HEADER TRANSFERASE/TRANSFERASE INHIBITOR 20-OCT-10 3PBB TITLE CRYSTAL STRUCTURE OF HUMAN SECRETORY GLUTAMINYL CYCLASE IN COMPLEX TITLE 2 WITH PBD150 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINYL-PEPTIDE CYCLOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FUNCTIONAL DOMAIN; COMPND 5 SYNONYM: GLUTAMINYL CYCLASE, QC, GLUTAMINYL-TRNA CYCLOTRANSFERASE, COMPND 6 GLUTAMYL CYCLASE, EC; COMPND 7 EC: 2.3.2.5; COMPND 8 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: QPCT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET 32A KEYWDS ALPHA/BETA PROTEIN, ALPHA/BETA-MIXED FOLD, GLUTAMINYL CYCLASE, KEYWDS 2 SECRETORY PATHWAY, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.F.HUANG,S.S.LIAW,W.L.HUANG,C.Y.CHIA,Y.C.LO,Y.L.CHEN,A.H.J.WANG REVDAT 3 01-NOV-23 3PBB 1 REMARK LINK REVDAT 2 03-AUG-11 3PBB 1 JRNL REVDAT 1 02-FEB-11 3PBB 0 JRNL AUTH K.F.HUANG,S.S.LIAW,W.L.HUANG,C.Y.CHIA,Y.C.LO,Y.L.CHEN, JRNL AUTH 2 A.H.J.WANG JRNL TITL STRUCTURES OF HUMAN GOLGI-RESIDENT GLUTAMINYL CYCLASE AND JRNL TITL 2 ITS COMPLEXES WITH INHIBITORS REVEAL A LARGE LOOP MOVEMENT JRNL TITL 3 UPON INHIBITOR BINDING JRNL REF J.BIOL.CHEM. V. 286 12439 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21288892 JRNL DOI 10.1074/JBC.M110.208595 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 49935 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2679 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3523 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 206 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.47000 REMARK 3 B22 (A**2) : -2.47000 REMARK 3 B33 (A**2) : 3.70000 REMARK 3 B12 (A**2) : -1.23000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.989 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5410 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7358 ; 1.863 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 638 ; 6.652 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 268 ;36.845 ;23.881 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 862 ;17.289 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;19.777 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 780 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4216 ; 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): 3230 ; 1.657 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5212 ; 2.698 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2180 ; 4.428 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2146 ; 6.336 ; 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): 5410 ; 2.315 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3PBB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53126 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.49200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2AFM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7M (NH4)2SO4, 4%(V/V) DIOXANE, 100MM REMARK 280 MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 77.87650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.96202 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.83867 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 77.87650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 44.96202 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.83867 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 77.87650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 44.96202 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.83867 