HEADER HYDROLASE/HYDROLASE INHIBITOR 08-JAN-14 4OC2 TITLE X-RAY STRUCTURE OF OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN A TITLE 2 COMPLEX WITH CEIBZL, A UREA-BASED INHIBITOR N~2~-{[(1S)-1-CARBOXYBUT- TITLE 3 3-YN-1-YL]CARBAMOYL}-N~6~-(4-IODOBENZOYL)-L-LYSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE CARBOXYPEPTIDASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL GROWTH-INHIBITING GENE 27 PROTEIN, FOLATE HYDROLASE 1, COMPND 5 FOLYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE, FGCP, GLUTAMATE COMPND 6 CARBOXYPEPTIDASE II, GCPII, MEMBRANE GLUTAMATE CARBOXYPEPTIDASE, COMPND 7 MGCP, N-ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE I, NAALADASE I, COMPND 8 PROSTATE-SPECIFIC MEMBRANE ANTIGEN, PSM, PSMA, PTEROYLPOLY-GAMMA- COMPND 9 GLUTAMATE CARBOXYPEPTIDASE; COMPND 10 EC: 3.4.17.21; COMPND 11 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: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SCHNEIDER'S S2 CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HYDROLASE, METALLOPEPTIDASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.PAVLICEK,J.PTACEK,J.CERNY,Y.BYUN,L.SKULTETYOVA,M.POMPER, AUTHOR 2 J.LUBKOWSKI,C.BARINKA REVDAT 2 29-JUL-20 4OC2 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 21-MAY-14 4OC2 0 JRNL AUTH J.PAVLICEK,J.PTACEK,J.CERNY,Y.BYUN,L.SKULTETYOVA,M.G.POMPER, JRNL AUTH 2 J.LUBKOWSKI,C.BARINKA JRNL TITL STRUCTURAL CHARACTERIZATION OF P1'-DIVERSIFIED UREA-BASED JRNL TITL 2 INHIBITORS OF GLUTAMATE CARBOXYPEPTIDASE II. JRNL REF BIOORG.MED.CHEM.LETT. V. 24 2340 2014 JRNL REFN ISSN 0960-894X JRNL PMID 24731280 JRNL DOI 10.1016/J.BMCL.2014.03.066 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 121587 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2494 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7881 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.2830 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 : 240 REMARK 3 SOLVENT ATOMS : 534 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.180 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6332 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8639 ; 1.683 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 744 ; 5.709 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 292 ;35.812 ;23.836 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1039 ;14.246 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;14.013 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 950 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4860 ; 0.010 ; 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): 3670 ; 1.120 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5999 ; 1.840 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2662 ; 2.896 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2640 ; 4.508 ; 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 55 A 750 REMARK 3 RESIDUE RANGE : A 817 A 820 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7841 49.7142 44.8868 REMARK 3 T TENSOR REMARK 3 T11: 0.0196 T22: 0.0673 REMARK 3 T33: 0.0560 T12: 0.0179 REMARK 3 T13: 0.0078 T23: -0.0312 REMARK 3 L TENSOR REMARK 3 L11: 0.6666 L22: 1.0753 REMARK 3 L33: 0.3760 L12: -0.3017 REMARK 3 L13: 0.0458 L23: 0.1267 REMARK 3 S TENSOR REMARK 3 S11: -0.0670 S12: 0.0303 S13: -0.0464 REMARK 3 S21: 0.0105 S22: 0.0864 S23: -0.1959 REMARK 3 S31: 0.0322 S32: 0.0767 S33: -0.0194 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 4OC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084303. