HEADER HYDROLASE 21-MAY-08 3D7F TITLE A HIGH RESOLUTION CRYSTAL STRUCTURE OF HUMAN GLUTAMATE TITLE 2 CARBOXYPEPTIDASE II (GCPII) IN A COMPLEX WITH DCIT, A UREA-BASED TITLE 3 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE CARBOXYPEPTIDASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTAMATE CARBOXYPEPTIDASE II, MEMBRANE GLUTAMATE COMPND 5 CARBOXYPEPTIDASE, MGCP, N-ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE COMPND 6 I, NAALADASE I, PTEROYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE, COMPND 7 FOLYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE, FGCP, FOLATE HYDROLASE 1, COMPND 8 PROSTATE-SPECIFIC MEMBRANE ANTIGEN, PSMA, PSM; COMPND 9 EC: 3.4.17.21; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: FOLH1, FOLH, NAALAD1, PSM, PSMA; SOURCE 5 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: SCHNEIDER'S S2 CELLS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROSTATE SPECIFIC MEMBRANE ANTIGEN; METALLOPEPTIDASE; FOLATE KEYWDS 2 HYDROLASE; GLUTAMATE CARBOXYPEPTIDASE II; NAALADASE, DCIT, UREA- KEYWDS 3 BASED INHIBITOR, CARBOXYPEPTIDASE, DIPEPTIDASE, GLYCOPROTEIN, KEYWDS 4 HYDROLASE, MEMBRANE, METAL-BINDING, METALLOPROTEASE, MULTIFUNCTIONAL KEYWDS 5 ENZYME, PROTEASE, SIGNAL-ANCHOR, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR J.LUBKOWSKI,C.BARINKA REVDAT 5 30-OCT-24 3D7F 1 REMARK REVDAT 4 30-AUG-23 3D7F 1 HETSYN REVDAT 3 29-JUL-20 3D7F 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 13-JUL-11 3D7F 1 VERSN REVDAT 1 30-DEC-08 3D7F 0 JRNL AUTH C.BARINKA,Y.BYUN,C.L.DUSICH,S.R.BANERJEE,Y.CHEN, JRNL AUTH 2 M.CASTANARES,A.P.KOZIKOWSKI,R.C.MEASE,M.G.POMPER,J.LUBKOWSKI JRNL TITL INTERACTIONS BETWEEN HUMAN GLUTAMATE CARBOXYPEPTIDASE II AND JRNL TITL 2 UREA-BASED INHIBITORS: STRUCTURAL CHARACTERIZATION JRNL REF J.MED.CHEM. V. 51 7737 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 19053759 JRNL DOI 10.1021/JM800765E REMARK 2 REMARK 2 RESOLUTION. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 142946 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1446 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6554 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 217 REMARK 3 SOLVENT ATOMS : 657 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.85000 REMARK 3 B22 (A**2) : -1.76000 REMARK 3 B33 (A**2) : 0.92000 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.345 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6113 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8298 ; 1.787 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 695 ;10.804 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 288 ;36.489 ;23.993 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1024 ;14.583 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;14.815 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 907 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4591 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3038 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4221 ; 0.325 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 610 ; 0.173 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.055 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 99 ; 0.270 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 44 ; 0.244 ; 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): 3532 ; 1.136 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5714 ; 1.788 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2851 ; 2.723 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2584 ; 4.081 ; 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): 4 ; 6.498 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 25 ; 8.015 ; 3.000 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: NULL REMARK 4 REMARK 4 3D7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 144557 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 2OOT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 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 50.71700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.02950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.27150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.71700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.02950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.27150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 50.71700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.02950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.27150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 50.71700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.02950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.27150 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: 12200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 130.05900 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2305 LIES ON A SPECIAL POSITION. 