PDB Short entry for 2ZCK HEADER IMMUNE SYSTEM 09-NOV-07 2ZCK TITLE CRYSTAL STRUCTURE OF A TERNARY COMPLEX BETWEEN PSA, A SUBSTRAT-ACYL TITLE 2 INTERMEDIATE AND AN ACTIVATING ANTIBODY CAVEAT 2ZCK LEU P 67 HAS WRONG CHIRALITY AT ATOM CA ASP L 28 HAS WRONG CAVEAT 2 2ZCK CHIRALITY AT ATOM CA TRP H 188 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 2ZCK CA NAG A 1 HAS WRONG CHIRALITY AT ATOM C1 MAN A 2 HAS WRONG CAVEAT 4 2ZCK CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROSTATE-SPECIFIC ANTIGEN; COMPND 3 CHAIN: P; COMPND 4 FRAGMENT: UNP RESIDUES 25-261; COMPND 5 SYNONYM: PSA, KALLIKREIN- 3, SEMENOGELASE, GAMMA-SEMINOPROTEIN, COMPND 6 SEMININ, P-30 ANTIGEN; COMPND 7 EC: 3.4.21.77; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: KGISSQY; COMPND 10 CHAIN: S; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: MONOCLONAL ANTIBODY 8G8F5 FAB; COMPND 14 CHAIN: L; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: MONOCLONAL ANTIBODY 8G8F5 FAB; COMPND 17 CHAIN: H SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: SEMINAL FLUIDS; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: PEPTIDE SYNTHESIS; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 STRAIN: BALB/CJYCO; SOURCE 14 OTHER_DETAILS: ASCITIC FLUIDS; SOURCE 15 MOL_ID: 4; SOURCE 16 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 17 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 18 ORGANISM_TAXID: 10090; SOURCE 19 STRAIN: BALB/CJYCO; SOURCE 20 OTHER_DETAILS: ASCITIC FLUIDS KEYWDS HUMAN PSA, ANTIBODIES, KALLIKREIN RELATED PEPTIDASES, PROSTATE KEYWDS 2 CANCER, GLYCOPROTEIN, HYDROLASE, PROTEASE, SECRETED, SERINE KEYWDS 3 PROTEASE, ZYMOGEN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.MENEZ,E.STURA,C.JOLIVET-REYNAUD REVDAT 6 01-NOV-23 2ZCK 1 HETSYN REVDAT 5 29-JUL-20 2ZCK 1 CAVEAT COMPND REMARK DBREF REVDAT 5 2 1 HETNAM LINK SITE ATOM REVDAT 4 13-JUL-11 2ZCK 1 VERSN REVDAT 3 24-FEB-09 2ZCK 1 VERSN REVDAT 2 18-MAR-08 2ZCK 1 JRNL REVDAT 1 29-JAN-08 2ZCK 0 JRNL AUTH S.MICHEL,B.H.MULLER,M.BOSSUS,F.DUCANCEL,C.JOLIVET-REYNAUD, JRNL AUTH 2 E.A.STURA JRNL TITL CRYSTAL STRUCTURE OF A TERNARY COMPLEX BETWEEN HUMAN JRNL TITL 2 PROSTATE-SPECIFIC ANTIGEN, ITS SUBSTRATE ACYL INTERMEDIATE JRNL TITL 3 AND AN ACTIVATING ANTIBODY JRNL REF J.MOL.BIOL. V. 376 1021 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18187150 JRNL DOI 10.1016/J.JMB.2007.11.052 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 16217 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 870 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1143 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5273 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.11000 REMARK 3 B22 (A**2) : 1.11000 REMARK 3 B33 (A**2) : -2.22000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.500 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.377 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.086 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.906 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5437 