HEADER IMMUNE SYSTEM 09-JUL-13 4LLW TITLE CRYSTAL STRUCTURE OF PERTUZUMAB CLAMBDA FAB WITH VARIABLE DOMAIN TITLE 2 REDESIGN (VRD2) AT 1.95A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUTATED PERTUZUMAB FAB HEAVY CHAIN; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN CLAMBDA; COMPND 7 CHAIN: B, D; 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 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS FAB, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.PUSTILNIK,S.M.LEWIS,X.WU,A.SERENO,F.HUANG,G.GUNTAS,A.LEAVER-FAY, AUTHOR 2 E.M.SMITH,C.HO,C.HANSEN-ESTRUCH,A.K.CHAMBERLAIN,S.M.TRUHLAR, AUTHOR 3 B.KUHLMAN,S.J.DEMAREST,S.ATWELL REVDAT 6 06-NOV-24 4LLW 1 REMARK REVDAT 5 26-JUN-19 4LLW 1 COMPND SOURCE REMARK DBREF REVDAT 5 2 1 SEQRES REVDAT 4 15-NOV-17 4LLW 1 REMARK REVDAT 3 26-MAR-14 4LLW 1 JRNL REVDAT 2 12-FEB-14 4LLW 1 JRNL REVDAT 1 29-JAN-14 4LLW 0 JRNL AUTH S.M.LEWIS,X.WU,A.PUSTILNIK,A.SERENO,F.HUANG,H.L.RICK, JRNL AUTH 2 G.GUNTAS,A.LEAVER-FAY,E.M.SMITH,C.HO,C.HANSEN-ESTRUCH, JRNL AUTH 3 A.K.CHAMBERLAIN,S.M.TRUHLAR,E.M.CONNER,S.ATWELL,B.KUHLMAN, JRNL AUTH 4 S.J.DEMAREST JRNL TITL GENERATION OF BISPECIFIC IGG ANTIBODIES BY STRUCTURE-BASED JRNL TITL 2 DESIGN OF AN ORTHOGONAL FAB INTERFACE. JRNL REF NAT.BIOTECHNOL. V. 32 191 2014 JRNL REFN ISSN 1087-0156 JRNL PMID 24463572 JRNL DOI 10.1038/NBT.2797 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 76928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3843 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6352 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 360 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4LLW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .97931 REMARK 200 MONOCHROMATOR : DIAMOND (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76929 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 35.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.71900 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 (%): 35.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8K + 200MM AMMONIUM SULFATE , REMARK 280 PH 7.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 35.58950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -125.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 133 REMARK 465 SER A 134 REMARK 465 LYS A 135 REMARK 465 SER A 136 REMARK 465 THR A 137 REMARK 465 SER A 138 REMARK 465 GLY A 139 REMARK 465 SER A 221 REMARK 465 CYS A 222 REMARK 465 ASP A 223 REMARK 465 LYS A 224 REMARK 465 THR A 225 REMARK 465 HIS A 226 REMARK 465 GLN B 168 REMARK 465 SER B 169 REMARK 465 ASN B 170 REMARK 465 GLU B 211 REMARK 465 CYS B 212 REMARK 465 SER C 134 REMARK 465 LYS C 135 REMARK 465 SER C 136 REMARK 465 THR C 137 REMARK 465 SER C 138 REMARK 465 GLY C 139 REMARK 465 SER C 221 REMARK 465 CYS C 222 REMARK 465 ASP C 223 REMARK 