HEADER TRANSFERASE/TRANSFERASE INHIBITOR 14-SEP-20 7K41 TITLE BACTERIAL O-GLCNACASE (OGA) WITH COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-GLCNACASE BT_4395; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N-ACETYLHEXOSAMINIDASE, COMPND 5 BETA-HEXOSAMINIDASE,HEXOSAMINIDASE B,N-ACETYL-BETA-GLUCOSAMINIDASE; COMPND 6 EC: 3.2.1.169; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 EXPRESSION_SYSTEM: BACTEROIDES THETAIOTAOMICRON; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 818 KEYWDS OGA, VIRTUAL SCREENING, STRUCTURE BASED DRUG DESIGN, SBDD, KEYWDS 2 TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.LANE,R.TJHEN,G.SNELL,B.SANG REVDAT 4 18-OCT-23 7K41 1 REMARK REVDAT 3 10-FEB-21 7K41 1 JRNL REVDAT 2 20-JAN-21 7K41 1 JRNL REVDAT 1 13-JAN-21 7K41 0 JRNL AUTH M.TAWADA,M.FUSHIMI,K.MASUDA,H.SUN,N.UCHIYAMA,Y.KOSUGI, JRNL AUTH 2 W.LANE,R.TJHEN,S.ENDO,T.KOIKE JRNL TITL DISCOVERY OF A NOVEL AND BRAIN-PENETRANT O -GLCNACASE JRNL TITL 2 INHIBITOR VIA VIRTUAL SCREENING, STRUCTURE-BASED ANALYSIS, JRNL TITL 3 AND RATIONAL LEAD OPTIMIZATION. JRNL REF J.MED.CHEM. V. 64 1103 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33404239 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01712 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 52602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.082 REMARK 3 FREE R VALUE TEST SET COUNT : 2673 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2152 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4759 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84800 REMARK 3 B22 (A**2) : -1.75900 REMARK 3 B33 (A**2) : 1.77600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.83800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.531 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4953 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6701 ; 1.356 ; 1.650 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 592 ; 6.921 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 267 ;35.602 ;23.745 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 829 ;16.973 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;14.812 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 618 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3876 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2278 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3377 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 233 ; 0.123 ; 0.200 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): 2364 ; 1.207 ; 2.737 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2950 ; 1.976 ; 4.094 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2589 ; 1.616 ; 2.891 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3749 ; 2.520 ; 4.242 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 2 A 2613 REMARK 3 ORIGIN FOR THE GROUP (A): -19.4176 -2.4944 15.4681 REMARK 3 T TENSOR REMARK 3 T11: 0.0236 T22: 0.0918 REMARK 3 T33: 0.0216 T12: 0.0410 REMARK 3 T13: 0.0005 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 2.3720 L22: 1.1959 REMARK 3 L33: 2.0473 L12: 0.7648 REMARK 3 L13: 1.4347 L23: 0.6197 REMARK 3 S TENSOR REMARK 3 S11: 0.0772 S12: 0.2630 S13: -0.1517 REMARK 3 S21: -0.0367 S22: 0.0790 S23: -0.0096 REMARK 3 S31: 0.0668 S32: 0.1619 S33: -0.1562 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7K41 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL 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 : 52607 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 41.