HEADER HYDROLASE 05-NOV-15 5ELY TITLE X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN TITLE 2 COMPLEX WITH A HYDROXAMATE INHIBITOR JHU242 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE CARBOXYPEPTIDASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 55-750; 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; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROSTATE-SPECIFIC MEMBRANE ANTIGEN, NAALADASE, PHOSPHORAMIDATE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.BARINKA,Z.NOVAKOVA,J.PAVLICEK REVDAT 3 29-JUL-20 5ELY 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 08-JUN-16 5ELY 1 JRNL REVDAT 1 27-APR-16 5ELY 0 JRNL AUTH Z.NOVAKOVA,K.WOZNIAK,A.JANCARIK,R.RAIS,Y.WU,J.PAVLICEK, JRNL AUTH 2 D.FERRARIS,B.HAVLINOVA,J.PTACEK,J.VAVRA,N.HIN,C.ROJAS, JRNL AUTH 3 P.MAJER,B.S.SLUSHER,T.TSUKAMOTO,C.BARINKA JRNL TITL UNPRECEDENTED BINDING MODE OF HYDROXAMATE-BASED INHIBITORS JRNL TITL 2 OF GLUTAMATE CARBOXYPEPTIDASE II: STRUCTURAL JRNL TITL 3 CHARACTERIZATION AND BIOLOGICAL ACTIVITY. JRNL REF J.MED.CHEM. V. 59 4539 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27074627 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01806 REMARK 2 REMARK 2 RESOLUTION. 1.81 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 94013 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT : 952 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) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6640 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5436 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 190 REMARK 3 SOLVENT ATOMS : 466 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.18000 REMARK 3 B22 (A**2) : -2.02000 REMARK 3 B33 (A**2) : 0.84000 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): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.350 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6118 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8346 ; 1.658 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 745 ; 6.207 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 279 ;36.169 ;23.871 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1006 ;14.650 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;15.023 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 900 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4738 ; 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): 3585 ; 1.014 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5846 ; 1.683 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2533 ; 2.577 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2487 ; 4.102 ; 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 750 REMARK 3 ORIGIN FOR THE GROUP (A): 17.5404 50.0822 45.0093 REMARK 3 T TENSOR REMARK 3 T11: 0.0430 T22: 0.0623 REMARK 3 T33: 0.0654 T12: 0.0118 REMARK 3 T13: 0.0082 T23: -0.0378 REMARK 3 L TENSOR REMARK 3 L11: 0.2546 L22: 0.5553 REMARK 3 L33: 0.0831 L12: -0.3111 REMARK 3 L13: 0.0591 L23: 0.0110 REMARK 3 S TENSOR REMARK 3 S11: -0.0377 S12: 0.0358 S13: 0.0171 REMARK 3 S21: 0.0360 S22: 0.0487 S23: -0.1098 REMARK 3 S31: 0.0142 S32: 0.0409 S33: -0.0110 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: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5ELY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000211143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-11 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 : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SAGITALLY BENDED SI111 DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 100.