465 LYS C 224 REMARK 465 THR C 225 REMARK 465 HIS C 226 REMARK 465 THR D 210 REMARK 465 GLU D 211 REMARK 465 CYS D 212 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 GLU A 1 CG CD OE1 OE2 REMARK 470 ARG A 63 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 65 CG CD CE NZ REMARK 470 LEU A 100 CG CD1 CD2 REMARK 470 ASP B 1 CG OD1 OD2 REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 LYS B 130 CG CD CE NZ REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 GLU B 184 CD OE1 OE2 REMARK 470 LYS B 187 CG CD CE NZ REMARK 470 LYS C 65 CD CE NZ REMARK 470 THR C 197 OG1 CG2 REMARK 470 LYS C 220 CG CD CE NZ REMARK 470 ASP D 1 CG OD1 OD2 REMARK 470 LYS D 107 CE NZ REMARK 470 GLN D 109 CD OE1 NE2 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 CYS A 146 CA - CB - SG ANGL. DEV. = 8.7 DEGREES REMARK 500 LEU A 184 CA - CB - CG ANGL. DEV. = 16.8 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 PHE A 104 55.07 -90.46 REMARK 500 SER A 162 18.51 59.91 REMARK 500 HIS A 206 79.94 -111.62 REMARK 500 SER B 30 -127.86 62.24 REMARK 500 ALA B 51 -29.96 69.19 REMARK 500 THR B 56 131.50 -39.17 REMARK 500 ALA B 84 -173.55 178.46 REMARK 500 PRO B 95 43.05 -103.76 REMARK 500 ALA B 131 139.23 -172.85 REMARK 500 ASP B 152 -122.33 52.10 REMARK 500 GLU B 199 -115.78 53.85 REMARK 500 PHE C 104 56.60 -92.65 REMARK 500 PRO C 173 161.47 -49.91 REMARK 500 SER D 30 -130.76 59.37 REMARK 500 ALA D 51 -41.51 68.95 REMARK 500 ALA D 84 -179.94 175.90 REMARK 500 ASP D 152 -106.84 48.42 REMARK 500 GLU D 199 -129.23 55.82 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 SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LLU RELATED DB: PDB REMARK 900 PARENT PERTUZUMAB CLAMBDA REMARK 900 RELATED ID: 4LLD RELATED DB: PDB REMARK 900 CH1-CL REMARK 900 RELATED ID: 4LLM RELATED DB: PDB REMARK 900 RELATED ID: 4LLQ RELATED DB: PDB REMARK 900 RELATED ID: 4LLY RELATED DB: PDB DBREF 4LLW A 1 226 PDB 4LLW 4LLW 1 226 DBREF 4LLW B 1 212 PDB 4LLW 4LLW 1 212 DBREF 4LLW C 1 226 PDB 4LLW 4LLW 1 226 DBREF 4LLW D 1 212 PDB 4LLW 4LLW 1 212 SEQRES 1 A 226 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 226 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 226 PHE THR PHE THR ASP TYR THR MET ASP TRP VAL ARG TYR SEQRES 4 A 226 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ASP VAL ASN SEQRES 5 A 226 PRO ASN SER GLY GLY SER ILE TYR ASN GLN ARG PHE LYS SEQRES 6 A 226 GLY ARG PHE THR LEU SER VAL ASP ARG SER LYS ASN THR SEQRES 7 A 226 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 A 226 ALA VAL TYR TYR CYS ALA ARG ASN LEU GLY PRO SER PHE SEQRES 9 A 226 TYR PHE ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 A 226 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 A 226 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 A 226 