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05266 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44690 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2CHN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M NAACETATE, 15% PEG 3350, 0.1 M REMARK 280 MES PH 6.0, 20% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 94.38550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.32300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 94.38550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.32300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC 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 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 A2779 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 GLY A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLN A 1 REMARK 465 ILE A 212 REMARK 465 LYS A 213 REMARK 465 LYS A 594 REMARK 465 MET A 595 REMARK 465 ILE A 596 REMARK 465 SER A 597 REMARK 465 ASN A 598 REMARK 465 VAL A 599 REMARK 465 GLU A 600 REMARK 465 GLN A 601 REMARK 465 ILE A 602 REMARK 465 LYS A 603 REMARK 465 ASN A 604 REMARK 465 LEU A 605 REMARK 465 PRO A 606 REMARK 465 LEU A 607 REMARK 465 GLN A 608 REMARK 465 VAL A 609 REMARK 465 LYS A 610 REMARK 465 ALA A 611 REMARK 465 ASN A 612 REMARK 465 ARG A 613 REMARK 465 VAL A 614 REMARK 465 LEU A 615 REMARK 465 ILE A 616 REMARK 465 SER A 617 REMARK 465 PRO A 618 REMARK 465 ALA A 619 REMARK 465 ASN A 620 REMARK 465 GLU A 621 REMARK 465 VAL A 622 REMARK 465 VAL A 623 REMARK 465 LYS A 624 REMARK 465 TRP A 625 REMARK 465 ALA A 626 REMARK 465 ALA A 627 REMARK 465 GLY A 628 REMARK 465 ASN A 629 REMARK 465 SER A 630 REMARK 465 VAL A 631 REMARK 465 GLU A 632 REMARK 465 ILE A 633 REMARK 465 GLU A 634 REMARK 465 LEU A 635 REMARK 465 ASP A 636 REMARK 465 ALA A 637 REMARK 465 ILE A 638 REMARK 465 TYR A 639 REMARK 465 PRO A 640 REMARK 465 GLY A 641 REMARK 465 GLU A 642 REMARK 465 ASN A 643 REMARK 465 ILE A 644 REMARK 465 GLN A 645 REMARK 465 ILE A 646 REMARK 465 ASN A 647 REMARK 465 PHE A 648 REMARK 465 GLY A 649 REMARK 465 LYS A 650 REMARK 465 ASP A 651 REMARK 465 ALA A 652 REMARK 465 PRO A 653 REMARK 465 CYS A 654 REMARK 465 THR A 655 REMARK 465 TRP A 656 REMARK 465 GLY A 657 REMARK 465 ARG A 658 REMARK 465 LEU A 659 REMARK 465 GLU A 660 REMARK 465 ILE A 661 REMARK 465 SER A 662 REMARK 465 THR A 663 REMARK 465 ASP A 664 REMARK 465 GLY A 665 REMARK 465 LYS A 666 REMARK 465 GLU A 667 REMARK 465 TRP A 668 REMARK 465 LYS A 669 REMARK 465 THR A 670 REMARK 465 VAL A 671 REMARK 465 ASP A 672 REMARK 465 LEU A 673 REMARK 465 LYS A 674 REMARK 465 GLN A 675 REMARK 465 LYS A 676 REMARK 465 GLU A 677 REMARK 465 SER A 678 REMARK 465 ARG A 679 REMARK 465 LEU A 680 REMARK 465 SER A 681 