HEADER HYDROLASE 12-MAR-14 4P4B TITLE X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN TITLE 2 COMPLEX WITH A PHOSPHORAMIDATE INHIBITOR CTT54 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE CARBOXYPEPTIDASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 44-750; COMPND 5 SYNONYM: CELL GROWTH-INHIBITING GENE 27 PROTEIN,FOLATE HYDROLASE 1, COMPND 6 FOLYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE,FGCP,GLUTAMATE COMPND 7 CARBOXYPEPTIDASE II,GCPII,MEMBRANE GLUTAMATE CARBOXYPEPTIDASE,MGCP,N- COMPND 8 ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE I,NAALADASE I,PROSTATE- COMPND 9 SPECIFIC MEMBRANE ANTIGEN,PSMA,PTEROYLPOLY-GAMMA-GLUTAMATE COMPND 10 CARBOXYPEPTIDASE; COMPND 11 EC: 3.4.17.21; COMPND 12 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: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SCHNEIDER'S S2 CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GLUTAMATE CARBOXYPEPTIDASE II (GCPII), NAALADASE, PROSTATE-SPECIFIC KEYWDS 2 MEMBRANE ANTIGEN, PHOSPHORAMIDATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.BARINKA REVDAT 5 13-NOV-24 4P4B 1 HETSYN LINK REVDAT 4 29-JUL-20 4P4B 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 20-JAN-16 4P4B 1 JRNL REVDAT 2 04-NOV-15 4P4B 1 JRNL REVDAT 1 20-MAY-15 4P4B 0 JRNL AUTH Z.NOVAKOVA,J.CERNY,C.J.CHOY,J.R.NEDROW,J.K.CHOI,J.LUBKOWSKI, JRNL AUTH 2 C.E.BERKMAN,C.BARINKA JRNL TITL DESIGN OF COMPOSITE INHIBITORS TARGETING GLUTAMATE JRNL TITL 2 CARBOXYPEPTIDASE II: THE IMPORTANCE OF EFFECTOR JRNL TITL 3 FUNCTIONALITIES. JRNL REF FEBS J. V. 283 130 2016 JRNL REFN ISSN 1742-464X JRNL PMID 26460595 JRNL DOI 10.1111/FEBS.13557 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 76914 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2380 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5186 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5529 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 234 REMARK 3 SOLVENT ATOMS : 513 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.06000 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): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.294 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6198 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8436 ; 1.680 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 725 ; 5.960 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 285 ;37.255 ;23.789 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1011 ;13.935 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;14.811 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 915 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4752 ; 0.009 ; 0.021 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): 3584 ; 0.904 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5837 ; 1.529 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2614 ; 2.533 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2598 ; 4.012 