1018 O HOH B 1022 2.10 REMARK 500 OE1 GLU B 7 O HOH B 802 2.12 REMARK 500 O HOH A 983 O HOH A 1052 2.14 REMARK 500 O HOH B 1000 O HOH B 1087 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 CYS B 117 CB CYS B 117 SG -0.135 REMARK 500 PRO C 2 N PRO C 2 CA -0.141 REMARK 500 PRO C 2 CD PRO C 2 N 0.152 REMARK 500 PRO C 2 C LYS C 3 N 0.158 REMARK 500 ARG C 4 C NH2 C 5 N 0.153 REMARK 500 PRO D 2 N PRO D 2 CA -0.128 REMARK 500 PRO D 2 CD PRO D 2 N 0.146 REMARK 500 PRO D 2 C LYS D 3 N 0.165 REMARK 500 ARG D 4 C NH2 D 5 N 0.164 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 B 112 -72.75 -89.24 REMARK 500 VAL B 137 -8.55 -145.44 REMARK 500 SER B 181 68.09 62.84 REMARK 500 VAL A 137 -13.06 -145.53 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 SAH B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 701 DBREF 6WH8 B 2 223 UNP Q9BV86 NTM1A_HUMAN 2 223 DBREF 6WH8 A 2 223 UNP Q9BV86 NTM1A_HUMAN 2 223 DBREF 6WH8 C 1 5 PDB 6WH8 6WH8 1 5 DBREF 6WH8 D 1 5 PDB 6WH8 6WH8 1 5 SEQADV 6WH8 MET B -17 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 GLY B -16 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER B -15 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER B -14 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS B -13 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS B -12 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS B -11 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS B -10 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS B -9 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS B -8 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER B -7 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER B -6 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 GLY B -5 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 LEU B -4 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 VAL B -3 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 PRO B -2 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 ARG B -1 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 GLY B 0 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER B 1 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 MET A -17 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 GLY A -16 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER A -15 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER A -14 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS A -13 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS A -12 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS A -11 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS A -10 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS A -9 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 HIS A -8 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER A -7 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER A -6 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 GLY A -5 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 LEU A -4 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 VAL A -3 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 