REMARK 465 ALA A 682 REMARK 465 GLY A 683 REMARK 465 LEU A 684 REMARK 465 GLN A 685 REMARK 465 LYS A 686 REMARK 465 ALA A 687 REMARK 465 PRO A 688 REMARK 465 VAL A 689 REMARK 465 LYS A 690 REMARK 465 PHE A 691 REMARK 465 VAL A 692 REMARK 465 ARG A 693 REMARK 465 PHE A 694 REMARK 465 THR A 695 REMARK 465 ASN A 696 REMARK 465 VAL A 697 REMARK 465 SER A 698 REMARK 465 ASP A 699 REMARK 465 GLU A 700 REMARK 465 GLU A 701 REMARK 465 GLN A 702 REMARK 465 GLN A 703 REMARK 465 VAL A 704 REMARK 465 TYR A 705 REMARK 465 LEU A 706 REMARK 465 ARG A 707 REMARK 465 GLN A 708 REMARK 465 PHE A 709 REMARK 465 VAL A 710 REMARK 465 LEU A 711 REMARK 465 THR A 712 REMARK 465 ILE A 713 REMARK 465 GLU A 714 REMARK 465 LYS A 715 REMARK 465 LYS A 716 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 LYS A 52 CB CG CD CE NZ REMARK 470 LYS A 53 CB CG CD CE NZ REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 LYS A 396 CD CE NZ REMARK 470 ARG A 408 NE CZ NH1 NH2 REMARK 470 TYR A 590 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS A 593 CG ND1 CD2 CE1 NE2 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 146 CG - CD - NE ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG A 146 NE - CZ - NH2 ANGL. DEV. = -3.4 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 SER A 46 38.49 -140.92 REMARK 500 LYS A 52 -5.46 -151.36 REMARK 500 PHE A 265 -57.32 -134.37 REMARK 500 ASP A 271 35.31 -154.45 REMARK 500 ASN A 273 -83.76 -87.58 REMARK 500 VAL A 346 55.85 -142.20 REMARK 500 ALA A 414 45.82 -145.15 REMARK 500 SER A 426 -41.47 -131.38 REMARK 500 SER A 426 -30.40 -137.05 REMARK 500 LYS A 455 -76.06 -43.70 REMARK 500 GLU A 456 32.31 -84.92 REMARK 500 TYR A 550 -65.24 -108.15 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 ASN A 292 TYR A 293 -148.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 2601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VUA A 2602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 2612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2613 DBREF 7K41 A 1 716 UNP Q89ZI2 OGA_BACTN 22 737 SEQADV 7K41 GLY A -2 UNP Q89ZI2 EXPRESSION TAG SEQADV 7K41 GLY A -1 UNP Q89ZI2 EXPRESSION TAG SEQADV 7K41 SER A 0 UNP Q89ZI2 EXPRESSION TAG SEQRES 1 A 719 GLY GLY SER GLN ASN VAL SER LEU GLN PRO PRO PRO GLN SEQRES 2 A 719 GLN LEU ILE VAL GLN ASN LYS THR ILE ASP LEU PRO ALA SEQRES 3 A 719 VAL TYR GLN LEU ASN GLY GLY GLU GLU ALA ASN PRO HIS SEQRES 4 A 719 ALA VAL LYS VAL LEU LYS GLU LEU LEU SER GLY LYS GLN SEQRES 5 A 719 SER SER LYS LYS GLY MET LEU ILE SER ILE GLY GLU LYS SEQRES 6 A 719 GLY ASP LYS SER VAL ARG LYS TYR SER ARG GLN ILE PRO SEQRES 7 A 719 ASP HIS LYS GLU GLY TYR TYR LEU SER VAL ASN GLU LYS SEQRES 8 A 719 GLU ILE VAL LEU ALA GLY ASN ASP GLU ARG GLY THR TYR SEQRES 9 A 719 TYR ALA LEU GLN THR PHE ALA GLN LEU LEU LYS ASP GLY SEQRES 10 A 719 LYS LEU PRO GLU VAL GLU ILE LYS ASP TYR PRO SER VAL SEQRES 11 A 719 ARG TYR ARG GLY VAL VAL GLU GLY PHE TYR GLY THR PRO SEQRES 12 A 719 TRP SER HIS GLN ALA ARG LEU SER GLN LEU LYS PHE TYR SEQRES 13 A 719 GLY LYS ASN LYS MET ASN THR TYR ILE TYR GLY PRO LYS SEQRES 14 A 719 ASP ASP PRO TYR HIS SER