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.92404 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 53.67733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 89.92404 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 53.67733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 89.92404 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 53.67733 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 THR A 183 REMARK 465 VAL A 184 REMARK 465 SER A 185 REMARK 465 ASP A 186 REMARK 465 SER A 187 REMARK 465 LYS A 188 REMARK 465 THR B 183 REMARK 465 VAL B 184 REMARK 465 SER B 185 REMARK 465 ASP B 186 REMARK 465 SER B 187 REMARK 465 LYS B 188 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA A 131 REMARK 475 ALA B 131 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 HOH B 595 O HOH B 630 1.90 REMARK 500 O HOH B 646 O HOH B 677 2.16 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 NH1 ARG B 312 O HOH A 500 9454 1.86 REMARK 500 OH TYR A 117 O HOH B 475 5565 2.10 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 TYR A 117 CZ TYR A 117 OH 0.104 REMARK 500 TYR A 117 CE2 TYR A 117 CD2 0.105 REMARK 500 GLU B 202 CB GLU B 202 CG 0.118 REMARK 500 ARG B 312 CG ARG B 312 CD 0.180 REMARK 500 TYR B 358 CD1 TYR B 358 CE1 0.103 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 ASP A 101 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 THR A 130 O - C - N ANGL. DEV. = -9.8 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 ARG A 77 43.32 -150.45 REMARK 500 LEU A 181 0.19 -69.57 REMARK 500 SER A 192 -152.51 -137.71 REMARK 500 LEU A 205 -62.29 -121.64 REMARK 500 SER A 212 157.66 170.97 REMARK 500 ASN A 263 47.16 -90.00 REMARK 500 SER A 264 9.24 -160.00 REMARK 500 ASP A 286 40.83 36.61 REMARK 500 ASN A 296 37.82 -64.13 REMARK 500 TRP A 329 123.79 -38.53 REMARK 500 SER B 34 82.14 -65.95 REMARK 500 ARG B 77 49.74 -143.19 REMARK 500 ASP B 101 58.40 -90.26 REMARK 500 ASN B 128 71.30 52.35 REMARK 500 SER B 160 44.25 -142.90 REMARK 500 SER B 212 157.96 167.44 REMARK 500 ASP B 305 -178.34 -172.01 REMARK 500 HIS B 360 59.18 76.84 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 B 297 SER B 298 143.93 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 THR A 130 -10.41 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 ZN A 391 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 159 OD2 REMARK 620 2 GLU A 202 OE2 105.3 REMARK 620 3 HIS A 330 NE2 94.9 109.9 REMARK 620 4 PBD A 380 NAM 126.4 109.9 109.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 392 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 159 OD2 REMARK 620 2 GLU B 202 OE2 101.8 REMARK 620 3 HIS B 330 NE2 96.9 113.5 REMARK 620 4 PBD B 381 NAM 122.0 114.8 106.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PBD A 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PBD B 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 392 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AFM RELATED DB: PDB REMARK 900 THE WILD-TYPE PROTEIN AT PH 6.5 REMARK 900 RELATED ID: 3PB4 RELATED DB: PDB REMARK 900 RELATED ID: 3PB6 RELATED DB: PDB REMARK 900 RELATED ID: 3PB7 RELATED DB: PDB REMARK 900 RELATED ID: 3PB8 RELATED DB: PDB REMARK 900 RELATED ID: 3PB9 RELATED DB: PDB REMARK 900 RELATED ID: 3PBE RELATED DB: PDB DBREF 3PBB A 33 361 UNP Q16769 QPCT_HUMAN 33 361 DBREF 3PBB B 33 361 UNP Q16769 QPCT_HUMAN 33 361 SEQRES 1 A 329 ALA SER ALA TRP PRO GLU GLU LYS ASN TYR HIS GLN PRO SEQRES 2 A 329 ALA ILE LEU ASN SER SER