PRO A -2 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 ARG A -1 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 GLY A 0 UNP Q9BV86 EXPRESSION TAG SEQADV 6WH8 SER A 1 UNP Q9BV86 EXPRESSION TAG SEQRES 1 B 241 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 241 LEU VAL PRO ARG GLY SER THR SER GLU VAL ILE GLU ASP SEQRES 3 B 241 GLU LYS GLN PHE TYR SER LYS ALA LYS THR TYR TRP LYS SEQRES 4 B 241 GLN ILE PRO PRO THR VAL ASP GLY MET LEU GLY GLY TYR SEQRES 5 B 241 GLY HIS ILE SER SER ILE ASP ILE ASN SER SER ARG LYS SEQRES 6 B 241 PHE LEU GLN ARG PHE LEU ARG GLU GLY PRO ASN LYS THR SEQRES 7 B 241 GLY THR SER CYS ALA LEU ASP CYS GLY ALA GLY ILE GLY SEQRES 8 B 241 ARG ILE THR LYS ARG LEU LEU LEU PRO LEU PHE ARG GLU SEQRES 9 B 241 VAL ASP MET VAL ASP ILE THR GLU ASP PHE LEU VAL GLN SEQRES 10 B 241 ALA LYS THR TYR LEU GLY GLU GLU GLY LYS ARG VAL ARG SEQRES 11 B 241 ASN TYR PHE CYS CYS GLY LEU GLN ASP PHE THR PRO GLU SEQRES 12 B 241 PRO ASP SER TYR ASP VAL ILE TRP ILE GLN TRP VAL ILE SEQRES 13 B 241 GLY HIS LEU THR ASP GLN HIS LEU ALA GLU PHE LEU ARG SEQRES 14 B 241 ARG CYS LYS GLY SER LEU ARG PRO ASN GLY ILE ILE VAL SEQRES 15 B 241 ILE LYS ASP ASN MET ALA GLN GLU GLY VAL ILE LEU ASP SEQRES 16 B 241 ASP VAL ASP SER SER VAL CYS ARG ASP LEU ASP VAL VAL SEQRES 17 B 241 ARG ARG ILE ILE CYS SER ALA GLY LEU SER LEU LEU ALA SEQRES 18 B 241 GLU GLU ARG GLN GLU ASN LEU PRO ASP GLU ILE TYR HIS SEQRES 19 B 241 VAL TYR SER PHE ALA LEU ARG SEQRES 1 A 241 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 241 LEU VAL PRO ARG GLY SER THR SER GLU VAL ILE GLU ASP SEQRES 3 A 241 GLU LYS GLN PHE TYR SER LYS ALA LYS THR TYR TRP LYS SEQRES 4 A 241 GLN ILE PRO PRO THR VAL ASP GLY MET LEU GLY GLY TYR SEQRES 5 A 241 GLY HIS ILE SER SER ILE ASP ILE ASN SER SER ARG LYS SEQRES 6 A 241 PHE LEU GLN ARG PHE LEU ARG GLU GLY PRO ASN LYS THR SEQRES 7 A 241 GLY THR SER CYS ALA LEU ASP CYS GLY ALA GLY ILE GLY SEQRES 8 A 241 ARG ILE THR LYS ARG LEU LEU LEU PRO LEU PHE ARG GLU SEQRES 9 A 241 VAL ASP MET VAL ASP ILE THR GLU ASP PHE LEU VAL GLN SEQRES 10 A 241 ALA LYS THR TYR LEU GLY GLU GLU GLY LYS ARG VAL ARG SEQRES 11 A 241 ASN TYR PHE CYS CYS GLY LEU GLN ASP PHE THR PRO GLU SEQRES 12 A 241 PRO ASP SER TYR ASP VAL ILE TRP ILE GLN TRP VAL ILE SEQRES 13 A 241 GLY HIS LEU THR ASP GLN HIS LEU ALA GLU PHE LEU ARG SEQRES 14 A 241 ARG CYS LYS GLY SER LEU ARG PRO ASN GLY ILE ILE VAL SEQRES 15 A 241 ILE LYS ASP ASN MET ALA GLN GLU GLY VAL ILE LEU ASP SEQRES 16 A 241 ASP VAL ASP SER SER VAL CYS ARG ASP LEU ASP VAL VAL SEQRES 17 A 241 ARG ARG ILE ILE CYS SER ALA GLY LEU SER LEU LEU ALA SEQRES 18 A 241 GLU GLU ARG GLN GLU ASN LEU PRO ASP GLU ILE TYR HIS SEQRES 19 A 241 VAL TYR SER PHE ALA LEU ARG SEQRES 1 C 5 4HP PRO LYS ARG NH2 SEQRES 1 D 5 4HP PRO LYS ARG NH2 HET 4HP C 1 17 HET NH2 C 5 3 HET 4HP D 1 17 HET NH2 D 5 3 HET SAH B 701 45 HET SAH A 701 45 HETNAM 4HP 4-HYDROXYPHENYLACETATE HETNAM NH2 AMINO GROUP HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 3 4HP 2(C8 H8 O3) FORMUL 3 NH2 2(H2 N) FORMUL 5 SAH 2(C14 H20 N6 O5 S) FORMUL 7 HOH *560(H2 O) HELIX 