ALA PRO ASN TRP ARG LEU PRO SEQRES 15 A 719 TYR PRO ASP LYS GLU ALA ALA GLN LEU GLN GLU LEU VAL SEQRES 16 A 719 ALA VAL ALA ASN GLU ASN GLU VAL ASP PHE VAL TRP ALA SEQRES 17 A 719 ILE HIS PRO GLY GLN ASP ILE LYS TRP ASN LYS GLU ASP SEQRES 18 A 719 ARG ASP LEU LEU LEU ALA LYS PHE GLU LYS MET TYR GLN SEQRES 19 A 719 LEU GLY VAL ARG SER PHE ALA VAL PHE PHE ASP ASP ILE SEQRES 20 A 719 SER GLY GLU GLY THR ASN PRO GLN LYS GLN ALA GLU LEU SEQRES 21 A 719 LEU ASN TYR ILE ASP GLU LYS PHE ALA GLN VAL LYS PRO SEQRES 22 A 719 ASP ILE ASN GLN LEU VAL MET CYS PRO THR GLU TYR ASN SEQRES 23 A 719 LYS SER TRP SER ASN PRO ASN GLY ASN TYR LEU THR THR SEQRES 24 A 719 LEU GLY ASP LYS LEU ASN PRO SER ILE GLN ILE MET TRP SEQRES 25 A 719 THR GLY ASP ARG VAL ILE SER ASP ILE THR ARG ASP GLY SEQRES 26 A 719 ILE SER TRP ILE ASN GLU ARG ILE LYS ARG PRO ALA TYR SEQRES 27 A 719 ILE TRP TRP ASN PHE PRO VAL SER ASP TYR VAL ARG ASP SEQRES 28 A 719 HIS LEU LEU LEU GLY PRO VAL TYR GLY ASN ASP THR THR SEQRES 29 A 719 ILE ALA LYS GLU MET SER GLY PHE VAL THR ASN PRO MET SEQRES 30 A 719 GLU HIS ALA GLU SER SER LYS ILE ALA ILE TYR SER VAL SEQRES 31 A 719 ALA SER TYR ALA TRP ASN PRO ALA LYS TYR ASP THR TRP SEQRES 32 A 719 GLN THR TRP LYS ASP ALA ILE ARG THR ILE LEU PRO SER SEQRES 33 A 719 ALA ALA GLU GLU LEU GLU CYS PHE ALA MET HIS ASN SER SEQRES 34 A 719 ASP LEU GLY PRO ASN GLY HIS GLY TYR ARG ARG GLU GLU SEQRES 35 A 719 SER MET ASP ILE GLN PRO ALA ALA GLU ARG PHE LEU LYS SEQRES 36 A 719 ALA PHE LYS GLU GLY LYS ASN TYR ASP LYS ALA ASP PHE SEQRES 37 A 719 GLU THR LEU GLN TYR THR PHE GLU ARG MET LYS GLU SER SEQRES 38 A 719 ALA ASP ILE LEU LEU MET ASN THR GLU ASN LYS PRO LEU SEQRES 39 A 719 ILE VAL GLU ILE THR PRO TRP VAL HIS GLN PHE LYS LEU SEQRES 40 A 719 THR ALA GLU MET GLY GLU GLU VAL LEU LYS MET VAL GLU SEQRES 41 A 719 GLY ARG ASN GLU SER TYR PHE LEU ARG LYS TYR ASN HIS SEQRES 42 A 719 VAL LYS ALA LEU GLN GLN GLN MET PHE TYR ILE ASP GLN SEQRES 43 A 719 THR SER ASN GLN ASN PRO TYR GLN PRO GLY VAL LYS THR SEQRES 44 A 719 ALA THR ARG VAL ILE LYS PRO LEU ILE ASP ARG THR PHE SEQRES 45 A 719 ALA THR VAL VAL LYS PHE PHE ASN GLN LYS PHE ASN ALA SEQRES 46 A 719 HIS LEU ASP ALA THR THR ASP TYR MET PRO HIS LYS MET SEQRES 47 A 719 ILE SER ASN VAL GLU GLN ILE LYS ASN LEU PRO LEU GLN SEQRES 48 A 719 VAL LYS ALA ASN ARG VAL LEU ILE SER PRO ALA ASN GLU SEQRES 49 A 719 VAL VAL LYS TRP ALA ALA GLY ASN SER VAL GLU ILE GLU SEQRES 50 A 719 LEU ASP ALA ILE TYR PRO GLY GLU ASN ILE GLN ILE ASN SEQRES 51 A 719 PHE GLY LYS ASP ALA PRO CYS THR TRP GLY ARG LEU GLU SEQRES 52 A 719 ILE SER THR ASP GLY LYS GLU TRP LYS THR VAL ASP LEU SEQRES 53 A 719 LYS GLN LYS GLU SER ARG LEU SER ALA GLY LEU GLN LYS SEQRES 54 A 719 ALA PRO VAL LYS PHE VAL ARG PHE THR ASN VAL SER ASP SEQRES 55 A 719 GLU GLU GLN GLN VAL TYR LEU ARG GLN PHE VAL LEU THR SEQRES 56 A 719 ILE GLU LYS LYS HET ACT A2601 4 HET VUA A2602 22 HET EDO A2603 4 HET EDO A2604 4 HET EDO A2605 4 HET EDO A2606 4 HET EDO A2607 4 HET EDO A2608 4 HET EDO A2609 4 HET EDO A2610 4 HET EDO A2611 4 HET ACT A2612 4 HET EDO A2613 4 HETNAM ACT ACETATE ION HETNAM VUA 