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 REMARK 200 MONOCHROMATOR : SI 220. ROSENBAUM-ROCK DOUBLE REMARK 200 -CRYSTAL MONOCHROMATOR. 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 : 124655 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.5.0109 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33% (V/V) PENTAERYTHRITOL PROPOXYLATE REMARK 280 PO/OH 5/4, 1% (W/V) PEG 3350, 100 MM TRIS-HCL, PH 8.0, VAPOR REMARK 280 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 50.66900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.12350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.53650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.66900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.12350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.53650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 50.66900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.12350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.53650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 50.66900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.12350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.53650 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: 13600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 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 130.24700 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 ARG A 42 REMARK 465 SER A 43 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 TYR A 151 N ASN A 153 1.94 REMARK 500 O GLU A 648 NE2 GLN A 651 2.03 REMARK 500 OD2 ASP A 666 O HOH A 1111 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1111 O HOH A 1365 2565 1.98 REMARK 500 O HOH A 1225 O HOH A 1359 2565 2.05 REMARK 500 OE2 GLU A 152 O HOH A 1335 7545 2.18 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 ARG A 370 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 440 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 673 NE - CZ - NH1 ANGL. DEV. = 4.5 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 GLU A 152 -14.22 -11.73 REMARK 500 PHE A 164 4.09 86.75 REMARK 500 ASN A 178 -125.49 57.75 REMARK 500 ASN A 178 -125.49 59.98 REMARK 500 LYS A 207 -42.37 71.21 REMARK 500 ASN A 262 -1.75 -146.01 REMARK 500 VAL A 382 -108.00 -129.81 REMARK 500 ALA A 452 64.27 -150.35 REMARK 500 ASP A 453 -158.70 -86.41 REMARK 500 SER A 454 124.79 -36.94 REMARK 500 SER A 517 -159.83 -128.68 REMARK 500 TRP A 541 73.15 -159.06 REMARK 500 ASP A 567 64.46 -155.89 REMARK 500 ASP A 683 13.04 57.12 REMARK 500 ASP A 683 11.19 57.12 REMARK 500 ASN A 698 97.09 -165.10 REMARK 500 PHE A 705 58.43 38.76 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 819 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 269 O REMARK 620 2 THR A 269 OG1 72.8 REMARK 620 3 TYR A 272 O 74.3 92.9 REMARK 620 4 GLU A 433 OE1 152.4 89.0 86.5 REMARK 620 5 GLU A 433 OE2 148.1 97.2 137.4 52.6 REMARK 620 6 GLU A 436 OE2 104.2 172.8 80.0 91.4 88.6 REMARK 620 7 HOH A 905 O 73.4 89.2 145.4 128.1 76.3 96.