ALA LEU ARG GLN ILE ALA GLU SEQRES 3 A 329 GLY THR SER ILE SER GLU MET TRP GLN ASN ASP LEU GLN SEQRES 4 A 329 PRO LEU LEU ILE GLU ARG TYR PRO GLY SER PRO GLY SER SEQRES 5 A 329 TYR ALA ALA ARG GLN HIS ILE MET GLN ARG ILE GLN ARG SEQRES 6 A 329 LEU GLN ALA ASP TRP VAL LEU GLU ILE ASP THR PHE LEU SEQRES 7 A 329 SER GLN THR PRO TYR GLY TYR ARG SER PHE SER ASN ILE SEQRES 8 A 329 ILE SER THR LEU ASN PRO THR ALA LYS ARG HIS LEU VAL SEQRES 9 A 329 LEU ALA CYS HIS TYR ASP SER LYS TYR PHE SER HIS TRP SEQRES 10 A 329 ASN ASN ARG VAL PHE VAL GLY ALA THR ASP SER ALA VAL SEQRES 11 A 329 PRO CYS ALA MET MET LEU GLU LEU ALA ARG ALA LEU ASP SEQRES 12 A 329 LYS LYS LEU LEU SER LEU LYS THR VAL SER ASP SER LYS SEQRES 13 A 329 PRO ASP LEU SER LEU GLN LEU ILE PHE PHE ASP GLY GLU SEQRES 14 A 329 GLU ALA PHE LEU HIS TRP SER PRO GLN ASP SER LEU TYR SEQRES 15 A 329 GLY SER ARG HIS LEU ALA ALA LYS MET ALA SER THR PRO SEQRES 16 A 329 HIS PRO PRO GLY ALA ARG GLY THR SER GLN LEU HIS GLY SEQRES 17 A 329 MET ASP LEU LEU VAL LEU LEU ASP LEU ILE GLY ALA PRO SEQRES 18 A 329 ASN PRO THR PHE PRO ASN PHE PHE PRO ASN SER ALA ARG SEQRES 19 A 329 TRP PHE GLU ARG LEU GLN ALA ILE GLU HIS GLU LEU HIS SEQRES 20 A 329 GLU LEU GLY LEU LEU LYS ASP HIS SER LEU GLU GLY ARG SEQRES 21 A 329 TYR PHE GLN ASN TYR SER TYR GLY GLY VAL ILE GLN ASP SEQRES 22 A 329 ASP HIS ILE PRO PHE LEU ARG ARG GLY VAL PRO VAL LEU SEQRES 23 A 329 HIS LEU ILE PRO SER PRO PHE PRO GLU VAL TRP HIS THR SEQRES 24 A 329 MET ASP ASP ASN GLU GLU ASN LEU ASP GLU SER THR ILE SEQRES 25 A 329 ASP ASN LEU ASN LYS ILE LEU GLN VAL PHE VAL LEU GLU SEQRES 26 A 329 TYR LEU HIS LEU SEQRES 1 B 329 ALA SER ALA TRP PRO GLU GLU LYS ASN TYR HIS GLN PRO SEQRES 2 B 329 ALA ILE LEU ASN SER SER ALA LEU ARG GLN ILE ALA GLU SEQRES 3 B 329 GLY THR SER ILE SER GLU MET TRP GLN ASN ASP LEU GLN SEQRES 4 B 329 PRO LEU LEU ILE GLU ARG TYR PRO GLY SER PRO GLY SER SEQRES 5 B 329 TYR ALA ALA ARG GLN HIS ILE MET GLN ARG ILE GLN ARG SEQRES 6 B 329 LEU GLN ALA ASP TRP VAL LEU GLU ILE ASP THR PHE LEU SEQRES 7 B 329 SER GLN THR PRO TYR GLY TYR ARG SER PHE SER ASN ILE SEQRES 8 B 329 ILE SER THR LEU ASN PRO THR ALA LYS ARG HIS LEU VAL SEQRES 9 B 329 LEU ALA CYS HIS TYR ASP SER LYS TYR PHE SER HIS TRP SEQRES 10 B 329 ASN ASN ARG VAL PHE VAL GLY ALA THR ASP SER ALA VAL SEQRES 11 B 329 PRO CYS ALA MET MET LEU GLU LEU ALA ARG ALA LEU ASP SEQRES 12 B 329 LYS LYS LEU LEU SER LEU LYS THR VAL SER ASP SER LYS SEQRES 13 B 329 PRO ASP LEU SER LEU GLN LEU ILE PHE PHE ASP GLY GLU SEQRES 14 B 329 GLU ALA PHE LEU HIS TRP SER PRO GLN ASP SER LEU TYR SEQRES 15 B 329 GLY SER ARG HIS LEU ALA ALA LYS MET ALA SER THR PRO SEQRES 16 B 329 HIS PRO PRO GLY ALA ARG GLY THR SER GLN LEU HIS GLY SEQRES 17 B 329 MET ASP LEU LEU VAL LEU LEU ASP LEU ILE GLY ALA PRO SEQRES 18 B 329 ASN PRO THR PHE PRO ASN PHE PHE PRO ASN SER ALA ARG SEQRES 19 B 329 TRP PHE GLU ARG LEU GLN ALA ILE GLU HIS GLU LEU HIS SEQRES 20 B 329 GLU LEU GLY LEU LEU LYS ASP HIS SER LEU GLU GLY ARG SEQRES 21 B 329 TYR PHE GLN ASN TYR SER TYR GLY GLY VAL ILE GLN ASP SEQRES 22 B 329 ASP HIS ILE PRO PHE LEU ARG ARG GLY VAL PRO VAL LEU SEQRES 23 B 329 HIS LEU ILE PRO SER PRO PHE PRO GLU VAL TRP HIS THR SEQRES 24 B 329 MET ASP ASP ASN GLU GLU ASN LEU ASP GLU SER THR ILE SEQRES 25 B 329 ASP ASN LEU ASN LYS ILE LEU GLN VAL PHE VAL LEU GLU SEQRES 26 B 329 TYR LEU HIS LEU HET PBD A 380 22 HET ZN A 391 1 HET PBD B 381 22 HET ZN B 392 1 HETNAM PBD 1-(3,4-DIMETHOXYPHENYL)-3-[3-(1H-IMIDAZOL-1-YL) HETNAM 