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.59 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, 2 % (W/V) PEG 3350, AND 100 MM TRIS-HCL, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K 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 50.53000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.41350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.19300 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.53000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.41350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.19300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 50.53000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.41350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.19300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 50.53000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.41350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.19300 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: 12100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 130.82700 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 ASN A 132 REMARK 465 GLU A 133 REMARK 465 ASP A 134 REMARK 465 GLY A 135 REMARK 465 ASN A 544 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 465 LYS A 699 REMARK 465 TYR A 700 REMARK 465 ALA A 701 REMARK 465 GLY A 702 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 CH3 ACT A 818 O HOH A 1238 1.88 REMARK 500 ND2 ASN A 260 O HOH A 902 2.03 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 OE1 GLU A 276 O2 BMA E 3 2565 2.19 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 VAL A 158 CB VAL A 158 CG1 0.133 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 536 NE - CZ - NH2 ANGL. DEV. = -3.3 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 ASN A 153 41.74 -101.32 REMARK 500 PHE A 164 5.14 84.12 REMARK 500 ASN A 178 -126.93 57.35 REMARK 500 LYS A 207 -50.74 81.96 REMARK 500 VAL A 382 -106.58 -134.19 REMARK 500 ALA A 452 57.68 -156.51 REMARK 500 SER A 454 120.82 -32.18 REMARK 500 SER A 454 120.88 -32.18 REMARK 500 TRP A 541 29.73 -75.50 REMARK 500 GLU A 542 48.98 -148.21 REMARK 500 ASP A 567 64.24 -155.10 REMARK 500 SER A 704 172.38 -56.25 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 HIS A 697 ASN A 698 144.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1365 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A1366 DISTANCE = 7.30 ANGSTROMS 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 73.5 REMARK 620 3 TYR A 272 O 73.1 92.6 REMARK 620 4 GLU A 433 OE1 150.2 88.3 84.8 REMARK 620 5 GLU A 433 OE2 149.5 96.5 137.1 53.9 REMARK 620 6 GLU A 436 OE2 102.8 173.2 80.8 92.7 89.5 REMARK 620 7 HOH A 966 O 75.0 91.3 145.1 130.0 76.5 93.