HEADER HYDROLASE 26-FEB-18 6FTZ TITLE COMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT FACTOR D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADIPSIN,C3 CONVERTASE ACTIVATOR,PROPERDIN FACTOR D; COMPND 5 EC: 3.4.21.46; COMPND 6 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: CFD, DF, PFD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SERINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.OSTERMANN REVDAT 2 17-JAN-24 6FTZ 1 REMARK REVDAT 1 06-JUN-18 6FTZ 0 JRNL AUTH A.VULPETTI,N.OSTERMANN,S.RANDL,T.YOON,A.MAC SWEENEY,F.CUMIN, JRNL AUTH 2 E.LORTHIOIS,S.RUDISSER,P.ERBEL,J.MAIBAUM JRNL TITL DISCOVERY AND DESIGN OF FIRST BENZYLAMINE-BASED LIGANDS JRNL TITL 2 BINDING TO AN UNLOCKED CONFORMATION OF THE COMPLEMENT FACTOR JRNL TITL 3 D. JRNL REF ACS MED CHEM LETT V. 9 490 2018 JRNL REFN ISSN 1948-5875 JRNL PMID 29795765 JRNL DOI 10.1021/ACSMEDCHEMLETT.8B00104 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 23386 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1169 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.16 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2628 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2356 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2497 REMARK 3 BIN R VALUE (WORKING SET) : 0.2334 REMARK 3 BIN FREE R VALUE : 0.2761 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.98 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 131 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1711 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.00060 REMARK 3 B22 (A**2) : -2.71400 REMARK 3 B33 (A**2) : -0.28650 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.92850 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.210 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.111 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.111 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.105 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.108 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1847 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2531 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 634 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 40 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 285 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1847 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 228 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2279 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.54 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.74 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 49.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.090 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.91 REMARK 200 R MERGE FOR SHELL (I) : 0.19700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.530 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: 5FBE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, 100 MM HEPES PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.98750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 244 REMARK 465 ALA A 245 REMARK 465 ALA A 246 REMARK 465 ALA A 247 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 HIS A 25 18.23 59.09 REMARK 500 ASP A 61 17.45 58.30 REMARK 500 ALA A 61B 100.14 -48.01 REMARK 500 ASP A 61C -50.57 130.14 REMARK 500 HIS A 171 -112.06 -101.50 REMARK 500 ARG A 187 -46.85 69.53 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 E7E A 301 DBREF 6FTZ A 16 243 UNP P00746 CFAD_HUMAN 26 253 SEQADV 6FTZ SER A 244 UNP P00746 EXPRESSION TAG SEQADV 6FTZ ALA A 245 UNP P00746 EXPRESSION TAG SEQADV 6FTZ ALA A 246 UNP P00746 EXPRESSION TAG SEQADV 6FTZ ALA A 247 UNP P00746 EXPRESSION TAG SEQRES 1 A 232 ILE LEU GLY GLY ARG GLU ALA GLU ALA HIS ALA ARG PRO SEQRES 2 A 232 TYR MET ALA SER VAL GLN LEU ASN GLY ALA HIS LEU CYS SEQRES 3 A 232 GLY GLY VAL LEU VAL ALA GLU GLN TRP VAL LEU SER ALA SEQRES 4 A 232 ALA HIS CYS LEU GLU ASP ALA ALA ASP GLY LYS VAL GLN SEQRES 5 A 232 VAL LEU LEU GLY ALA HIS SER LEU SER GLN PRO GLU PRO SEQRES 6 A 232 SER LYS ARG LEU TYR ASP VAL LEU ARG ALA VAL PRO HIS SEQRES 7 A 232 PRO ASP SER GLN PRO ASP THR ILE ASP HIS ASP LEU LEU SEQRES 8 A 232 LEU LEU GLN LEU SER GLU LYS ALA THR LEU GLY PRO ALA SEQRES 9 A 232 VAL ARG PRO LEU PRO TRP GLN ARG VAL ASP ARG ASP VAL SEQRES 10 A 232 ALA PRO GLY THR LEU CYS ASP VAL ALA GLY TRP GLY ILE SEQRES 11 A 232 VAL ASN HIS ALA GLY ARG ARG PRO ASP SER LEU GLN HIS SEQRES 12 A 232 VAL LEU LEU PRO VAL LEU ASP ARG ALA THR CYS ASN ARG SEQRES 13 A 232 ARG THR HIS HIS ASP GLY ALA ILE THR GLU ARG LEU MET SEQRES 14 A 232 CYS ALA GLU SER ASN ARG ARG ASP SER CYS LYS GLY ASP SEQRES 15 A 232 SER GLY GLY PRO LEU VAL CYS GLY GLY VAL LEU GLU GLY SEQRES 16 A 232 VAL VAL THR SER GLY SER ARG VAL CYS GLY ASN ARG LYS SEQRES 17 A 232 LYS PRO GLY ILE TYR THR ARG VAL ALA SER TYR ALA ALA SEQRES 18 A 232 TRP ILE ASP SER VAL LEU ALA SER ALA ALA ALA HET E7E A 301 23 HETNAM E7E ~{N}4-[3-(AMINOMETHYL)PHENYL]-1~{H}-INDOLE-2,4- HETNAM 2 E7E DICARBOXAMIDE FORMUL 2 E7E C17 H16 N4 O2 FORMUL 3 HOH *209(H2 O) HELIX 1 AA1 ALA A 55 LEU A 59 5 5 HELIX 2 AA2 ASP A 164 ASN A 169 1 6 HELIX 3 AA3 TYR A 234 ALA A 243 1 10 SHEET 1 AA1 8 ARG A 20 GLU A 21 0 SHEET 2 AA1 8 GLN A 156 LEU A 163 -1 O HIS A 157 N ARG A 20 SHEET 3 AA1 8 LEU A 180 ALA A 183 -1 O CYS A 182 N LEU A 163 SHEET 4 AA1 8 GLY A 226 ARG A 230 -1 O TYR A 228 N MET A 181 SHEET 5 AA1 8 VAL A 208 VAL A 213 -1 N VAL A 212 O THR A 229 SHEET 6 AA1 8 PRO A 198 CYS A 201 -1 N LEU A 199 O GLU A 210 SHEET 7 AA1 8 LEU A 135 GLY A 140 -1 N ASP A 137 O VAL A 200 SHEET 8 AA1 8 GLN A 156 LEU A 163 -1 O LEU A 160 N CYS A 136 SHEET 1 AA2 7 MET A 30 LEU A 35 0 SHEET 2 AA2 7 ALA A 39 LEU A 46 -1 O CYS A 42 N VAL A 33 SHEET 3 AA2 7 TRP A 51 SER A 54 -1 O LEU A 53 N VAL A 45 SHEET 4 AA2 7 LEU A 104 LEU A 108 -1 O LEU A 106 N VAL A 52 SHEET 5 AA2 7 ARG A 81 PRO A 90 -1 N VAL A 89 O LEU A 105 SHEET 6 AA2 7 VAL A 64 LEU A 68 -1 N VAL A 66 O TYR A 83 SHEET 7 AA2 7 MET A 30 LEU A 35 -1 N SER A 32 O LEU A 67 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 2 CYS A 136 CYS A 201 1555 1555 2.04 SSBOND 3 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 4 CYS A 191 CYS A 220 1555 1555 2.03 SITE 1 AC1 12 ASP A 189 SER A 190 CYS A 191 LYS A 192 SITE 2 AC1 12 SER A 195 VAL A 213 THR A 214 SER A 215 SITE 3 AC1 12 SER A 217 ARG A 218 VAL A 219 HOH A 411 CRYST1 55.220 49.975 39.370 90.00 106.07 90.00 P 1 21 1 2 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 0.018109 0.000000 0.005217 0.00000 SCALE2 0.000000 0.020010 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026433 0.00000