1 AA1 SER B 1 VAL B 5 5 5 HELIX 2 AA2 ASP B 8 GLN B 22 1 15 HELIX 3 AA3 THR B 26 LEU B 31 1 6 HELIX 4 AA4 TYR B 34 HIS B 36 5 3 HELIX 5 AA5 ILE B 37 ARG B 51 1 15 HELIX 6 AA6 PHE B 52 ARG B 54 5 3 HELIX 7 AA7 GLY B 73 LEU B 79 1 7 HELIX 8 AA8 THR B 93 LEU B 104 1 12 HELIX 9 AA9 GLY B 105 LYS B 109 5 5 HELIX 10 AB1 GLY B 118 PHE B 122 5 5 HELIX 11 AB2 VAL B 137 LEU B 141 5 5 HELIX 12 AB3 THR B 142 SER B 156 1 15 HELIX 13 AB4 ASP B 186 ALA B 197 1 12 HELIX 14 AB5 SER A 1 ILE A 6 1 6 HELIX 15 AB6 ASP A 8 GLN A 22 1 15 HELIX 16 AB7 THR A 26 LEU A 31 1 6 HELIX 17 AB8 TYR A 34 HIS A 36 5 3 HELIX 18 AB9 ILE A 37 GLU A 55 1 19 HELIX 19 AC1 GLY A 73 LEU A 79 1 7 HELIX 20 AC2 THR A 93 LEU A 104 1 12 HELIX 21 AC3 GLY A 105 LYS A 109 5 5 HELIX 22 AC4 GLY A 118 PHE A 122 5 5 HELIX 23 AC5 VAL A 137 LEU A 141 5 5 HELIX 24 AC6 THR A 142 SER A 156 1 15 HELIX 25 AC7 LEU A 187 ALA A 197 1 11 SHEET 1 AA1 7 VAL B 111 CYS B 116 0 SHEET 2 AA1 7 GLU B 86 ASP B 91 1 N MET B 89 O PHE B 115 SHEET 3 AA1 7 CYS B 64 CYS B 68 1 N ALA B 65 O ASP B 88 SHEET 4 AA1 7 TYR B 129 GLN B 135 1 O TRP B 133 N LEU B 66 SHEET 5 AA1 7 LEU B 157 MET B 169 1 O VAL B 164 N ILE B 134 SHEET 6 AA1 7 HIS B 216 ARG B 223 -1 O PHE B 220 N ILE B 165 SHEET 7 AA1 7 SER B 200 ARG B 206 -1 N LEU B 202 O ALA B 221 SHEET 1 AA2 2 VAL B 174 ASP B 177 0 SHEET 2 AA2 2 SER B 182 ARG B 185 -1 O SER B 182 N ASP B 177 SHEET 1 AA3 7 VAL A 111 CYS A 116 0 SHEET 2 AA3 7 GLU A 86 ASP A 91 1 N MET A 89 O PHE A 115 SHEET 3 AA3 7 CYS A 64 CYS A 68 1 N ASP A 67 O ASP A 88 SHEET 4 AA3 7 TYR A 129 GLN A 135 1 O TRP A 133 N LEU A 66 SHEET 5 AA3 7 LEU A 157 ALA A 170 1 O VAL A 164 N ILE A 132 SHEET 6 AA3 7 SER A 182 ASP A 186 1 O ARG A 185 N ALA A 170 SHEET 7 AA3 7 VAL A 174 ASP A 177 -1 N ASP A 177 O SER A 182 SHEET 1 AA4 7 VAL A 111 CYS A 116 0 SHEET 2 AA4 7 GLU A 86 ASP A 91 1 N MET A 89 O PHE A 115 SHEET 3 AA4 7 CYS A 64 CYS A 68 1 N ASP A 67 O ASP A 88 SHEET 4 AA4 7 TYR A 129 GLN A 135 1 O TRP A 133 N LEU A 66 SHEET 5 AA4 7 LEU A 157 ALA A 170 1 O VAL A 164 N ILE A 132 SHEET 6 AA4 7 HIS A 216 ARG A 223 -1 O LEU A 222 N ILE A 163 SHEET 7 AA4 7 SER A 200 ARG A 206 -1 N SER A 200 O ARG A 223 LINK C8 4HP C 1 N PRO C 2 1555 1555 1.45 LINK C ARG C 4 N NH2 C 5 1555 1555 1.49 LINK C8 4HP D 1 N PRO D 2 1555 1555 1.47 LINK C ARG D 4 N NH2 D 5 1555 1555 1.50 CISPEP 1 GLY A 56 PRO A 57 0 -1.78 SITE 1 AC1 20 TRP B 20 MET B 30 GLY B 69 GLY B 71 SITE 2 AC1 20 ILE B 75 ASP B 91 ILE B 92 THR B 93 SITE 3 AC1 20 PHE B 96 CYS B 117 GLY B 118 LEU B 119 SITE 4 AC1 20 GLN B 120 GLN B 135 TRP B 136 VAL B 137 SITE 5 AC1 20 HIS B 140 HOH B 848 HOH B 905 HOH B 940 SITE 1 AC2 18 TRP A 20 MET A 30 GLY A 69 GLY A 71 SITE 2 AC2 18 ILE A 75 ASP A 91 ILE A 92 THR A 93 SITE 3 AC2 18 PHE A 96 GLY A 118 LEU A 119 GLN A 120 SITE 4 AC2 18 GLN A 135 TRP A 136 VAL A 137 HIS A 140 SITE 5 AC2 18 HOH A 862 HOH A 876 CRYST1 106.867 106.867 205.431 90.00 90.00 120.00 P 65 2 2 24 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 0.009357 0.005403 0.000000 0.00000 SCALE2 0.000000 0.010805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004868 0.00000