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4732 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7414 ; 1.733 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11094 ; 0.974 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 688 ; 8.335 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;35.733 ;24.533 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 863 ;18.849 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.009 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 835 ; 0.241 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6031 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1035 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1199 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5134 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2578 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3066 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 130 ; 0.166 ; 0.200 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): 22 ; 0.178 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.161 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.173 ; 0.200 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): 4338 ; 1.136 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1403 ; 0.064 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5586 ; 1.149 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2318 ; 1.578 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1828 ; 2.342 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ZCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000027800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, XFIT REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17100 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 70.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.12700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.51900 REMARK 200 R SYM FOR SHELL (I) : 0.58300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: XFIT REMARK 200 STARTING MODEL: PDB ENTRY 2ZCH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL GROWN IN 14% MPEG550, 100MM REMARK 280 HEPES (PH7.2), THEN SOAKED IN PEG400, 100MM TRIS-HCL (PH7.3), REMARK 280 10MM ZNCL2, 0.28 MG/ML MU-KGISSQY-AFC, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 119.09000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.38250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.38250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.54500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.38250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.38250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 178.63500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.38250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.38250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.54500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.38250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.38250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 178.63500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 119.09000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, S, L, H, 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 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 SER P 195 O THR P 213 1.85 REMARK 500 O HOH L 221 O HOH L 223 1.91 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 LEU P 67 N - CA - C ANGL. DEV. = 18.6 DEGREES REMARK 500 ARG H 94 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PRO H 219 C - N - CA ANGL. DEV. = 22.3 DEGREES REMARK 500 PRO H 219 C - N - CD ANGL. DEV. = -19.1 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 VAL P 41 -75.38 161.17 REMARK 500 LEU P 67 -65.09 -92.82 REMARK 500 HIS P 70 -55.65 -124.09 REMARK 500 SER P 99 31.42 -86.99 REMARK 500 ASP P 102 79.19 -66.22 REMARK 500 GLU P 148 106.54 78.15 REMARK 500 GLN P 210 -35.34 -133.30 REMARK 500 SER P 214 -118.20 146.46 REMARK 500 ASN P 246 56.77 -140.56 REMARK 500 ASP L 28 -37.45 61.39 REMARK 500 LEU L 47 -61.32 -94.54 REMARK 500 ALA L 51 -47.58 69.96 REMARK 500 ALA L 60 -5.09 -55.40 REMARK 500 GLN L 76 119.71 -178.92 REMARK 500 ALA L 111 139.03 -175.35 REMARK 500 ALA L 130 116.43 -161.34 REMARK 500 ASP L 151 108.52 49.58 REMARK 500 SER L 153 78.17 -57.67 REMARK 500 ARG L 155 84.54 176.61 REMARK 500 ASN L 157 82.02 101.41 REMARK 500 GLN L 166 109.29 -45.00 REMARK 500 GLU L 187 32.20 -81.31 REMARK 500 ASN L 190 -115.29 -81.92 REMARK 500 LYS L 199 0.74 -42.80 REMARK 500 SER L 201 -95.44 -129.47 REMARK 500 ARG L 211 72.91 48.73 REMARK 500 ASN L 212 74.49 43.63 REMARK 500 GLU L 213 97.33 4.63 REMARK 500 GLN H 6 -112.51 -85.16 REMARK 500 PRO H 41 -53.63 -29.27 REMARK 500 GLU H 61 81.55 -69.81 REMARK 500 MET H 62 -42.99 168.43 REMARK 500 SER H 82A -89.99 -100.83 REMARK 500 SER H 84 119.89 60.65 REMARK 500 ASP H 86 -34.47 171.29 REMARK 500 ASN H 100 19.51 59.23 REMARK 500 GLU H 100C 51.39 32.38 REMARK 500 SER H 113 -74.23 -21.92 REMARK 500 ALA H 114 16.11 -159.00 REMARK 500 LYS H 115 -131.91 16.58 REMARK 500 THR H 116 81.41 -150.97 REMARK 500 LEU H 124 77.26 -113.77 REMARK 500 PRO H 126 150.60 -39.37 REMARK 500 VAL H 127 -88.55 -16.76 REMARK 500 CYS H 128 -171.83 64.96 REMARK 500 LEU H 138 -168.50 -114.25 REMARK 500 SER H 149 68.16 102.73 REMARK 500 SER H 161 51.42 -109.53 REMARK 500 GLN H 171 -36.81 -150.18 REMARK 500 TRP H 188 -141.02 -30.32 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. 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 ALA P 39 VAL P 41 -73.07 REMARK 500 THR P 213 SER P 214 -63.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZCH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PSA COMPLEXED WITH ANTIBODY 8G8F5 AT REMARK 900 PH7.2 REMARK 900 RELATED ID: 2ZCL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PSA COMPLEXED WITH ANTIBODY 8G8F5 AT REMARK 900 PH5.5 REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR CHAIN L AND H DOES NOT CURRENTLY REMARK 999 EXIST. DBREF 2ZCK P 16 247 UNP P07288 KLK3_HUMAN 25 261 DBREF 2ZCK S 498 504 PDB 2ZCK 2ZCK 498 504 DBREF 2ZCK L 1 214 PDB 2ZCK 2ZCK 1 214 DBREF 2ZCK H 1 221 PDB 2ZCK 2ZCK 1 221 SEQRES 1 P 237 ILE VAL GLY