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 55 A 1766 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6771 49.5117 44.5873 REMARK 3 T TENSOR REMARK 3 T11: 0.0159 T22: 0.0502 REMARK 3 T33: 0.0432 T12: 0.0167 REMARK 3 T13: 0.0058 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.6528 L22: 1.0580 REMARK 3 L33: 0.4088 L12: -0.2905 REMARK 3 L13: -0.0003 L23: 0.0802 REMARK 3 S TENSOR REMARK 3 S11: -0.0621 S12: 0.0199 S13: -0.0440 REMARK 3 S21: 0.0122 S22: 0.0649 S23: -0.1659 REMARK 3 S31: 0.0461 S32: 0.0812 S33: -0.0028 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 : 1.40 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 4P4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200677. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79458 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33% (V/V) PENTAERYTHRITOL PROPOXYLATE REMARK 280 PO/OH 5/4, 0.5 % (W/V) PEG 3350, AND 100 MM TRIS-HCL, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 50.81700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.15350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.28850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.81700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.15350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.28850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 50.81700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.15350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.28850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 50.81700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.15350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.28850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 130.30700 REMARK 350 BIOMT3 2 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 LYS A 44 REMARK 465 SER A 45 REMARK 465 SER A 46 REMARK 465 ASN A 47 REMARK 465 GLU A 48 REMARK 465 ALA A 49 REMARK 465 THR A 50 REMARK 465 ASN A 51 REMARK 465 ILE A 52 REMARK 465 THR A 53 REMARK 465 PRO A 54 REMARK 465 ASP A 654 REMARK 465 LYS A 655 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 A 656 O HOH A 902 1.96 REMARK 500 OE1 GLU A 486 O HOH A 1198 2.01 REMARK 500 O HOH A 1110 O HOH A 1367 2.03 REMARK 500 OG SER A 656 O HOH A 902 2.12 REMARK 500 NZ LYS A 617 O HOH A 1313 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 171 CD GLU A 171 OE2 0.184 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 164 4.98 81.83 REMARK 500 ASN A 178 -126.43 61.22 REMARK 500 LYS A 207 -44.42 77.80 REMARK 500 VAL A 382 -108.30 -130.31 REMARK 500 ALA A 452 59.32 -149.83 REMARK 500 ASP A 453 -157.62 -85.77 REMARK 500 SER A 454 119.48 -35.39 REMARK 500 SER A 517 -154.08 -151.28 REMARK 500 ASP A 567 64.17 -154.99 REMARK 500 ASN A 698 96.03 -168.37 REMARK 500 PHE A 705 59.39 36.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 803 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 269 O REMARK 620 2 THR A 269 OG1 72.1 REMARK 620 3 TYR A 272 O 72.7 91.6 REMARK 620 4 GLU A 433 OE1 149.8 87.7 86.0 REMARK 620 5 GLU A 433 OE2 149.6 98.8 137.5 53.7 REMARK 620 6 GLU A 436 OE2 103.3 171.9 80.6 93.9 88.5 REMARK 620 7 HOH A1003 O 72.9 87.4 144.2 129.6 77.8 97.