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 377 NE2 REMARK 620 2 ASP A 387 OD1 96.6 REMARK 620 3 ASP A 453 OD1 85.8 91.3 REMARK 620 4 ASP A 453 OD2 94.0 144.3 55.5 REMARK 620 5 5PU A 817 OAD 96.3 109.6 158.4 102.9 REMARK 620 6 HOH A1126 O 176.0 85.2 90.5 82.4 86.4 REMARK 620 N 1 2 3 4 5 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 152.7 REMARK 620 3 GLU A 425 OE2 97.3 56.0 REMARK 620 4 HIS A 553 NE2 92.7 87.4 100.9 REMARK 620 5 5PU A 817 OAD 99.8 86.9 89.4 162.7 REMARK 620 6 5PU A 817 OAC 102.9 104.4 156.1 90.7 74.9 REMARK 620 N 1 2 3 4 5 DBREF 5ELY A 55 750 UNP Q04609 FOLH1_HUMAN 55 750 SEQRES 1 A 696 LYS HIS ASN MET LYS ALA PHE LEU ASP GLU LEU LYS ALA SEQRES 2 A 696 GLU ASN ILE LYS LYS PHE LEU TYR ASN PHE THR GLN ILE SEQRES 3 A 696 PRO HIS LEU ALA GLY THR GLU GLN ASN PHE GLN LEU ALA SEQRES 4 A 696 LYS GLN ILE GLN SER GLN TRP LYS GLU PHE GLY LEU ASP SEQRES 5 A 696 SER VAL GLU LEU ALA HIS TYR ASP VAL LEU LEU SER TYR SEQRES 6 A 696 PRO ASN LYS THR HIS PRO ASN TYR ILE SER ILE ILE ASN SEQRES 7 A 696 GLU ASP GLY ASN GLU ILE PHE ASN THR SER LEU PHE GLU SEQRES 8 A 696 PRO PRO PRO PRO GLY TYR GLU ASN VAL SER ASP ILE VAL SEQRES 9 A 696 PRO PRO PHE SER ALA PHE SER PRO GLN GLY MET PRO GLU SEQRES 10 A 696 GLY ASP LEU VAL TYR VAL ASN TYR ALA ARG THR GLU ASP SEQRES 11 A 696 PHE PHE LYS LEU GLU ARG ASP MET LYS ILE ASN CYS SER SEQRES 12 A 696 GLY LYS ILE VAL ILE ALA ARG TYR GLY LYS VAL PHE ARG SEQRES 13 A 696 GLY ASN LYS VAL LYS ASN ALA GLN LEU ALA GLY ALA LYS SEQRES 14 A 696 GLY VAL ILE LEU TYR SER ASP PRO ALA ASP TYR PHE ALA SEQRES 15 A 696 PRO GLY VAL LYS SER TYR PRO ASP GLY TRP ASN LEU PRO SEQRES 16 A 696 GLY GLY GLY VAL GLN ARG GLY ASN ILE LEU ASN LEU ASN SEQRES 17 A 696 GLY ALA GLY ASP PRO LEU THR PRO GLY TYR PRO ALA ASN SEQRES 18 A 696 GLU TYR ALA TYR ARG ARG GLY ILE ALA GLU ALA VAL GLY SEQRES 19 A 696 LEU PRO SER ILE PRO VAL HIS PRO ILE GLY TYR TYR ASP SEQRES 20 A 696 ALA GLN LYS LEU LEU GLU LYS MET GLY GLY SER ALA PRO SEQRES 21 A 696 PRO ASP SER SER TRP ARG GLY SER LEU LYS VAL PRO TYR SEQRES 22 A 696 ASN VAL GLY PRO GLY PHE THR GLY ASN PHE SER THR GLN SEQRES 23 A 696 LYS VAL LYS MET HIS ILE HIS SER THR ASN GLU VAL THR SEQRES 24 A 696 ARG ILE TYR ASN VAL ILE GLY THR LEU ARG GLY ALA VAL SEQRES 25 A 696 GLU PRO ASP ARG TYR VAL ILE LEU GLY GLY HIS ARG ASP SEQRES 26 A 696 SER TRP VAL PHE GLY GLY ILE ASP PRO GLN SER GLY ALA SEQRES 27 A 696 ALA VAL VAL HIS GLU ILE VAL ARG SER PHE GLY THR LEU SEQRES 28 A 696 LYS LYS GLU GLY TRP ARG PRO ARG ARG THR ILE LEU PHE SEQRES 29 A 696 ALA SER TRP ASP ALA GLU GLU PHE GLY LEU LEU GLY SER SEQRES 30 A 696 THR GLU TRP ALA GLU GLU ASN SER ARG LEU LEU GLN GLU SEQRES 31 A 696 ARG GLY VAL ALA TYR ILE ASN ALA ASP SER SER ILE GLU SEQRES 32 A 696 GLY ASN TYR THR LEU ARG VAL ASP CYS THR PRO LEU MET SEQRES 33 A 696 TYR SER LEU VAL HIS ASN LEU THR LYS GLU LEU LYS SER SEQRES 34 A 696 PRO ASP GLU GLY PHE GLU GLY LYS SER LEU TYR GLU SER SEQRES 35 A 696 TRP THR LYS LYS SER PRO SER PRO GLU PHE SER GLY MET SEQRES 36 A 696 PRO ARG ILE SER LYS LEU GLY SER GLY ASN ASP PHE GLU SEQRES 37 A 696 VAL PHE PHE GLN ARG LEU GLY ILE ALA SER GLY ARG ALA SEQRES 38 A 696 ARG TYR THR LYS ASN TRP GLU THR ASN LYS PHE SER GLY SEQRES 39 A 696 TYR PRO LEU TYR HIS SER VAL TYR GLU THR TYR GLU LEU SEQRES 40 A 696 VAL GLU LYS PHE TYR ASP PRO MET PHE LYS TYR HIS LEU SEQRES 41 A 696 THR VAL ALA GLN VAL ARG GLY GLY MET VAL PHE GLU LEU SEQRES 42 A 696 ALA ASN SER ILE VAL LEU PRO PHE ASP CYS ARG ASP TYR SEQRES 43 A 696 ALA VAL VAL LEU ARG LYS TYR ALA ASP LYS ILE TYR SER SEQRES 44 A 696 ILE SER MET LYS HIS PRO GLN GLU MET LYS THR TYR SER SEQRES 45 