GLY TRP GLU CYS GLU LYS HIS SER GLN PRO SEQRES 2 P 237 TRP GLN VAL LEU VAL ALA SER ARG GLY ARG ALA VAL CYS SEQRES 3 P 237 GLY GLY VAL LEU VAL HIS PRO GLN TRP VAL LEU THR ALA SEQRES 4 P 237 ALA HIS CYS ILE ARG ASN LYS SER VAL ILE LEU LEU GLY SEQRES 5 P 237 ARG HIS SER LEU PHE HIS PRO GLU ASP THR GLY GLN VAL SEQRES 6 P 237 PHE GLN VAL SER HIS SER PHE PRO HIS PRO LEU TYR ASP SEQRES 7 P 237 MET SER LEU LEU LYS ASN ARG PHE LEU ARG PRO GLY ASP SEQRES 8 P 237 ASP SER SER HIS ASP LEU MET LEU LEU ARG LEU SER GLU SEQRES 9 P 237 PRO ALA GLU LEU THR ASP ALA VAL LYS VAL MET ASP LEU SEQRES 10 P 237 PRO THR GLN GLU PRO ALA LEU GLY THR THR CYS TYR ALA SEQRES 11 P 237 SER GLY TRP GLY SER ILE GLU PRO GLU GLU PHE LEU THR SEQRES 12 P 237 PRO LYS LYS LEU GLN CYS VAL ASP LEU HIS VAL ILE SER SEQRES 13 P 237 ASN ASP VAL CYS ALA GLN VAL HIS PRO GLN LYS VAL THR SEQRES 14 P 237 LYS PHE MET LEU CYS ALA GLY ARG TRP THR GLY GLY LYS SEQRES 15 P 237 SER THR CYS SER GLY ASP SER GLY GLY PRO LEU VAL CYS SEQRES 16 P 237 ASN GLY VAL LEU GLN GLY ILE THR SER TRP GLY SER GLU SEQRES 17 P 237 PRO CYS ALA LEU PRO GLU ARG PRO SER LEU TYR THR LYS SEQRES 18 P 237 VAL VAL HIS TYR ARG LYS TRP ILE LYS ASP THR ILE VAL SEQRES 19 P 237 ALA ASN PRO SEQRES 1 S 7 LYS GLY ILE SER SER GLN TYR SEQRES 1 L 218 ASP ILE VAL LEU THR GLN SER PRO ALA SER LEU ALA VAL SEQRES 2 L 218 SER LEU GLY GLN ARG ALA THR ILE SER CYS LYS ALA SER SEQRES 3 L 218 GLN SER VAL ASP PHE ASP GLY ASP SER TYR MET ASN TRP SEQRES 4 L 218 TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU LEU ILE SEQRES 5 L 218 PHE ALA ALA SER ASN LEU ALA SER GLY ILE PRO ALA ARG SEQRES 6 L 218 LEU SER GLY SER GLY SER GLY THR ASP PHE THR LEU ASN SEQRES 7 L 218 ILE GLN PRO VAL GLU GLU GLU ASP ALA ALA THR TYR TYR SEQRES 8 L 218 CYS GLN GLN SER ASN GLU ASP PRO TYR THR PHE GLY GLY SEQRES 9 L 218 GLY THR LYS LEU GLU ILE LYS ARG ALA ASP ALA ALA PRO SEQRES 10 L 218 THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU THR SEQRES 11 L 218 SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN PHE SEQRES 12 L 218 TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SEQRES 13 L 218 SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR ASP SEQRES 14 L 218 GLN ASP SER LYS ASP SER THR TYR SER MET SER SER THR SEQRES 15 L 218 LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SER SEQRES 16 L 218 TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER PRO SEQRES 17 L 218 ILE VAL LYS SER PHE ASN ARG ASN GLU CYS SEQRES 1 H 230 GLN VAL GLN LEU GLN GLN SER GLY ASP ASP LEU VAL LYS SEQRES 2 H 230 PRO GLY ALA SER VAL LYS LEU SER CYS LYS ALA SER GLY SEQRES 3 H 230 TYR THR PHE THR THR TYR TYR ILE ASN TRP MET ARG GLN SEQRES 4 H 230 ARG PRO GLY GLN GLY LEU GLU TRP ILE GLY ARG ILE ALA SEQRES 5 H 230 PRO ALA SER GLY THR THR TYR SER SER GLU MET PHE LYS SEQRES 6 H 230 ASP LYS ALA THR LEU THR VAL ASP THR SER SER ASN THR SEQRES 7 H 230 ALA TYR ILE GLN LEU SER SER LEU SER SER GLU ASP SER SEQRES 8 H 230 ALA VAL TYR PHE CYS ALA ARG ALA ASP TYR GLY PHE ASN SEQRES 9 H 230 SER GLY GLU ALA MET ASP TYR TRP GLY GLN GLY THR