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 377 NE2 REMARK 620 2 ASP A 387 OD1 107.6 REMARK 620 3 ASP A 453 OD2 101.9 120.0 REMARK 620 4 2G2 A 820 OAL 112.9 117.8 95.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 387 OD2 REMARK 620 2 GLU A 425 OE1 156.6 REMARK 620 3 GLU A 425 OE2 102.4 54.3 REMARK 620 4 HIS A 553 NE2 99.7 88.2 110.3 REMARK 620 5 2G2 A 820 OAG 104.6 95.7 135.6 99.1 REMARK 620 N 1 2 3 4 DBREF 4P4B A 44 750 UNP Q04609 FOLH1_HUMAN 44 750 SEQRES 1 A 707 LYS SER SER ASN GLU ALA THR ASN ILE THR PRO LYS HIS SEQRES 2 A 707 ASN MET LYS ALA PHE LEU ASP GLU LEU LYS ALA GLU ASN SEQRES 3 A 707 ILE LYS LYS PHE LEU TYR ASN PHE THR GLN ILE PRO HIS SEQRES 4 A 707 LEU ALA GLY THR GLU GLN ASN PHE GLN LEU ALA LYS GLN SEQRES 5 A 707 ILE GLN SER GLN TRP LYS GLU PHE GLY LEU ASP SER VAL SEQRES 6 A 707 GLU LEU ALA HIS TYR ASP VAL LEU LEU SER TYR PRO ASN SEQRES 7 A 707 LYS THR HIS PRO ASN TYR ILE SER ILE ILE ASN GLU ASP SEQRES 8 A 707 GLY ASN GLU ILE PHE ASN THR SER LEU PHE GLU PRO PRO SEQRES 9 A 707 PRO PRO GLY TYR GLU ASN VAL SER ASP ILE VAL PRO PRO SEQRES 10 A 707 PHE SER ALA PHE SER PRO GLN GLY MET PRO GLU GLY ASP SEQRES 11 A 707 LEU VAL TYR VAL ASN TYR ALA ARG THR GLU ASP PHE PHE SEQRES 12 A 707 LYS LEU GLU ARG ASP MET LYS ILE ASN CYS SER GLY LYS SEQRES 13 A 707 ILE VAL ILE ALA ARG TYR GLY LYS VAL PHE ARG GLY ASN SEQRES 14 A 707 LYS VAL LYS ASN ALA GLN LEU ALA GLY ALA LYS GLY VAL SEQRES 15 A 707 ILE LEU TYR SER ASP PRO ALA ASP TYR PHE ALA PRO GLY SEQRES 16 A 707 VAL LYS SER TYR PRO ASP GLY TRP ASN LEU PRO GLY GLY SEQRES 17 A 707 GLY VAL GLN ARG GLY ASN ILE LEU ASN LEU ASN GLY ALA SEQRES 18 A 707 GLY ASP PRO LEU THR PRO GLY TYR PRO ALA ASN GLU TYR SEQRES 19 A 707 ALA TYR ARG ARG GLY ILE ALA GLU ALA VAL GLY LEU PRO SEQRES 20 A 707 SER ILE PRO VAL HIS PRO ILE GLY TYR TYR ASP ALA GLN SEQRES 21 A 707 LYS LEU LEU GLU LYS MET GLY GLY SER ALA PRO PRO ASP SEQRES 22 A 707 SER SER TRP ARG GLY SER LEU LYS VAL PRO TYR ASN VAL SEQRES 23 A 707 GLY PRO GLY PHE THR GLY ASN PHE SER THR GLN LYS VAL SEQRES 24 A 707 LYS MET HIS ILE HIS SER THR ASN GLU VAL THR ARG ILE SEQRES 25 A 707 TYR ASN VAL ILE GLY THR LEU ARG GLY ALA VAL GLU PRO SEQRES 26 A 707 ASP ARG TYR VAL ILE LEU GLY GLY HIS ARG ASP SER TRP SEQRES 27 A 707 VAL PHE GLY GLY ILE ASP PRO GLN SER GLY ALA ALA VAL SEQRES 28 A 707 VAL HIS GLU ILE VAL ARG SER PHE GLY THR LEU LYS LYS SEQRES 29 A 707 GLU GLY TRP ARG PRO ARG ARG THR ILE LEU PHE ALA SER SEQRES 30 A 707 TRP ASP ALA GLU GLU PHE GLY LEU LEU GLY SER THR GLU SEQRES 31 A 707 TRP ALA GLU GLU ASN SER ARG LEU LEU GLN GLU ARG GLY SEQRES 32 A 707 VAL ALA TYR ILE ASN ALA ASP SER SER ILE GLU GLY ASN SEQRES 33 A 707 TYR THR LEU ARG VAL ASP CYS THR PRO LEU MET TYR SER SEQRES 34 A 707 LEU VAL HIS ASN LEU THR LYS GLU LEU LYS SER