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 LYS A 545 REMARK 465 PHE A 546 REMARK 465 SER A 547 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 OH TYR A 242 O HOH A 2416 2.01 REMARK 500 O HOH A 2012 O HOH A 2417 2.09 REMARK 500 O HOH A 2191 O HOH A 2292 2.14 REMARK 500 OD1 ASN A 589 O HOH A 2417 2.17 REMARK 500 OD2 ASP A 666 O HOH A 1986 2.18 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 1986 O HOH A 2331 2565 1.93 REMARK 500 O HOH A 2034 O HOH A 2161 2565 1.95 REMARK 500 OG SER A 656 O HOH A 2128 4566 2.06 REMARK 500 O SER A 656 O HOH A 2128 4566 2.11 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 PRO A 243 C - N - CD ANGL. DEV. = -15.6 DEGREES REMARK 500 ARG A 370 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 370 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 673 NE - CZ - NH2 ANGL. DEV. = -4.1 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 HIS A 124 74.15 -151.14 REMARK 500 PHE A 164 5.59 84.82 REMARK 500 ASN A 178 -126.53 58.55 REMARK 500 LYS A 207 -46.34 72.75 REMARK 500 VAL A 382 -107.41 -127.15 REMARK 500 ALA A 452 61.09 -150.47 REMARK 500 ASP A 453 -154.31 -84.08 REMARK 500 SER A 454 126.55 -37.66 REMARK 500 SER A 517 -159.22 -152.13 REMARK 500 ASP A 567 64.42 -153.21 REMARK 500 ASP A 683 12.85 59.69 REMARK 500 ASN A 698 99.96 -168.93 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 TYR A 242 PRO A 243 44.01 REMARK 500 GLY A 330 PRO A 331 49.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR A 242 10.15 REMARK 500 GLY A 330 13.06 REMARK 500 ASP A 387 10.31 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 A1753 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 269 O REMARK 620 2 THR A 269 OG1 73.2 REMARK 620 3 TYR A 272 O 74.6 92.2 REMARK 620 4 GLU A 433 OE1 151.3 87.9 85.1 REMARK 620 5 GLU A 433 OE2 149.9 98.7 135.4 52.5 REMARK 620 6 GLU A 436 OE2 104.9 172.4 80.2 90.9 86.5 REMARK 620 7 HOH A1774 O 73.7 90.9 145.7 129.1 77.6 95.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1752 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 377 NE2 REMARK 620 2 ASP A 387 OD1 108.1 REMARK 620 3 ASP A 453 OD2 103.0 119.1 REMARK 620 4 HOH A2352 O 106.5 106.6 112.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1751 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 387 OD2 REMARK 620 2 GLU A 425 OE2 102.8 REMARK 620 3 HIS A 553 NE2 89.4 100.7 REMARK 620 4 HOH A2352 O 100.5 93.1 160.8 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D7D RELATED DB: PDB REMARK 900 RELATED ID: 3D7G RELATED DB: PDB REMARK 900 RELATED ID: 3D7H RELATED DB: PDB DBREF 3D7F A 44 750 UNP Q04609 FOLH1_HUMAN 44 750 SEQADV 3D7F ARG A 42 UNP Q04609 EXPRESSION TAG SEQADV 3D7F 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 3D7F ASN A 76 ASN GLYCOSYLATION SITE MODRES 3D7F ASN A 121 ASN GLYCOSYLATION SITE MODRES 3D7F ASN A 140 ASN GLYCOSYLATION SITE MODRES 3D7F ASN A 195 ASN GLYCOSYLATION SITE MODRES 3D7F ASN A 459 ASN GLYCOSYLATION SITE MODRES 3D7F ASN A 476 ASN GLYCOSYLATION SITE MODRES 3D7F ASN A 638 ASN GLYCOSYLATION SITE 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 BMA D 3 11 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET NAG A1757 14 HET NAG A1759 14 HET NAG A1760 14 HET ZN A1751 1 HET ZN A1752 1 HET CA A1753 1 HET CL A1754 1 HET YBY A 1 26 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 YBY N-{[(1S)-1-CARBOXY-2-(4-HYDROXY-3-IODOPHENYL) HETNAM 2 YBY ETHYL]CARBAMOYL}-L-GLUTAMIC ACID 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 HETSYN YBY (S)-2-(3-((S)-1-CARBOXY-2-(4-HYDROXY-3-IODOPHENYL) HETSYN 2 YBY ETHYL)UREIDO)PENTANEDIOIC ACID FORMUL 2 NAG 11(C8 H15 N O6) FORMUL 4 BMA 2(C6 H12 O6) FORMUL 5 MAN C6 H12 O6 FORMUL 9 ZN 2(ZN 2+) FORMUL 11 CA CA 2+ FORMUL 12 CL CL 1- FORMUL 13 YBY C15 H17 I N2 O8 FORMUL 14 HOH *657(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 PHE A 103 1 18 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 GLU A 480 1 11 HELIX 15 15 SER A 492 SER A 501 1 10 HELIX 16 16 ASP A 520 ARG A 527 1 8 HELIX 17 17 THR A 558 TYR A 566 1 9 HELIX 18 18 PHE A 570 SER A 590 1 21 HELIX 19 19 ASP A 596 MET A 616 1 21 HELIX 20 20 HIS A 618 TYR A 625 1 8 HELIX 21 21 PHE A 629 PHE A 653 1 25 HELIX 22 22 ASN A 657 ALA A 674 1 18 HELIX 23 23 PHE A 705 PHE A 713 1 9 HELIX 24 24 ASP A 714 LYS A 718 5 5 HELIX 25 25 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 LEU A 374 O LEU A 417 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 PHE A 139 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 N GLY A 256 O 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 ALA A 203 SHEET 4 D 4 VAL A 294 ILE A 297 1 O ILE A 297 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 1.44 LINK ND2 ASN A 121 C1 NAG A1757 1555 1555 1.45 LINK ND2 ASN A 140 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 195 C1 NAG A1759 1555 1555 1.45 LINK ND2 ASN A 459 C1 NAG A1760 1555 1555 1.46 LINK ND2 ASN A 476 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 638 C1 NAG E 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.43 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.43 LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.45 LINK O THR A 269 CA CA A1753 1555 1555 2.42 LINK OG1 THR A 269 CA CA A1753 1555 1555 2.46 LINK O TYR A 272 CA CA A1753 1555 1555 2.32 LINK NE2 HIS A 377 ZN ZN A1752 1555 1555 2.02 LINK OD2 ASP A 387 ZN ZN A1751 1555 1555 2.02 LINK OD1 ASP A 387 ZN ZN A1752 1555 1555 1.95 LINK OE2 GLU A 425 ZN ZN A1751 1555 1555 2.15 LINK OE1 GLU A 433 CA CA A1753 1555 1555 2.48 LINK OE2 GLU A 433 CA CA A1753 1555 1555 2.50 LINK OE2 GLU A 436 CA CA A1753 1555 1555 2.35 LINK OD2 ASP A 453 ZN ZN A1752 1555 1555 1.94 LINK NE2 HIS A 553 ZN ZN A1751 1555 1555 2.05 LINK ZN ZN A1751 O HOH A2352 1555 1555 2.03 LINK ZN ZN A1752 O HOH A2352 1555 1555 1.98 LINK CA CA A1753 O HOH A1774 1555 1555 2.39 CISPEP 1 ASP A 387 PRO A 388 0 29.11 CRYST1 101.434 130.059 158.543 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 0.009859 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006307 0.00000