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 A 226 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 A 226 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 A 226 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 A 226 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 A 226 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER SEQRES 18 A 226 CYS ASP LYS THR HIS SEQRES 1 B 212 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 B 212 SER VAL GLY ASP ARG VAL THR ILE THR CYS LYS ALA SER SEQRES 3 B 212 GLN ASP VAL SER ILE GLY VAL ALA TRP TYR GLN ARG LYS SEQRES 4 B 212 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR SER ALA SER SEQRES 5 B 212 TYR ARG TYR THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 212 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 B 212 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 B 212 TYR ILE TYR PRO TYR THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 B 212 GLU ILE LYS GLY GLN PRO LYS ALA ALA PRO SER VAL THR SEQRES 10 B 212 LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA ASN LYS SEQRES 11 B 212 ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR PRO GLY SEQRES 12 B 212 ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER PRO VAL SEQRES 13 B 212 LYS ALA GLY VAL GLU THR THR THR PRO SER LYS GLN SER SEQRES 14 B 212 ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER LEU THR SEQRES 15 B 212 PRO GLU GLN TRP LYS SER HIS ARG SER TYR SER CYS GLN SEQRES 16 B 212 VAL THR HIS GLU GLY SER THR VAL GLU LYS THR VAL ALA SEQRES 17 B 212 PRO THR GLU CYS SEQRES 1 C 226 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 226 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 226 PHE THR PHE THR ASP TYR THR MET ASP TRP VAL ARG TYR SEQRES 4 C 226 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ASP VAL ASN SEQRES 5 C 226 PRO ASN SER GLY GLY SER ILE TYR ASN GLN ARG PHE LYS SEQRES 6 C 226 GLY ARG PHE THR LEU SER VAL ASP ARG SER LYS ASN THR SEQRES 7 C 226 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 C 226 ALA VAL TYR TYR CYS ALA ARG ASN LEU GLY PRO SER PHE SEQRES 9 C 226 TYR PHE ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 C 226 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 C 226 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 C 226 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 C 226 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 C 226 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 C 226 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 C 226 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 C 226 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER SEQRES 18 C 226 CYS ASP LYS THR HIS SEQRES 1 D 212 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 D 212 SER VAL GLY ASP ARG VAL THR ILE THR CYS LYS ALA SER SEQRES 3 