HEADER GENE REGULATION 29-AUG-24 7HHJ TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF HRP-2 PWWP TITLE 2 DOMAIN IN COMPLEX WITH Z100642432 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: HDGF-RELATED PROTEIN 2,HRP-2,HEPATOMA-DERIVED GROWTH FACTOR COMPND 5 2,HDGF-2; COMPND 6 ENGINEERED: YES; COMPND 7 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: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS INHIBITOR, FRAGMENT SCREENING, EPIGENETIC READER, METHYLLYSINE, PWWP, KEYWDS 2 DIAMOND LIGHT SOURCE, I04-1, PANDDA, XCHEM, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR T.VANTIEGHEM,E.OSIPOV,D.FEARON,A.DOUANGAMATH,F.VON DELFT,S.STRELKOV REVDAT 1 06-NOV-24 7HHJ 0 JRNL AUTH T.VANTIEGHEM,N.A.ASLAM,E.M.OSIPOV,M.AKELE,S.VAN BELLE, JRNL AUTH 2 S.BEELEN,M.DREXLER,T.PAULOVCAKOVA,V.LUX,D.FEARON, JRNL AUTH 3 A.DOUANGAMATH,F.VON DELFT,F.CHRIST,V.VEVERKA,P.VERWILST, JRNL AUTH 4 A.VAN AERSCHOT,Z.DEBYSER,S.V.STRELKOV JRNL TITL RATIONAL FRAGMENT-BASED DESIGN OF COMPOUNDS TARGETING THE JRNL TITL 2 PWWP DOMAIN OF THE HRP FAMILY. JRNL REF EUR.J.MED.CHEM. V. 280 16960 2024 JRNL REFN ISSN 0223-5234 JRNL PMID 39461037 JRNL DOI 10.1016/J.EJMECH.2024.116960 REMARK 2 REMARK 2 RESOLUTION. 1.78 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25867 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1399 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) : 1.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1892 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3710 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2139 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -1.05000 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): 0.141 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.107 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2292 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3116 ; 1.578 ; 1.836 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 265 ; 8.137 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 6 ; 6.402 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 315 ;13.898 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 285 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1910 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1070 ; 3.663 ; 4.076 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1332 ; 5.149 ; 7.281 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1222 ; 4.432 ; 4.360 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): 3632 ;10.094 ;59.200 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7HHJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1001407481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918076 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27335 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 52.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 2.64200 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG MME 2000; 0.15 M AMMONIUM REMARK 280 SULFATE; 0.1 M SODIUM ACETATE PH 4.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K 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 20.70000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.70000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.99000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 0 REMARK 465 GLY B 0 REMARK 465 ALA B 29 REMARK 465 ASP B 30 REMARK 465 GLY B 31 REMARK 465 ALA B 32 REMARK 465 GLY C 0 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 HIS C 3 REMARK 465 ASP C 30 REMARK 465 GLY C 31 REMARK 465 ALA C 32 REMARK 465 VAL C 33 REMARK 465 LYS C 34 REMARK 465 SER C 93 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 LYS A 73 CD CE NZ REMARK 470 LYS A 75 NZ REMARK 470 LYS B 16 CE NZ REMARK 470 ILE B 28 CG1 CG2 CD1 REMARK 470 LYS B 34 CG CD CE NZ REMARK 470 GLN B 85 CG CD OE1 NE2 REMARK 470 LYS C 6 CG CD CE NZ REMARK 470 ASP C 27 CG OD1 OD2 REMARK 470 ILE C 28 CG1 CG2 CD1 REMARK 470 LYS C 56 CG CD CE NZ REMARK 470 LYS C 63 CG CD CE NZ REMARK 470 LYS C 70 NZ REMARK 470 LYS C 73 CG CD CE NZ REMARK 470 LYS C 75 CE NZ 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 O HOH B 244 O HOH B 276 1.74 REMARK 500 O HOH A 281 O HOH A 290 1.78 REMARK 500 O HOH A 226 O HOH C 205 1.82 REMARK 500 O2 SO4 A 104 O HOH A 201 1.91 REMARK 500 O HOH C 216 O HOH C 255 1.98 REMARK 500 O HOH C 206 O HOH C 236 1.99 REMARK 500 O HOH B 241 O HOH B 283 2.03 REMARK 500 OD1 ASP C 26 O HOH C 201 2.05 REMARK 500 O HOH C 256 O HOH C 265 2.06 REMARK 500 OD1 ASP A 