A 696 VAL SER PHE ASP SER LEU PHE SER ALA VAL LYS ASN PHE SEQRES 46 A 696 THR GLU ILE ALA SER LYS PHE SER GLU ARG LEU GLN ASP SEQRES 47 A 696 PHE ASP LYS SER ASN PRO ILE VAL LEU ARG MET MET ASN SEQRES 48 A 696 ASP GLN LEU MET PHE LEU GLU ARG ALA PHE ILE ASP PRO SEQRES 49 A 696 LEU GLY LEU PRO ASP ARG PRO PHE TYR ARG HIS VAL ILE SEQRES 50 A 696 TYR ALA PRO SER SER HIS ASN LYS TYR ALA GLY GLU SER SEQRES 51 A 696 PHE PRO GLY ILE TYR ASP ALA LEU PHE ASP ILE GLU SER SEQRES 52 A 696 LYS VAL ASP PRO SER LYS ALA TRP GLY GLU VAL LYS ARG SEQRES 53 A 696 GLN ILE TYR VAL ALA ALA PHE THR VAL GLN ALA ALA ALA SEQRES 54 A 696 GLU THR LEU SER GLU VAL ALA 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 MAN E 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 807 14 HET NAG A 810 14 HET 5PU A 817 20 HET ACT A 818 4 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 5PU 4-[(2~{R})-2-CARBOXY-5-(OXIDANYLAMINO)-5-OXIDANYLIDENE- HETNAM 2 5PU PENTYL]BENZOIC ACID HETNAM ACT ACETATE ION HETSYN 5PU JHU242 FORMUL 2 NAG 10(C8 H15 N O6) FORMUL 5 BMA C6 H12 O6 FORMUL 5 MAN C6 H12 O6 FORMUL 6 ZN 2(ZN 2+) FORMUL 8 CA CA 2+ FORMUL 9 CL CL 1- FORMUL 12 5PU C13 H15 N O6 FORMUL 13 ACT C2 H3 O2 1- FORMUL 14 HOH *466(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 GLY A 104 1 19 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 ARG A 527 1 7 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 ASP A 652 1 24 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 PHE A 139 ASN A 140 0 SHEET 2 AA2 4 TYR A 127 ILE A 131 -1 N ILE A 130 O PHE A 139 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 ILE A 226 N ALA A 203 SHEET 4 AA4 4 VAL A 294 ILE A 297 1 O HIS A 295 N LEU A 227 LINK ND2 ASN A 76 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 121 C1 NAG A 807 1555 1555 1.44 LINK ND2 ASN A 140 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 459 C1 NAG A 810 1555 1555 1.45 LINK ND2 ASN A 476 C1 NAG D 1 1555 1555 1.43 LINK ND2 ASN A 638 C1 NAG E 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 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 1.43 LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.45 LINK O THR A 269 CA CA A 803 1555 1555 2.40 LINK OG1 THR A 269 CA CA A 803 1555 1555 2.46 LINK O TYR A 272 CA CA A 803 1555 1555 2.35 LINK NE2 HIS A 377 ZN ZN A 802 1555 1555 2.04 LINK OD2 ASP A 387 ZN ZN A 801 1555 1555 2.01 LINK OD1 ASP A 387 ZN ZN A 802 1555 1555 2.07 LINK OE1 GLU A 425 ZN ZN A 801 1555 1555 2.51 LINK OE2 GLU A 425 ZN ZN A 801 1555 1555 2.00 LINK OE1 GLU A 433 CA CA A 803 1555 1555 2.40 LINK OE2 GLU A 433 CA CA A 803 1555 1555 2.40 LINK OE2 GLU A 436 CA CA A 803 1555 1555 2.30 LINK OD1 ASP A 453 ZN ZN A 802 1555 1555 2.51 LINK OD2 ASP A 453 ZN ZN A 802 1555 1555 2.09 LINK NE2 HIS A 553 ZN ZN A 801 1555 1555 2.11 LINK ZN ZN A 801 OAD 5PU A 817 1555 1555 2.30 LINK ZN ZN A 801 OAC 5PU A 817 1555 1555 2.10 LINK ZN ZN A 802 OAD 5PU A 817 1555 1555 1.98 LINK ZN ZN A 802 O HOH A1126 1555 1555 2.16 LINK CA CA A 803 O HOH A 966 1555 1555 2.50 CISPEP 1 TYR A 242 PRO A 243 0 9.96 CISPEP 2 GLY A 330 PRO A 331 0 -1.15 CISPEP 3 ASP A 387 PRO A 388 0 2.85 CRYST1 101.060 130.827 158.386 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 0.009895 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006314 0.00000