D 212 GLN ASP VAL SER ILE GLY VAL ALA TRP TYR GLN ARG LYS SEQRES 4 D 212 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR SER ALA SER SEQRES 5 D 212 TYR ARG TYR THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 D 212 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 D 212 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 D 212 TYR ILE TYR PRO TYR THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 D 212 GLU ILE LYS GLY GLN PRO LYS ALA ALA PRO SER VAL THR SEQRES 10 D 212 LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA ASN LYS SEQRES 11 D 212 ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR PRO GLY SEQRES 12 D 212 ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER PRO VAL SEQRES 13 D 212 LYS ALA GLY VAL GLU THR THR THR PRO SER LYS GLN SER SEQRES 14 D 212 ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER LEU THR SEQRES 15 D 212 PRO GLU GLN TRP LYS SER HIS ARG SER TYR SER CYS GLN SEQRES 16 D 212 VAL THR HIS GLU GLY SER THR VAL GLU LYS THR VAL ALA SEQRES 17 D 212 PRO THR GLU CYS HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HET SO4 B 301 5 HET SO4 C 501 5 HET SO4 C 502 5 HET SO4 C 503 5 HET SO4 C 504 5 HET SO4 C 505 5 HET SO4 D 301 5 HET SO4 D 302 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 11(O4 S 2-) FORMUL 16 HOH *360(H2 O) HELIX 1 1 THR A 28 TYR A 32 5 5 HELIX 2 2 ARG A 74 LYS A 76 5 3 HELIX 3 3 ARG A 87 THR A 91 5 5 HELIX 4 4 SER A 162 ALA A 164 5 3 HELIX 5 5 SER A 193 LEU A 195 5 3 HELIX 6 6 LYS A 207 ASN A 210 5 4 HELIX 7 7 GLN B 79 PHE B 83 5 5 HELIX 8 8 SER B 122 ALA B 128 1 7 HELIX 9 9 THR B 182 HIS B 189 1 8 HELIX 10 10 THR C 28 TYR C 32 5 5 HELIX 11 11 GLN C 62 LYS C 65 5 4 HELIX 12 12 ARG C 74 LYS C 76 5 3 HELIX 13 13 ARG C 87 THR C 91 5 5 HELIX 14 14 SER C 162 ALA C 164 5 3 HELIX 15 15 SER C 193 GLN C 198 1 6 HELIX 16 16 LYS C 207 ASN C 210 5 4 HELIX 17 17 GLN D 79 PHE D 83 5 5 HELIX 18 18 SER D 122 ALA D 128 1 7 HELIX 19 19 THR D 182 HIS D 189 1 8 SHEET 1 A 4 GLN A 3 SER A 7 0 SHEET 2 A 4 LEU A 18 SER A 25 -1 O ALA A 23 N VAL A 5 SHEET 3 A 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 A 4 PHE A 68 ASP A 73 -1 N THR A 69 O GLN A 82 SHEET 1 B 6 GLY A 10 VAL A 12 0 SHEET 2 B 6 THR A 113 VAL A 117 1 O THR A 116 N GLY A 10 SHEET 3 B 6 ALA A 92 ASN A 99 -1 N TYR A 94 O THR A 113 SHEET 4 B 6 MET A 34 ALA A 40 -1 N TYR A 39 O VAL A 93 SHEET 5 B 6 GLY A 44 ASN A 52 -1 O VAL A 48 N TRP A 36 SHEET 6 B 6 GLY A 57 TYR A 60 -1 O GLY A 57 N ASN A 52 SHEET 1 C 4 GLY A 10 VAL A 12 0 SHEET 2 C 4 THR A 113 VAL A 117 1 O THR A 116 N GLY A 10 SHEET 3 C 4 ALA A 92 ASN A 99 -1 N TYR A 94 O THR A 113 SHEET 4 C 4 PHE A 106 TRP A 109 -1 O TYR A 108 N ARG A 98 SHEET 1 D 4 SER A 126 LEU A 130 0 SHEET 2 D 4 THR A 141 TYR A 151 -1 O LYS A 149 N SER A 126 SHEET 3 D 4 TYR A 182 PRO A 191 -1 O