PRO ASP SEQRES 35 A 707 GLU GLY PHE GLU GLY LYS SER LEU TYR GLU SER TRP THR SEQRES 36 A 707 LYS LYS SER PRO SER PRO GLU PHE SER GLY MET PRO ARG SEQRES 37 A 707 ILE SER LYS LEU GLY SER GLY ASN ASP PHE GLU VAL PHE SEQRES 38 A 707 PHE GLN ARG LEU GLY ILE ALA SER GLY ARG ALA ARG TYR SEQRES 39 A 707 THR LYS ASN TRP GLU THR ASN LYS PHE SER GLY TYR PRO SEQRES 40 A 707 LEU TYR HIS SER VAL TYR GLU THR TYR GLU LEU VAL GLU SEQRES 41 A 707 LYS PHE TYR ASP PRO MET PHE LYS TYR HIS LEU THR VAL SEQRES 42 A 707 ALA GLN VAL ARG GLY GLY MET VAL PHE GLU LEU ALA ASN SEQRES 43 A 707 SER ILE VAL LEU PRO PHE ASP CYS ARG ASP TYR ALA VAL SEQRES 44 A 707 VAL LEU ARG LYS TYR ALA ASP LYS ILE TYR SER ILE SER SEQRES 45 A 707 MET LYS HIS PRO GLN GLU MET LYS THR TYR SER VAL SER SEQRES 46 A 707 PHE ASP SER LEU PHE SER ALA VAL LYS ASN PHE THR GLU SEQRES 47 A 707 ILE ALA SER LYS PHE SER GLU ARG LEU GLN ASP PHE ASP SEQRES 48 A 707 LYS SER ASN PRO ILE VAL LEU ARG MET MET ASN ASP GLN SEQRES 49 A 707 LEU MET PHE LEU GLU ARG ALA PHE ILE ASP PRO LEU GLY SEQRES 50 A 707 LEU PRO ASP ARG PRO PHE TYR ARG HIS VAL ILE TYR ALA SEQRES 51 A 707 PRO SER SER HIS ASN LYS TYR ALA GLY GLU SER PHE PRO SEQRES 52 A 707 GLY ILE TYR ASP ALA LEU PHE ASP ILE GLU SER LYS VAL SEQRES 53 A 707 ASP PRO SER LYS ALA TRP GLY GLU VAL LYS ARG GLN ILE SEQRES 54 A 707 TYR VAL ALA ALA PHE THR VAL GLN ALA ALA ALA GLU THR SEQRES 55 A 707 LEU SER GLU VAL ALA MODRES 4P4B NAG B 1 NAG -D MODRES 4P4B NAG B 2 NAG -D MODRES 4P4B NAG C 1 NAG -D MODRES 4P4B NAG C 2 NAG -D MODRES 4P4B NAG D 1 NAG -D MODRES 4P4B NAG D 2 NAG -D MODRES 4P4B NAG A 811 NAG -D MODRES 4P4B NAG A 812 NAG -D MODRES 4P4B NAG E 1 NAG -D MODRES 4P4B NAG E 2 NAG -D MODRES 4P4B NAG F 1 NAG -D MODRES 4P4B NAG F 2 NAG -D MODRES 4P4B MAN F 4 MAN -D HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET MAN F 4 11 HET ZN A 801 1 HET ZN A 802 1 HET CA A 803 1 HET CL A 804 1 HET NAG A 811 14 HET NAG A 812 14 HET 2G2 A 820 29 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM 2G2 L-GAMMA-GLUTAMYL-O-[(S)-{[(1S)-1,3- HETNAM 2 2G2 DICARBOXYPROPYL]AMINO}(HYDROXY)PHOSPHORYL]-L-SERINE 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 12(C8 H15 N O6) FORMUL 5 BMA 2(C6 H12 O6) FORMUL 6 MAN C6 H12 O6 FORMUL 7 ZN 2(ZN 2+) FORMUL 9 CA CA 2+ FORMUL 10 CL CL 1- FORMUL 13 2G2 C13 H22 N3 O12 P FORMUL 14 HOH *513(H2 O) HELIX 1 AA1 ASN A 57 LEU A 65 1 9 HELIX 2 AA2 LYS A 66 PHE A 77 1 12 HELIX 3 AA3 THR A 86 PHE A 103 1 18 HELIX 4 AA4 ARG A 181 ASP A 191 1 11 HELIX 5 AA5 PHE A 209 ALA A 220 1 12 HELIX 6 AA6 ASP A 230 PHE A 235 1 6 HELIX 7 AA7 GLY A 282 ALA A 286 5 5 HELIX 8 AA8 GLY A 298 GLU A 307 1 10 HELIX 9 AA9 ASP A 316 ARG A 320 5 5 HELIX 10 AB1 THR A 334 SER A 338 5 5 HELIX 11 AB2 PRO A 388 GLU A 408 1 21 HELIX 12 AB3 ALA A 423 GLY A 427 5 5 HELIX 13 AB4 LEU A 428 ASN A 438 1 11 HELIX 14 AB5 ASN A 438 ARG A 445 1 8 HELIX 15 AB6 MET A 470 GLU A 480 1 11 HELIX 16 AB7 SER A 492 SER A 501 1 10 HELIX 17 AB8 PHE A 521 GLN A 526 1 