HEADER GENE REGULATION 29-AUG-24 7HHK TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF HRP-2 PWWP TITLE 2 DOMAIN IN COMPLEX WITH Z1247413608 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 7HHK 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. 1.94 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20129 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1123 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1462 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2140 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.15000 REMARK 3 B22 (A**2) : -0.78000 REMARK 3 B33 (A**2) : -0.37000 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): 0.188 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.181 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.179 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.826 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2310 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3147 ; 1.816 ; 1.826 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 266 ; 8.315 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 6 ; 5.934 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 302 ;14.293 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 295 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1871 ; 0.009 ; 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): 1073 ; 4.567 ; 4.283 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1345 ; 6.087 ; 7.647 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1237 ; 5.515 ; 4.510 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): 3640 ;11.004 ;66.060 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 7HHK 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_1001407482. 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 : 21315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 79.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 2.40000 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 20.67500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.14000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.14000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.67500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.01000 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 ALA C 29 REMARK 465 ASP C 30 REMARK 465 GLY C 31 REMARK 465 ALA C 32 REMARK 465 VAL C 33 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 TYR A 18 CD1 REMARK 470 LYS A 70 CE NZ 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 LYS B 65 CD CE NZ REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 GLU B 79 CD OE1 OE2 REMARK 470 GLN B 85 CG CD OE1 NE2 REMARK 470 LYS C 6 CE NZ REMARK 470 ASP C 27 CG OD1 OD2 REMARK 470 ILE C 28 CG1 CG2 CD1 REMARK 470 LYS C 34 CG CD CE NZ 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 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 A 232 O HOH C 206 1.71 REMARK 500 O HOH B 250 O HOH B 271 1.88 REMARK 500 O HOH A 233 O HOH A 289 1.94 REMARK 500 OD1 ASP C 26 O HOH C 201 1.99 REMARK 500 O HOH C 253 O HOH C 260 2.05 REMARK 500 O HOH C 205 O HOH C 258 2.05 REMARK 500 O PRO A 37 O HOH A 201 2.07 REMARK 500 O2 SO4 A 105 O HOH A 202 2.08 REMARK 500 OD1 ASP C 9 O HOH C 202 2.12 REMARK 500 O HOH A 208 O HOH A 299 2.14 REMARK 500 O ASP B 66 NZ LYS B 70 2.17 REMARK 500 OE1 GLN A 85 O HOH A 203 2.17 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 B 268 O HOH C 238 4435 2.01 REMARK 500 O HOH A 219 O HOH A 263 4545 2.06 REMARK 500 NH2 ARG C 74 O3 LPU A 104 4535 2.18 REMARK 500 O HOH A 303 O HOH C 209 4435 2.18 REMARK 500 O HOH A 269 O HOH A 309 4545 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 TYR A 18 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 LEU A 53 CB - CG - CD1 ANGL. DEV. = -11.6 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 64.37 -151.72 REMARK 500 ASN B 38 -10.79 77.64 REMARK 500 ASN B 87 54.61 -162.97 REMARK 500 ASN C 87 50.87 -166.02 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 VAL B 11 PHE B 12 148.43 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 A 316 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 317 DISTANCE = 8.23 ANGSTROMS DBREF 7HHK A 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 DBREF 7HHK B 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 DBREF 7HHK C 1 93 UNP Q7Z4V5 HDGR2_HUMAN 1 93 SEQADV 7HHK GLY A 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 7HHK SER A 64 UNP Q7Z4V5 CYS 64 ENGINEERED MUTATION SEQADV 7HHK GLY B 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 7HHK SER B 64 UNP Q7Z4V5 CYS 64 ENGINEERED MUTATION SEQADV 7HHK GLY C 0 UNP Q7Z4V5 EXPRESSION TAG SEQADV 7HHK 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 LPU A 104 11 HET SO4 A 105 5 HET SO4 B 101 5 HET SO4 B 102 5 HET LPU B 103 11 HET SO4 C 101 5 HET LPU C 102 11 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM LPU 1-(METHANESULFONYL)PIPERIDIN-4-OL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 SO4 6(O4 S 2-) FORMUL 6 EDO C2 H6 O2 FORMUL 7 LPU 3(C6 H13 N O3 S) FORMUL 14 HOH *263(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 ALA A 13 O TRP A 21 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 ALA C 13 O TRP C 21 SHEET 5 AA3 5 LEU C 58 PRO C 60 -1 O PHE C 59 N PHE C 12 CRYST1 41.350 42.020 158.280 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 0.024184 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023798 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006318 0.00000