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 818 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 377 NE2 REMARK 620 2 ASP A 387 OD1 109.3 REMARK 620 3 ASP A 453 OD2 100.6 117.4 REMARK 620 4 HOH A1348 O 111.1 106.7 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 817 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 387 OD2 REMARK 620 2 GLU A 425 OE2 100.5 REMARK 620 3 GLU A 425 OE1 155.9 56.7 REMARK 620 4 HIS A 553 NE2 91.6 101.8 86.5 REMARK 620 5 2QQ A 821 OAD 107.4 151.1 96.4 85.1 REMARK 620 6 HOH A1348 O 97.2 95.5 92.9 158.8 73.9 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OC0 RELATED DB: PDB REMARK 900 RELATED ID: 4OC1 RELATED DB: PDB REMARK 900 RELATED ID: 4OC3 RELATED DB: PDB REMARK 900 RELATED ID: 4OC4 RELATED DB: PDB REMARK 900 RELATED ID: 4OC5 RELATED DB: PDB DBREF 4OC2 A 44 750 UNP Q04609 FOLH1_HUMAN 44 750 SEQADV 4OC2 ARG A 42 UNP Q04609 EXPRESSION TAG SEQADV 4OC2 SER A 43 UNP Q04609 EXPRESSION TAG SEQRES 1 A 709 ARG SER LYS SER SER ASN GLU ALA THR ASN ILE THR PRO SEQRES 2 A 709 LYS HIS ASN MET LYS ALA PHE LEU ASP GLU LEU LYS ALA SEQRES 3 A 709 GLU ASN ILE LYS LYS PHE LEU TYR ASN PHE THR GLN ILE SEQRES 4 A 709 PRO HIS LEU ALA GLY THR GLU GLN ASN PHE GLN LEU ALA SEQRES 5 A 709 LYS GLN ILE GLN SER GLN TRP LYS GLU PHE GLY LEU ASP SEQRES 6 A 709 SER VAL GLU LEU ALA HIS TYR ASP VAL LEU LEU SER TYR SEQRES 7 A 709 PRO ASN LYS THR HIS PRO ASN TYR ILE SER ILE ILE ASN SEQRES 8 A 709 GLU ASP GLY ASN GLU ILE PHE ASN THR SER LEU PHE GLU SEQRES 9 A 709 PRO PRO PRO PRO GLY TYR GLU ASN VAL SER ASP ILE VAL SEQRES 10 A 709 PRO PRO PHE SER ALA PHE SER PRO GLN GLY MET PRO GLU SEQRES 11 A 709 GLY ASP LEU VAL TYR VAL ASN TYR ALA ARG THR GLU ASP SEQRES 12 A 709 PHE PHE LYS LEU GLU ARG ASP MET LYS ILE ASN CYS SER SEQRES 13 A 709 GLY LYS ILE VAL ILE ALA ARG TYR GLY LYS VAL PHE ARG SEQRES 14 A 709 GLY ASN LYS VAL LYS ASN ALA GLN LEU ALA GLY ALA LYS SEQRES 15 A 709 GLY VAL ILE LEU TYR SER ASP PRO ALA ASP TYR PHE ALA SEQRES 16 A 709 PRO GLY VAL LYS SER TYR PRO ASP GLY TRP ASN LEU PRO SEQRES 17 A 709 GLY GLY GLY VAL GLN ARG GLY ASN ILE LEU ASN LEU ASN SEQRES 18 A 709 GLY ALA GLY ASP PRO LEU THR PRO GLY TYR PRO ALA ASN SEQRES 19 A 709 GLU TYR ALA TYR ARG ARG GLY ILE ALA GLU ALA VAL GLY SEQRES 20 A 709 LEU PRO SER ILE PRO VAL HIS PRO ILE GLY TYR TYR ASP SEQRES 21 A 709 ALA GLN LYS LEU LEU GLU LYS MET GLY GLY SER ALA PRO SEQRES 22 A 709 PRO ASP SER SER TRP ARG GLY SER LEU LYS VAL PRO TYR SEQRES 23 A 709 ASN VAL GLY PRO GLY PHE THR GLY ASN PHE SER THR GLN SEQRES 24 A 709 LYS VAL LYS MET HIS ILE HIS SER THR ASN GLU VAL THR SEQRES 25 A 709 ARG ILE TYR ASN VAL ILE GLY THR LEU ARG GLY ALA VAL SEQRES 26 A 709 GLU PRO ASP ARG TYR VAL ILE LEU GLY GLY HIS ARG ASP SEQRES 27 A 709 SER TRP VAL PHE GLY GLY ILE ASP PRO GLN SER GLY ALA SEQRES 28 A 709 ALA VAL VAL HIS GLU ILE VAL ARG SER PHE GLY THR LEU SEQRES 29 A 709 LYS LYS GLU GLY TRP ARG PRO ARG ARG THR ILE LEU PHE SEQRES 30 A 709 ALA SER