6 HELIX 18 AB9 THR A 558 TYR A 566 1 9 HELIX 19 AC1 PHE A 570 SER A 590 1 21 HELIX 20 AC2 ASP A 596 MET A 616 1 21 HELIX 21 AC3 HIS A 618 TYR A 625 1 8 HELIX 22 AC4 PHE A 629 PHE A 653 1 25 HELIX 23 AC5 ASN A 657 PHE A 675 1 19 HELIX 24 AC6 PHE A 705 PHE A 713 1 9 HELIX 25 AC7 ASP A 714 LYS A 718 5 5 HELIX 26 AC8 ASP A 720 THR A 745 1 26 SHEET 1 AA1 7 SER A 107 TYR A 119 0 SHEET 2 AA1 7 THR A 349 LEU A 362 -1 O ASN A 357 N ALA A 111 SHEET 3 AA1 7 ARG A 414 TRP A 421 -1 O PHE A 418 N GLY A 360 SHEET 4 AA1 7 GLU A 367 HIS A 377 1 N LEU A 374 O LEU A 417 SHEET 5 AA1 7 GLY A 446 ASN A 451 1 O ILE A 450 N ILE A 373 SHEET 6 AA1 7 ALA A 531 THR A 538 1 O GLY A 533 N ASN A 451 SHEET 7 AA1 7 THR A 461 CYS A 466 -1 N THR A 461 O THR A 538 SHEET 1 AA2 4 GLU A 137 ASN A 140 0 SHEET 2 AA2 4 TYR A 127 ILE A 131 -1 N ILE A 130 O ILE A 138 SHEET 3 AA2 4 LYS A 341 HIS A 345 -1 O LYS A 343 N SER A 129 SHEET 4 AA2 4 GLU A 171 GLY A 172 -1 N GLY A 172 O VAL A 342 SHEET 1 AA3 2 SER A 162 ALA A 163 0 SHEET 2 AA3 2 GLY A 256 ASN A 257 1 N GLY A 256 O ALA A 163 SHEET 1 AA4 4 LEU A 174 TYR A 176 0 SHEET 2 AA4 4 ILE A 200 ARG A 204 1 O ILE A 202 N VAL A 175 SHEET 3 AA4 4 GLY A 224 TYR A 228 1 O GLY A 224 N VAL A 201 SHEET 4 AA4 4 VAL A 294 ILE A 297 1 O HIS A 295 N LEU A 227 SHEET 1 AA5 2 TYR A 692 SER A 695 0 SHEET 2 AA5 2 ASN A 698 SER A 704 -1 O GLU A 703 N ALA A 693 LINK ND2 ASN A 76 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 121 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN A 140 C1 NAG D 1 1555 1555 1.46 LINK ND2 ASN A 195 C1 NAG A 811 1555 1555 1.46 LINK ND2 ASN A 459 C1 NAG A 812 1555 1555 1.45 LINK ND2 ASN A 476 C1 NAG E 1 1555 1555 1.43 LINK ND2 ASN A 638 C1 NAG F 1 1555 1555 1.43 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.41 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.44 LINK O3 BMA F 3 C1 MAN F 4 1555 1555 1.45 LINK O THR A 269 CA CA A 803 1555 1555 2.38 LINK OG1 THR A 269 CA CA A 803 1555 1555 2.47 LINK O TYR A 272 CA CA A 803 1555 1555 2.36 LINK NE2 HIS A 377 ZN ZN A 802 1555 1555 2.01 LINK OD2 ASP A 387 ZN ZN A 801 1555 1555 1.97 LINK OD1 ASP A 387 ZN ZN A 802 1555 1555 2.02 LINK OE1 GLU A 425 ZN ZN A 801 1555 1555 2.53 LINK OE2 GLU A 425 ZN ZN A 801 1555 1555 2.07 LINK OE1 GLU A 433 CA CA A 803 1555 1555 2.40 LINK OE2 GLU A 433 CA CA A 803 1555 1555 2.49 LINK OE2 GLU A 436 CA CA A 803 1555 1555 2.28 LINK OD2 ASP A 453 ZN ZN A 802 1555 1555 1.91 LINK NE2 HIS A 553 ZN ZN A 801 1555 1555 2.00 LINK ZN ZN A 801 OAG 2G2 A 820 1555 1555 1.97 LINK ZN ZN A 802 OAL 2G2 A 820 1555 1555 1.88 LINK CA CA A 803 O HOH A1003 1555 1555 2.42 CISPEP 1 TYR A 242 PRO A 243 0 4.49 CISPEP 2 GLY A 330 PRO A 331 0 -1.57 CISPEP 3 ASP A 387 PRO A 388 0 7.15 CRYST1 101.634 130.307 158.577 90.00 90.00 90.00 I 2 2 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 0.009839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007674 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006306 0.00000