SER SEQRES 10 H 230 VAL THR VAL SER SER ALA LYS THR THR ALA PRO PRO VAL SEQRES 11 H 230 TYR PRO LEU ALA PRO VAL CYS GLY ASP THR THR GLY SER SEQRES 12 H 230 SER VAL THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO SEQRES 13 H 230 GLU SER VAL THR LEU LEU TRP ASN SER GLY SER LEU SER SEQRES 14 H 230 SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER ASP SEQRES 15 H 230 LEU TYR THR LEU SER SER SER VAL THR VAL THR SER SER SEQRES 16 H 230 THR TRP PRO SER GLN SER ILE THR CYS ASN VAL ALA HIS SEQRES 17 H 230 PRO ALA SER SER THR LYS VAL ASP LYS LYS ILE VAL PRO SEQRES 18 H 230 ARG ASP CYS GLY CYS LYS PRO CYS ILE MODRES 2ZCK ASN P 61 ASN GLYCOSYLATION SITE HET NAG A 1 14 HET MAN A 2 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 5 NAG C8 H15 N O6 FORMUL 5 MAN C6 H12 O6 FORMUL 6 HOH *31(H2 O) HELIX 1 1 ALA P 55 ILE P 59 5 5 HELIX 2 2 ASP P 95 LYS P 95E 5 6 HELIX 3 3 SER P 164 HIS P 172 1 9 HELIX 4 4 TYR P 235 ALA P 245 1 11 HELIX 5 5 GLU L 79 ALA L 83 5 5 HELIX 6 6 SER L 121 THR L 126 1 6 HELIX 7 7 LYS L 183 GLU L 187 1 5 HELIX 8 8 THR H 28 TYR H 32 5 5 HELIX 9 9 THR H 73 SER H 75 5 3 SHEET 1 A 6 TRP P 20 GLU P 21 0 SHEET 2 A 6 GLN P 156 VAL P 162 -1 O CYS P 157 N TRP P 20 SHEET 3 A 6 THR P 135 GLY P 140 -1 N CYS P 136 O LEU P 160 SHEET 4 A 6 PRO P 198 CYS P 201 -1 O VAL P 200 N TYR P 137 SHEET 5 A 6 VAL P 208 SER P 217 -1 O VAL P 208 N CYS P 201 SHEET 6 A 6 SER S 501 GLN S 503 -1 O SER S 502 N GLY P 216 SHEET 1 B 6 TRP P 20 GLU P 21 0 SHEET 2 B 6 GLN P 156 VAL P 162 -1 O CYS P 157 N TRP P 20 SHEET 3 B 6 MET P 180 GLY P 184 -1 O GLY P 184 N HIS P 161 SHEET 4 B 6 SER P 227 LYS P 231 -1 O TYR P 229 N LEU P 181 SHEET 5 B 6 VAL P 208 SER P 217 -1 N ILE P 212 O THR P 230 SHEET 6 B 6 SER S 501 GLN S 503 -1 O SER S 502 N GLY P 216 SHEET 1 C 7 GLN P 30 SER P 35 0 SHEET 2 C 7 ARG P 38 HIS P 48 -1 O CYS P 42 N VAL P 33 SHEET 3 C 7 TRP P 51 THR P 54 -1 O LEU P 53 N VAL P 45 SHEET 4 C 7 MET P 104 LEU P 108 -1 O MET P 104 N THR P 54 SHEET 5 C 7 VAL P 82 PRO P 90 -1 N PHE P 89 O LEU P 105 SHEET 6 C 7 VAL P 64 LEU P 66 -1 N ILE P 65 O PHE P 83 SHEET 7 C 7 GLN P 30 SER P 35 -1 N ALA P 34 O VAL P 64 SHEET 1 D 4 LEU L 4 SER L 7 0 SHEET 2 D 4 ALA L 19 ALA L 25 -1 O LYS L 24 N THR L 5 SHEET 3 D 4 ASP L 70 ILE L 75 -1 O ILE L 75 N ALA L 19 SHEET 4 D 4 LEU L 62 SER L 67 -1 N SER L 63 O ASN L 74 SHEET 1 E 6 SER L 10 VAL L 13 0 SHEET 2 E 6 LYS L 103 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 E 6 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 E 6 MET L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 E 6 LYS L 45 PHE L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 E 6 ASN L 53 LEU L 54 -1 O ASN L 53 N PHE L 49 SHEET 1 F 4 SER L 10 VAL L 13 0 SHEET 2 F 4 LYS L 103 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 F 4 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 F 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 G 2 ASP L 27C PHE L 27D 0 SHEET 2 G 2 ASP L 30 SER L 31 -1 O ASP L 30 N PHE L 27D SHEET 1 H 4 THR L 114 PHE L 118 0 SHEET 2 H 4 GLY