TRP ASP ALA GLU GLU PHE GLY LEU LEU GLY SER SEQRES 31 A 709 THR GLU TRP ALA GLU GLU ASN SER ARG LEU LEU GLN GLU SEQRES 32 A 709 ARG GLY VAL ALA TYR ILE ASN ALA ASP SER SER ILE GLU SEQRES 33 A 709 GLY ASN TYR THR LEU ARG VAL ASP CYS THR PRO LEU MET SEQRES 34 A 709 TYR SER LEU VAL HIS ASN LEU THR LYS GLU LEU LYS SER SEQRES 35 A 709 PRO ASP GLU GLY PHE GLU GLY LYS SER LEU TYR GLU SER SEQRES 36 A 709 TRP THR LYS LYS SER PRO SER PRO GLU PHE SER GLY MET SEQRES 37 A 709 PRO ARG ILE SER LYS LEU GLY SER GLY ASN ASP PHE GLU SEQRES 38 A 709 VAL PHE PHE GLN ARG LEU GLY ILE ALA SER GLY ARG ALA SEQRES 39 A 709 ARG TYR THR LYS ASN TRP GLU THR ASN LYS PHE SER GLY SEQRES 40 A 709 TYR PRO LEU TYR HIS SER VAL TYR GLU THR TYR GLU LEU SEQRES 41 A 709 VAL GLU LYS PHE TYR ASP PRO MET PHE LYS TYR HIS LEU SEQRES 42 A 709 THR VAL ALA GLN VAL ARG GLY GLY MET VAL PHE GLU LEU SEQRES 43 A 709 ALA ASN SER ILE VAL LEU PRO PHE ASP CYS ARG ASP TYR SEQRES 44 A 709 ALA VAL VAL LEU ARG LYS TYR ALA ASP LYS ILE TYR SER SEQRES 45 A 709 ILE SER MET LYS HIS PRO GLN GLU MET LYS THR TYR SER SEQRES 46 A 709 VAL SER PHE ASP SER LEU PHE SER ALA VAL LYS ASN PHE SEQRES 47 A 709 THR GLU ILE ALA SER LYS PHE SER GLU ARG LEU GLN ASP SEQRES 48 A 709 PHE ASP LYS SER ASN PRO ILE VAL LEU ARG MET MET ASN SEQRES 49 A 709 ASP GLN LEU MET PHE LEU GLU ARG ALA PHE ILE ASP PRO SEQRES 50 A 709 LEU GLY LEU PRO ASP ARG PRO PHE TYR ARG HIS VAL ILE SEQRES 51 A 709 TYR ALA PRO SER SER HIS ASN LYS TYR ALA GLY GLU SER SEQRES 52 A 709 PHE PRO GLY ILE TYR ASP ALA LEU PHE ASP ILE GLU SER SEQRES 53 A 709 LYS VAL ASP PRO SER LYS ALA TRP GLY GLU VAL LYS ARG SEQRES 54 A 709 GLN ILE TYR VAL ALA ALA PHE THR VAL GLN ALA ALA ALA SEQRES 55 A 709 GLU THR LEU SER GLU VAL ALA MODRES 4OC2 ASN A 76 ASN GLYCOSYLATION SITE MODRES 4OC2 ASN A 140 ASN GLYCOSYLATION SITE MODRES 4OC2 ASN A 638 ASN GLYCOSYLATION SITE MODRES 4OC2 ASN A 476 ASN GLYCOSYLATION SITE MODRES 4OC2 ASN A 121 ASN GLYCOSYLATION SITE MODRES 4OC2 ASN A 195 ASN GLYCOSYLATION SITE MODRES 4OC2 ASN A 459 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET FUC C 2 10 HET NAG D 1 14 HET NAG D 2 14 HET FUC D 3 10 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 NAG A 808 14 HET NAG A 809 14 HET ZN A 817 1 HET ZN A 818 1 HET CA A 819 1 HET CL A 820 1 HET 2QQ A 821 29 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM 2QQ N~2~-{[(1S)-1-CARBOXYBUT-3-YN-1-YL]CARBAMOYL}-N~6~-(4- HETNAM 2 2QQ IODOBENZOYL)-L-LYSINE FORMUL 2 NAG 11(C8 H15 N O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 5 BMA 2(C6 H12 O6) FORMUL 6 MAN C6 H12 O6 FORMUL 9 ZN 2(ZN 2+) FORMUL 11 CA CA 2+ FORMUL 12 CL CL 1- FORMUL 13 2QQ C19 H22 I N3 O6 FORMUL 14 HOH *534(H2 O) HELIX 1 1 ASN A 57 LEU A 65 1 9 HELIX 2 2 LYS A 66 THR A 78 1 13 HELIX 3 3 THR A 86 GLY A 104 1 19 HELIX 4 4 ARG A 181 ASP A 191 1 11 HELIX 5 5 PHE A 209 ALA A 220 1 12 HELIX 6 6 ASP A 230 PHE A 235 1 6 HELIX 7 7 GLY A 282 ALA A 286 5 5 HELIX 8 8 GLY A 298 GLU A 307 1 10 HELIX 9 9 ASP A 316 ARG A 320 5 5 HELIX 10 10 THR A 334 SER A 338 5 5 HELIX 11 11 PRO A 388 GLU A 408 1 21 HELIX 12 12 ALA A 423 GLY A 427 5 5 HELIX 13 13 LEU A 428 ARG A 445 1 18 HELIX 14 14 MET A 470 