62 O HOH A 202 2.08 REMARK 500 O HOH B 212 O HOH B 273 2.13 REMARK 500 O HOH B 261 O HOH B 276 2.14 REMARK 500 O4 SO4 A 104 O HOH A 203 2.14 REMARK 500 O HOH B 210 O HOH B 231 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 237 O HOH C 229 4435 2.19 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 MET B 15 CG - SD - CE ANGL. DEV. = 10.4 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 ASN A 87 66.78 -154.23 REMARK 500 ASN B 38 -11.24 80.29 REMARK 500 PRO B 60 127.52 -37.62 REMARK 500 ASN B 87 62.08 -157.53 REMARK 500 ASN C 87 57.12 -159.38 REMARK 500 ALA C 90 -173.26 -68.33 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 C 74 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 7HHJ A 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 DBREF 7HHJ B 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 DBREF 7HHJ C 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 SEQADV 7HHJ GLY A 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 7HHJ SER A 64 UNP Q7Z4V5 CYS 64 ENGINEERED MUTATION SEQADV 7HHJ GLY B 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 7HHJ SER B 64 UNP Q7Z4V5 CYS 64 ENGINEERED MUTATION SEQADV 7HHJ GLY C 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 7HHJ SER C 64 UNP Q7Z4V5 CYS 64 ENGINEERED MUTATION SEQRES 1 A 94 GLY MET PRO HIS ALA PHE LYS PRO GLY ASP LEU VAL PHE SEQRES 2 A 94 ALA LYS MET LYS GLY TYR PRO HIS TRP PRO ALA ARG ILE SEQRES 3 A 94 ASP ASP ILE ALA ASP GLY ALA VAL LYS PRO PRO PRO ASN SEQRES 4 A 94 LYS TYR PRO ILE PHE PHE PHE GLY THR HIS GLU THR ALA SEQRES 5 A 94 PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR ASP LYS SER SEQRES 6 A 94 LYS ASP LYS TYR GLY LYS PRO ASN LYS ARG LYS GLY PHE SEQRES 7 A 94 ASN GLU GLY LEU TRP GLU ILE GLN ASN ASN PRO HIS ALA SEQRES 8 A 94 SER TYR SER SEQRES 1 B 94 GLY MET PRO HIS ALA PHE LYS PRO GLY ASP LEU VAL PHE SEQRES 2 B 94 ALA LYS MET LYS GLY TYR PRO HIS TRP PRO ALA ARG ILE SEQRES 3 B 94 ASP ASP ILE ALA ASP GLY ALA VAL LYS PRO PRO PRO ASN SEQRES 4 B 94 LYS TYR PRO ILE PHE PHE PHE GLY THR HIS GLU THR ALA SEQRES 5 B 94 PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR ASP LYS SER SEQRES 6 B 94 LYS ASP LYS TYR GLY LYS PRO ASN LYS ARG LYS GLY PHE SEQRES 7 B 94 ASN GLU GLY LEU TRP GLU ILE GLN ASN ASN PRO HIS ALA SEQRES 8 B 94 SER TYR SER SEQRES 1 C 94 GLY MET PRO HIS ALA PHE LYS PRO GLY ASP LEU VAL PHE SEQRES 2 C 94 ALA LYS MET LYS GLY TYR PRO HIS TRP PRO ALA ARG ILE SEQRES 3 C 94 ASP ASP ILE ALA ASP GLY ALA VAL LYS PRO PRO PRO ASN SEQRES 4 C 94 LYS TYR PRO ILE PHE PHE PHE GLY THR HIS GLU THR ALA SEQRES 5 C 94 PHE LEU GLY PRO LYS ASP LEU PHE PRO TYR ASP LYS SER SEQRES 6 C 94 LYS ASP LYS TYR GLY LYS PRO ASN LYS ARG LYS GLY PHE SEQRES 7 C 94 ASN GLU GLY LEU TRP GLU ILE GLN ASN ASN PRO HIS ALA SEQRES 8 C 94 SER TYR SER HET SO4 A 101 5 HET SO4 A 102 5 HET EDO A 103 4 HET SO4 A 104 5 HET SO4 B 101 5 HET SO4 B 102 5 HET WJ7 B 103 13 HET EDO C 101 4 HET SO4 C 102 5 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM WJ7 2-BROMO-4-FLUORO-N,N-DIMETHYLBENZAMIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 SO4 6(O4 S 2-) FORMUL 6 EDO 2(C2 H6 O2) FORMUL 10 WJ7 C9 H9 BR F N O FORMUL 13 HOH *268(H2 O) HELIX 1 AA1 GLY A 54 LYS A 56 5 3 HELIX 2 AA2 TYR A 61 GLY A 69 1 9 HELIX 3 AA3 GLY A 76 ASN A 87 1 12 HELIX 4 AA4 GLY B 54 LYS B 56 5 3 HELIX 5 AA5 TYR B 61 GLY B 69 1 9 HELIX 6 AA6 GLY B 76 ASN B 87 1 12 HELIX 7 AA7 GLY C 54 LYS C 56 5 3 HELIX 8 AA8 TYR C 61 GLY C 69 1 9 HELIX 9 AA9 GLY C 76 ASN C 87 1 12 SHEET 1 AA1 5 THR A 50 LEU A 53 0 SHEET 2 AA1 5 TYR A 40 PHE A 44 -1 N ILE A 42 O ALA A 51 SHEET 3 AA1 5 TRP A 21 ILE A 25 -1 N ARG A 24 O PHE A 43 SHEET 4 AA1 5 LEU A 10 ALA A 13 -1 N VAL A 11 O ALA A 23 SHEET 5 AA1 5 LEU A 58 PRO A 60 -1 O PHE A 59 N PHE A 12 SHEET 1 AA2 5 THR B 50 LEU B 53 0 SHEET 2 AA2 5 TYR B 40 PHE B 44 -1 N ILE B 42 O ALA B 51 SHEET 3 AA2 5 TRP B 21 ILE B 25 -1 N ARG B 24 O PHE B 43 SHEET 4 AA2 5 LEU B 10 ALA B 13 -1 N ALA B 13 O TRP B 21 SHEET 5 AA2 5 LEU B 58 PRO B 60 -1 O PHE B 59 N PHE B 12 SHEET 1 AA3 5 THR C 50 LEU C 53 0 SHEET 2 AA3 5 TYR C 40 PHE C 44 -1 N TYR C 40 O LEU C 53 SHEET 3 AA3 5 TRP C 21 ILE C 25 -1 N ARG C 24 O PHE C 43 SHEET 4 AA3 5 LEU C 10 ALA C 13 -1 N VAL C 11 O ALA C 23 SHEET 5 AA3 5 LEU C 58 PRO C 60 -1 O PHE C 59 N PHE C 12 CRYST1 41.400 41.980 157.860 90.00 90.00 90.00 P 21 21 21 12 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 0.024155 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006335 0.00000