2 PBD PROPYL]THIOUREA HETNAM ZN ZINC ION FORMUL 3 PBD 2(C15 H20 N4 O2 S) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *284(H2 O) HELIX 1 1 ALA A 35 PRO A 37 5 3 HELIX 2 2 GLU A 38 HIS A 43 1 6 HELIX 3 3 ASN A 49 THR A 60 1 12 HELIX 4 4 SER A 61 ASP A 69 1 9 HELIX 5 5 LEU A 70 LEU A 74 5 5 HELIX 6 6 SER A 81 ARG A 97 1 17 HELIX 7 7 HIS A 148 ARG A 152 5 5 HELIX 8 8 SER A 160 LEU A 174 1 15 HELIX 9 9 LEU A 174 LEU A 179 1 6 HELIX 10 10 SER A 180 LYS A 182 5 3 HELIX 11 11 LEU A 213 SER A 225 1 13 HELIX 12 12 PHE A 261 ASN A 263 5 3 HELIX 13 13 SER A 264 LEU A 281 1 18 HELIX 14 14 HIS A 307 ARG A 312 1 6 HELIX 15 15 ASN A 335 LEU A 339 5 5 HELIX 16 16 ASP A 340 LEU A 359 1 20 HELIX 17 17 ALA B 35 PRO B 37 5 3 HELIX 18 18 GLU B 38 HIS B 43 1 6 HELIX 19 19 ASN B 49 THR B 60 1 12 HELIX 20 20 SER B 61 ASP B 69 1 9 HELIX 21 21 LEU B 70 LEU B 74 5 5 HELIX 22 22 SER B 81 ARG B 97 1 17 HELIX 23 23 HIS B 148 ARG B 152 5 5 HELIX 24 24 SER B 160 LEU B 174 1 15 HELIX 25 25 LEU B 174 SER B 180 1 7 HELIX 26 26 LEU B 213 SER B 225 1 13 HELIX 27 27 SER B 236 HIS B 239 5 4 HELIX 28 28 PHE B 261 ASN B 263 5 3 HELIX 29 29 SER B 264 GLU B 280 1 17 HELIX 30 30 HIS B 307 ARG B 312 1 6 HELIX 31 31 ASN B 335 LEU B 339 5 5 HELIX 32 32 ASP B 340 HIS B 360 1 21 SHEET 1 A 6 VAL A 103 THR A 113 0 SHEET 2 A 6 GLY A 116 THR A 126 -1 O ILE A 124 N GLU A 105 SHEET 3 A 6 LEU A 191 PHE A 198 -1 O LEU A 195 N SER A 125 SHEET 4 A 6 ARG A 133 HIS A 140 1 N CYS A 139 O PHE A 198 SHEET 5 A 6 MET A 241 LEU A 247 1 O VAL A 245 N ALA A 138 SHEET 6 A 6 VAL A 317 LEU A 320 1 O LEU A 318 N LEU A 244 SHEET 1 B 2 PHE A 257 PRO A 258 0 SHEET 2 B 2 PHE A 294 GLN A 295 1 O GLN A 295 N PHE A 257 SHEET 1 C 6 VAL B 103 THR B 113 0 SHEET 2 C 6 GLY B 116 THR B 126 -1 O THR B 126 N VAL B 103 SHEET 3 C 6 LEU B 191 PHE B 198 -1 O LEU B 195 N SER B 125 SHEET 4 C 6 ARG B 133 HIS B 140 1 N CYS B 139 O PHE B 198 SHEET 5 C 6 MET B 241 LEU B 247 1 O LEU B 247 N ALA B 138 SHEET 6 C 6 VAL B 317 LEU B 320 1 O LEU B 318 N LEU B 244 SHEET 1 D 2 PHE B 257 PRO B 258 0 SHEET 2 D 2 PHE B 294 GLN B 295 1 O GLN B 295 N PHE B 257 LINK OD2 ASP A 159 ZN ZN A 391 1555 1555 2.07 LINK OE2 GLU A 202 ZN ZN A 391 1555 1555 2.03 LINK NE2 HIS A 330 ZN ZN A 391 1555 1555 2.11 LINK NAM PBD A 380 ZN ZN A 391 1555 1555 2.14 LINK OD2 ASP B 159 ZN ZN B 392 1555 1555 2.02 LINK OE2 GLU B 202 ZN ZN B 392 1555 1555 1.88 LINK NE2 HIS B 330 ZN ZN B 392 1555 1555 2.10 LINK NAM PBD B 381 ZN ZN B 392 1555 1555 2.02 CISPEP 1 ASP A 159 SER A 160 0 -7.13 CISPEP 2 HIS A 228 PRO A 229 0 -6.94 CISPEP 3 SER A 323 PRO A 324 0 1.54 CISPEP 4 ASP B 159 SER B 160 0 4.86 CISPEP 5 HIS B 228 PRO B 229 0 -1.14 CISPEP 6 SER B 323 PRO B 324 0 17.71 SITE 1 AC1 14 TYR A 115 TYR A 145 ASP A 159 GLU A 201 SITE 2 AC1 14 GLU A 202 TRP A 207 ASP A 248 TYR A 299 SITE 3 AC1 14 GLN A 304 SER A 323 PHE A 325 HIS A 330 SITE 4 AC1 14 ZN A 391 HOH A 632 SITE 1 AC2 4 ASP A 159 GLU A 202 HIS A 330 PBD A 380 SITE 1 AC3 15 TYR B 115 ARG B 118 TYR B 145 ASP B 159 SITE 2 AC3 15 GLU B 201 GLU B 202 TRP B 207 ASP B 248 SITE 3 AC3 15 GLN B 304 SER B 323 PHE B 325 TRP B 329 SITE 4 AC3 15 HIS B 330 ZN B 392 HOH B 602 SITE 1 AC4 4 ASP B 159 GLU B 202 HIS B 330 PBD B 381 CRYST1 155.753 155.753 80.516 90.00 90.00 120.00 H 3 18 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 0.006420 0.003707 0.000000 0.00000 SCALE2 0.000000 0.007414 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012420 0.00000