LEU A 481 1 12 HELIX 15 15 SER A 492 SER A 501 1 10 HELIX 16 16 PHE A 521 ARG A 527 1 7 HELIX 17 17 TRP A 541 LYS A 545 5 5 HELIX 18 18 THR A 558 TYR A 566 1 9 HELIX 19 19 PHE A 570 SER A 590 1 21 HELIX 20 20 ASP A 596 MET A 616 1 21 HELIX 21 21 HIS A 618 TYR A 625 1 8 HELIX 22 22 PHE A 629 ASP A 652 1 24 HELIX 23 23 ASN A 657 ALA A 674 1 18 HELIX 24 24 PHE A 705 PHE A 713 1 9 HELIX 25 25 ASP A 714 LYS A 718 5 5 HELIX 26 26 ASP A 720 THR A 745 1 26 SHEET 1 A 7 SER A 107 TYR A 119 0 SHEET 2 A 7 THR A 349 LEU A 362 -1 O ASN A 357 N ALA A 111 SHEET 3 A 7 ARG A 414 TRP A 421 -1 O PHE A 418 N GLY A 360 SHEET 4 A 7 GLU A 367 HIS A 377 1 N VAL A 372 O THR A 415 SHEET 5 A 7 GLY A 446 ASN A 451 1 O ILE A 450 N ILE A 373 SHEET 6 A 7 ALA A 531 THR A 538 1 O GLY A 533 N ASN A 451 SHEET 7 A 7 THR A 461 CYS A 466 -1 N THR A 461 O THR A 538 SHEET 1 B 4 GLU A 137 ASN A 140 0 SHEET 2 B 4 TYR A 127 ILE A 131 -1 N ILE A 130 O ILE A 138 SHEET 3 B 4 LYS A 341 HIS A 345 -1 O LYS A 343 N SER A 129 SHEET 4 B 4 GLU A 171 GLY A 172 -1 N GLY A 172 O VAL A 342 SHEET 1 C 2 SER A 162 ALA A 163 0 SHEET 2 C 2 GLY A 256 ASN A 257 1 O GLY A 256 N ALA A 163 SHEET 1 D 4 LEU A 174 TYR A 176 0 SHEET 2 D 4 ILE A 200 ARG A 204 1 O ILE A 202 N VAL A 175 SHEET 3 D 4 GLY A 224 TYR A 228 1 O ILE A 226 N VAL A 201 SHEET 4 D 4 VAL A 294 ILE A 297 1 O HIS A 295 N LEU A 227 SHEET 1 E 2 TYR A 692 SER A 695 0 SHEET 2 E 2 ASN A 698 SER A 704 -1 O ALA A 701 N SER A 695 LINK ND2 ASN A 76 C1 NAG B 1 1555 1555 1.42 LINK ND2 ASN A 121 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 140 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN A 195 C1 NAG A 808 1555 1555 1.44 LINK ND2 ASN A 459 C1 NAG A 809 1555 1555 1.45 LINK ND2 ASN A 476 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN A 638 C1 NAG F 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O6 NAG C 1 C1 FUC C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.46 LINK O6 NAG D 1 C1 FUC D 3 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.44 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.42 LINK O3 BMA F 3 C1 MAN F 4 1555 1555 1.46 LINK O THR A 269 CA CA A 819 1555 1555 2.42 LINK OG1 THR A 269 CA CA A 819 1555 1555 2.50 LINK O TYR A 272 CA CA A 819 1555 1555 2.30 LINK NE2 HIS A 377 ZN ZN A 818 1555 1555 2.01 LINK OD2 ASP A 387 ZN ZN A 817 1555 1555 2.09 LINK OD1 ASP A 387 ZN ZN A 818 1555 1555 1.93 LINK OE2 GLU A 425 ZN ZN A 817 1555 1555 2.15 LINK OE1 GLU A 425 ZN ZN A 817 1555 1555 2.42 LINK OE1 GLU A 433 CA CA A 819 1555 1555 2.44 LINK OE2 GLU A 433 CA CA A 819 1555 1555 2.48 LINK OE2 GLU A 436 CA CA A 819 1555 1555 2.28 LINK OD2 ASP A 453 ZN ZN A 818 1555 1555 1.93 LINK NE2 HIS A 553 ZN ZN A 817 1555 1555 2.03 LINK ZN ZN A 817 OAD 2QQ A 821 1555 1555 2.67 LINK ZN ZN A 817 O HOH A1348 1555 1555 1.99 LINK ZN ZN A 818 O HOH A1348 1555 1555 1.94 LINK CA CA A 819 O HOH A 905 1555 1555 2.47 CISPEP 1 TYR A 242 PRO A 243 0 13.65 CISPEP 2 GLY A 330 PRO A 331 0 -0.23 CISPEP 3 ASP A 387 PRO A 388 0 8.98 CRYST1 101.338 130.247 159.073 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 0.009868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006286 0.00000