4-(4-METHYLPIPERIDIN-1-YL)-N-(2-PHENYLETHYL)PYRIMIDIN- HETNAM 2 VUA 2-AMINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ACT 2(C2 H3 O2 1-) FORMUL 3 VUA C18 H24 N4 FORMUL 4 EDO 10(C2 H6 O2) FORMUL 15 HOH *154(H2 O) HELIX 1 AA1 ASN A 34 LEU A 45 1 12 HELIX 2 AA2 ASP A 64 SER A 71 5 8 HELIX 3 AA3 ASP A 96 LEU A 111 1 16 HELIX 4 AA4 SER A 142 ASN A 156 1 15 HELIX 5 AA5 ASP A 168 SER A 172 5 5 HELIX 6 AA6 PRO A 174 LEU A 178 5 5 HELIX 7 AA7 PRO A 181 ASN A 198 1 18 HELIX 8 AA8 ASN A 215 LEU A 232 1 18 HELIX 9 AA9 SER A 245 THR A 249 5 5 HELIX 10 AB1 ASN A 250 PHE A 265 1 16 HELIX 11 AB2 ASN A 292 LEU A 301 1 10 HELIX 12 AB3 THR A 319 LYS A 331 1 13 HELIX 13 AB4 ILE A 362 LYS A 364 5 3 HELIX 14 AB5 ALA A 377 SER A 379 5 3 HELIX 15 AB6 SER A 380 ASN A 393 1 14 HELIX 16 AB7 PRO A 394 TYR A 397 5 4 HELIX 17 AB8 ASP A 398 LEU A 411 1 14 HELIX 18 AB9 ALA A 414 HIS A 424 1 11 HELIX 19 AC1 ILE A 443 GLU A 456 1 14 HELIX 20 AC2 ASP A 461 MET A 484 1 24 HELIX 21 AC3 ASN A 488 GLY A 518 1 31 HELIX 22 AC4 ASN A 520 SER A 545 1 26 HELIX 23 AC5 VAL A 560 ASN A 581 1 22 SHEET 1 AA1 7 GLN A 11 ASP A 20 0 SHEET 2 AA1 7 LYS A 115 ASP A 123 -1 O LEU A 116 N ILE A 19 SHEET 3 AA1 7 TYR A 81 VAL A 85 -1 N LEU A 83 O ILE A 121 SHEET 4 AA1 7 GLU A 89 GLY A 94 -1 O ALA A 93 N TYR A 82 SHEET 5 AA1 7 MET A 55 GLU A 61 1 N SER A 58 O LEU A 92 SHEET 6 AA1 7 VAL A 24 ASN A 28 1 N ASN A 28 O ILE A 57 SHEET 7 AA1 7 LYS A 48 GLN A 49 1 O LYS A 48 N TYR A 25 SHEET 1 AA2 9 TYR A 129 VAL A 133 0 SHEET 2 AA2 9 THR A 160 TYR A 163 1 O ILE A 162 N VAL A 132 SHEET 3 AA2 9 ASP A 201 ILE A 206 1 O VAL A 203 N TYR A 161 SHEET 4 AA2 9 SER A 236 PHE A 240 1 O ALA A 238 N ILE A 206 SHEET 5 AA2 9 LEU A 275 CYS A 278 1 O VAL A 276 N VAL A 239 SHEET 6 AA2 9 GLN A 306 TRP A 309 1 O GLN A 306 N MET A 277 SHEET 7 AA2 9 ALA A 334 TRP A 338 1 O TRP A 337 N TRP A 309 SHEET 8 AA2 9 MET A 366 THR A 371 1 O VAL A 370 N TRP A 338 SHEET 9 AA2 9 TYR A 129 VAL A 133 1 N GLY A 131 O THR A 371 CISPEP 1 GLN A 6 PRO A 7 0 -10.54 CISPEP 2 ALA A 173 PRO A 174 0 -8.52 CISPEP 3 PHE A 340 PRO A 341 0 4.85 SITE 1 AC1 1 TRP A 400 SITE 1 AC2 12 GLY A 135 TYR A 137 ASP A 242 TYR A 282 SITE 2 AC2 12 ASN A 290 VAL A 314 ILE A 315 TRP A 337 SITE 3 AC2 12 ASN A 339 ASP A 344 TYR A 345 EDO A2604 SITE 1 AC3 4 ASP A 262 GLN A 267 ILE A 272 ASN A 273 SITE 1 AC4 4 GLY A 135 LYS A 166 ASP A 242 VUA A2602 SITE 1 AC5 5 ASN A 290 ASP A 344 ARG A 347 TYR A 550 SITE 2 AC5 5 GLN A 551 SITE 1 AC6 4 TYR A 137 GLY A 138 ARG A 347 HOH A2782 SITE 1 AC7 5 GLY A 357 TYR A 397 THR A 399 HOH A2722 SITE 2 AC7 5 HOH A2762 SITE 1 AC8 2 ASP A 317 ARG A 437 SITE 1 AC9 4 GLY A 434 TYR A 435 ARG A 436 ARG A 437 SITE 1 AD1 4 PRO A 430 ASN A 431 GLY A 434 ARG A 436 SITE 1 AD2 3 SER A 4 ARG A 408 HOH A2748 SITE 1 AD3 6 ARG A 98 ASN A 196 GLU A 199 VAL A 200 SITE 2 AD3 6 ASP A 201 HOH A2739 SITE 1 AD4 3 GLN A 105 LYS A 155 HOH A2784 CRYST1 188.771 52.646 84.464 90.00 99.69 90.00 C 1 2 1 4 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 0.005297 0.000000 0.000905 0.00000 SCALE2 0.000000 0.018995 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012011 0.00000