LEU A 184 N VAL A 148 SHEET 4 D 4 VAL A 169 THR A 171 -1 N HIS A 170 O VAL A 187 SHEET 1 E 4 SER A 126 LEU A 130 0 SHEET 2 E 4 THR A 141 TYR A 151 -1 O LYS A 149 N SER A 126 SHEET 3 E 4 TYR A 182 PRO A 191 -1 O LEU A 184 N VAL A 148 SHEET 4 E 4 VAL A 175 LEU A 176 -1 N VAL A 175 O SER A 183 SHEET 1 F 3 THR A 157 TRP A 160 0 SHEET 2 F 3 TYR A 200 HIS A 206 -1 O ASN A 205 N THR A 157 SHEET 3 F 3 THR A 211 VAL A 217 -1 O THR A 211 N HIS A 206 SHEET 1 G 4 MET B 4 SER B 7 0 SHEET 2 G 4 VAL B 19 ALA B 25 -1 O LYS B 24 N THR B 5 SHEET 3 G 4 ASP B 70 ILE B 75 -1 O LEU B 73 N ILE B 21 SHEET 4 G 4 PHE B 62 SER B 67 -1 N SER B 65 O THR B 72 SHEET 1 H 6 SER B 10 ALA B 13 0 SHEET 2 H 6 THR B 102 ILE B 106 1 O GLU B 105 N LEU B 11 SHEET 3 H 6 ALA B 84 GLN B 90 -1 N ALA B 84 O VAL B 104 SHEET 4 H 6 VAL B 33 ARG B 38 -1 N ARG B 38 O THR B 85 SHEET 5 H 6 LYS B 45 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 H 6 TYR B 53 ARG B 54 -1 O TYR B 53 N TYR B 49 SHEET 1 I 4 SER B 115 PHE B 119 0 SHEET 2 I 4 THR B 132 ASP B 139 -1 O LEU B 136 N THR B 117 SHEET 3 I 4 TYR B 173 SER B 180 -1 O LEU B 179 N LEU B 133 SHEET 4 I 4 THR B 164 PRO B 165 -1 N THR B 164 O ALA B 174 SHEET 1 J 4 SER B 154 GLU B 161 0 SHEET 2 J 4 VAL B 145 ALA B 151 -1 N VAL B 145 O GLU B 161 SHEET 3 J 4 TYR B 192 HIS B 198 -1 O GLN B 195 N ALA B 148 SHEET 4 J 4 SER B 201 VAL B 207 -1 O VAL B 203 N VAL B 196 SHEET 1 K 4 GLN C 3 SER C 7 0 SHEET 2 K 4 LEU C 18 SER C 25 -1 O ALA C 23 N VAL C 5 SHEET 3 K 4 THR C 78 MET C 83 -1 O LEU C 81 N LEU C 20 SHEET 4 K 4 PHE C 68 ASP C 73 -1 N THR C 69 O GLN C 82 SHEET 1 L 6 LEU C 11 VAL C 12 0 SHEET 2 L 6 THR C 113 VAL C 117 1 O THR C 116 N VAL C 12 SHEET 3 L 6 ALA C 92 LEU C 100 -1 N ALA C 92 O VAL C 115 SHEET 4 L 6 MET C 34 ALA C 40 -1 N VAL C 37 O TYR C 95 SHEET 5 L 6 GLY C 44 VAL C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 L 6 SER C 58 TYR C 60 -1 O ILE C 59 N ASP C 50 SHEET 1 M 4 LEU C 11 VAL C 12 0 SHEET 2 M 4 THR C 113 VAL C 117 1 O THR C 116 N VAL C 12 SHEET 3 M 4 ALA C 92 LEU C 100 -1 N ALA C 92 O VAL C 115 SHEET 4 M 4 SER C 103 TRP C 109 -1 O TYR C 108 N ARG C 98 SHEET 1 N 4 SER C 126 LEU C 130 0 SHEET 2 N 4 THR C 141 TYR C 151 -1 O LYS C 149 N SER C 126 SHEET 3 N 4 TYR C 182 PRO C 191 -1 O LEU C 184 N VAL C 148 SHEET 4 N 4 VAL C 169 THR C 171 -1 N HIS C 170 O VAL C 187 SHEET 1 O 4 SER C 126 LEU C 130 0 SHEET 2 O 4 THR C 141 TYR C 151 -1 O LYS C 149 N SER C 126 SHEET 3 O 4 TYR C 182 PRO C 191 -1 O LEU C 184 N VAL C 148 SHEET 4 O 4 VAL C 175 LEU C 176 -1 N VAL C 175 O SER C 183 SHEET 1 P 3 THR C 157 TRP C 160 0 SHEET 2 P 3 ILE C 201 HIS C 206 -1 O ASN C 205 N THR C 157 SHEET 3 P 3 THR C 211 LYS C 216 -1 O VAL C 213 N VAL C 204 SHEET 1 Q 4 MET D 4 SER D 7 0 SHEET 2 Q 4 VAL D 19 ALA D 25 -1 O LYS D 24 N THR D 5 SHEET 3 Q 4 ASP D 70 ILE D 75 -1 O LEU D 73 N ILE D 21 SHEET 4 Q 4 PHE D 62 SER D 67 -1 N SER D 65 O THR D 72 SHEET 1 R 6 SER D 10 ALA D 13 0 SHEET 2 R 6 THR D 102 ILE D 106 1 O GLU D 105 N LEU D 11 SHEET 3 R 6 ALA D 84 GLN D 90 -1 N ALA D 84 O VAL D 104 SHEET 4 R 6 VAL D 33 ARG D 38 -1 N ARG D 38 O THR D 85 SHEET 5 R 6 LYS D 45 TYR D 49 -1 O LEU D 47 N TRP D 35 SHEET 6 R 6 TYR D 53 ARG D 54 -1 O TYR D 53 N TYR D 49 SHEET 1 S 4 SER D 10 ALA D 13 0 SHEET 2 S 4 THR D 102 ILE D 106 1 O GLU D 105 N LEU D 11 SHEET 3 S 4 ALA D 84 GLN D 90 -1 N ALA D 84 O VAL D 104 SHEET 4 S 4 THR D 97 PHE D 98 -1 O THR D 97 N GLN D 90 SHEET 1 T 4 SER D 115 PHE D 119 0 SHEET 2 T 4 ALA D 131 PHE D 140 -1 O LEU D 136 N THR D 117 SHEET 3 T 4 TYR D 173 LEU D 181 -1 O ALA D 175 N ILE D 137 SHEET 4 T 4 VAL D 160 THR D 162 -1 N GLU D 161 O TYR D 178 SHEET 1 U 4 SER D 115 PHE D 119 0 SHEET 2 U 4 ALA D 131 PHE D 140 -1 O LEU D 136 N THR D 117 SHEET 3 U 4 TYR D 173 LEU D 181 -1 O ALA D 175 N ILE D 137 SHEET 4 U 4 SER D 166 LYS D 167 -1 N SER D 166 O ALA D 174 SHEET 1 V 4 SER D 154 PRO D 155 0 SHEET 2 V 4 THR D 146 ALA D 151 -1 N ALA D 151 O SER D 154 SHEET 3 V 4 TYR D 192 HIS D 198 -1 O GLN D 195 N ALA D 148 SHEET 4 V 4 SER D 201 VAL D 207 -1 O VAL D 203 N VAL D 196 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.10 SSBOND 2 CYS A 146 CYS A 202 1555 1555 2.03 SSBOND 3 CYS B 23 CYS B 88 1555 1555 2.06 SSBOND 4 CYS B 135 CYS B 194 1555 1555 2.03 SSBOND 5 CYS C 22 CYS C 96 1555 1555 2.10 SSBOND 6 CYS C 146 CYS C 202 1555 1555 2.05 SSBOND 7 CYS D 23 CYS D 88 1555 1555 2.08 SSBOND 8 CYS D 135 CYS D 194 1555 1555 2.03 CISPEP 1 PHE A 152 PRO A 153 0 -7.16 CISPEP 2 GLU A 154 PRO A 155 0 -0.96 CISPEP 3 SER B 7 PRO B 8 0 2.06 CISPEP 4 TYR B 94 PRO B 95 0 10.75 CISPEP 5 LYS C 43 GLY C 44 0 -10.32 CISPEP 6 PHE C 152 PRO C 153 0 -4.09 CISPEP 7 GLU C 154 PRO C 155 0 -3.20 CISPEP 8 SER D 7 PRO D 8 0 -4.47 CISPEP 9 TYR D 94 PRO D 95 0 -2.31 CISPEP 10 TYR D 141 PRO D 142 0 2.96 SITE 1 AC1 9 TYR A 39 PRO A 41 GLY A 42 LYS A 43 SITE 2 AC1 9 GLY A 44 TYR B 87 LYS B 103 HOH B 422 SITE 3 AC1 9 HOH B 467 SITE 1 AC2 4 VAL A 72 ASP A 73 ARG A 74 SER A 75 SITE 1 AC3 3 PHE A 27 THR A 28 TYR A 32 SITE 1 AC4 2 HIS A 170 SER B 138 SITE 1 AC5 4 HIS C 170 HOH C 629 GLN D 168 SER D 169 SITE 1 AC6 5 GLN C 177 SER C 178 HOH C 616 GLY D 159 SITE 2 AC6 5 GLU D 161 SITE 1 AC7 4 LYS C 149 ASP C 150 GLN C 177 LYS D 130 SITE 1 AC8 3 ASP C 73 ARG C 74 SER C 75 SITE 1 AC9 3 PHE C 27 THR C 28 TYR C 32 SITE 1 BC1 3 PRO D 59 ARG D 61 GLU D 81 SITE 1 BC2 5 TYR C 39 ARG D 38 PRO D 40 GLY D 41 SITE 2 BC2 5 HOH D 476 CRYST1 85.596 71.179 90.924 90.00 99.28 90.00 P 1 21 1 4 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 0.011683 0.000000 0.001909 0.00000 SCALE2 0.000000 0.014049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011144 0.00000