L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 H 4 TYR L 173 THR L 182 -1 O MET L 175 N LEU L 136 SHEET 4 H 4 VAL L 159 LEU L 160 -1 N LEU L 160 O THR L 178 SHEET 1 I 3 ILE L 144 TRP L 148 0 SHEET 2 I 3 TYR L 192 HIS L 198 -1 O GLU L 195 N LYS L 147 SHEET 3 I 3 VAL L 206 PHE L 209 -1 O PHE L 209 N TYR L 192 SHEET 1 J 4 GLN H 3 GLN H 5 0 SHEET 2 J 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 J 4 THR H 77 LEU H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 J 4 ALA H 67 ASP H 72 -1 N THR H 70 O TYR H 79 SHEET 1 K 6 ASP H 10 VAL H 12 0 SHEET 2 K 6 SER H 108 VAL H 111 1 O SER H 108 N ASP H 10 SHEET 3 K 6 ALA H 88 ALA H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 K 6 TYR H 33 GLN H 39 -1 N ASN H 35 O ALA H 93 SHEET 5 K 6 LEU H 45 ILE H 51 -1 O ILE H 48 N TRP H 36 SHEET 6 K 6 THR H 57 SER H 59 -1 O TYR H 58 N ARG H 50 SHEET 1 L 4 ASP H 10 VAL H 12 0 SHEET 2 L 4 SER H 108 VAL H 111 1 O SER H 108 N ASP H 10 SHEET 3 L 4 ALA H 88 ALA H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 L 4 MET H 100E TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 M 4 VAL H 121 PRO H 123 0 SHEET 2 M 4 SER H 135 TYR H 145 -1 O LEU H 141 N TYR H 122 SHEET 3 M 4 TYR H 175 THR H 184 -1 O TYR H 175 N TYR H 145 SHEET 4 M 4 VAL H 163 THR H 165 -1 N HIS H 164 O SER H 180 SHEET 1 N 4 VAL H 121 PRO H 123 0 SHEET 2 N 4 SER H 135 TYR H 145 -1 O LEU H 141 N TYR H 122 SHEET 3 N 4 TYR H 175 THR H 184 -1 O TYR H 175 N TYR H 145 SHEET 4 N 4 VAL H 169 LEU H 170 -1 N VAL H 169 O THR H 176 SHEET 1 O 3 THR H 151 TRP H 154 0 SHEET 2 O 3 THR H 194 ALA H 198 -1 O ALA H 198 N THR H 151 SHEET 3 O 3 LYS H 205 LYS H 209 -1 O VAL H 206 N VAL H 197 SSBOND 1 CYS P 22 CYS P 157 1555 1555 2.04 SSBOND 2 CYS P 42 CYS P 58 1555 1555 2.03 SSBOND 3 CYS P 136 CYS P 201 1555 1555 2.06 SSBOND 4 CYS P 168 CYS P 182 1555 1555 2.03 SSBOND 5 CYS P 191 CYS P 220 1555 1555 2.07 SSBOND 6 CYS L 23 CYS L 88 1555 1555 2.06 SSBOND 7 CYS L 134 CYS L 194 1555 1555 2.05 SSBOND 8 CYS H 22 CYS H 92 1555 1555 2.05 SSBOND 9 CYS H 140 CYS H 195 1555 1555 2.03 LINK ND2 ASN P 61 C1 NAG A 1 1555 1555 1.46 LINK O4 NAG A 1 C1 MAN A 2 1555 1555 1.47 CISPEP 1 GLU P 218 PRO P 219 0 0.80 CISPEP 2 SER L 7 PRO L 8 0 -1.35 CISPEP 3 GLN L 76 PRO L 77 0 -1.50 CISPEP 4 ASP L 94 PRO L 95 0 0.32 CISPEP 5 TYR L 140 PRO L 141 0 -3.69 CISPEP 6 GLN L 156 ASN L 157 0 -6.57 CISPEP 7 THR L 200 SER L 201 0 -11.19 CISPEP 8 THR L 202 SER L 203 0 -17.80 CISPEP 9 GLU L 213 CYS L 214 0 6.41 CISPEP 10 SER H 83 SER H 84 0 27.63 CISPEP 11 SER H 113 ALA H 114 0 -22.61 CISPEP 12 VAL H 127 CYS H 128 0 -13.68 CISPEP 13 CYS H 128 GLY H 129 0 -2.14 CISPEP 14 GLY H 129 ASP H 130 0 3.57 CISPEP 15 THR H 132 GLY H 133 0 -5.53 CISPEP 16 PHE H 146 PRO H 147 0 -0.83 CISPEP 17 SER H 203 THR H 204 0 6.70 CISPEP 18 ARG H 213 ASP H 214 0 7.07 CISPEP 19 ASP H 214 CYS H 215 0 5.99 CISPEP 20 LYS H 218 PRO H 219 0 -2.88 CRYST1 86.765 86.765 238.180 90.00 90.00 90.00 P 41 21 2 8 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 0.011525 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004199 0.00000