HEADER HYDROLASE 14-SEP-23 8QK5 TITLE STRUCTURE OF K. PNEUMONIAE LPXH IN COMPLEX WITH EBL-3647 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-2,3-DIACYLGLUCOSAMINE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: LPXH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: AI; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMIDS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-26B(+) KEYWDS LIPID A BIOSYNTHESIS PATHWAY ENDOTOXIN UDP-DIACYL-GLUCOSAMINE LIPID X KEYWDS 2 GRAM-NEGATIVE BACTERIA LIPOPOLYSACCHARIDES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SOORIYAARACHCHI,T.BERGFORS,T.A.JONES,S.L.MOWBRAY REVDAT 1 17-APR-24 8QK5 0 JRNL AUTH D.L.HUSEBY,S.CAO,E.ZAMARATSKI,S.SOORIYAARACHCHI,S.AHMAD, JRNL AUTH 2 T.BERGFORS,L.KRASNOVA,J.PELSS,M.IKAUNIEKS,E.LOZA, JRNL AUTH 3 M.KATKEVICS,O.BOBILEVA,H.CIRULE,B.GUKALOVA,S.GRINBERGA, JRNL AUTH 4 M.BACKLUND,I.SIMOFF,A.T.LEBER,T.BERRUGA-FERNANDEZ,D.ANTONOV, JRNL AUTH 5 V.R.KONDA,S.LINDSTROM,G.OLANDERS,P.BRANDT,P.BARANCZEWSKI, JRNL AUTH 6 C.VINGSBO LUNDBERG,E.LIEPINSH,E.SUNA,T.A.JONES,S.L.MOWBRAY, JRNL AUTH 7 D.HUGHES,A.KARLEN JRNL TITL ANTIBIOTIC CLASS WITH POTENT IN VIVO ACTIVITY TARGETING JRNL TITL 2 LIPOPOLYSACCHARIDE SYNTHESIS IN GRAM-NEGATIVE BACTERIA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 74121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38579010 JRNL DOI 10.1073/PNAS.2317274121 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 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) : 29.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22624 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) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1219 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) : 1592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1844 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : 0.77000 REMARK 3 B33 (A**2) : -2.50000 REMARK 3 B12 (A**2) : 0.38000 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): 0.172 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.083 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1956 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1698 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2652 ; 1.335 ; 1.635 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3934 ; 0.466 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 227 ; 6.892 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ; 6.540 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 297 ;14.209 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 287 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2223 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 405 ; 0.001 ; 0.020 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): 914 ; 4.255 ; 4.902 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 914 ; 4.250 ; 4.902 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1139 ; 5.433 ; 7.315 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1140 ; 5.431 ; 7.319 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1042 ; 4.452 ; 5.210 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 991 ; 4.425 ; 5.224 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1440 ; 5.965 ; 7.715 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2135 ; 7.618 ;56.671 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2058 ; 7.566 ;56.891 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8QK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292133191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965459 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 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) : 2.00 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: BIPYRAMIDAL CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS III - G11 1.2 % CHOLIC ACID REMARK 280 DERIVATIVES MIX 0.1 M BUFFER SYSTEM 3 8.5 50 % PRECIPITANT MIX 3, REMARK 280 PH 8.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 95.89733 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 191.79467 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 143.84600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 239.74333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.94867 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 95.89733 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 191.79467 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 239.74333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 143.84600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 47.94867 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: 2250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL 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 BIOMT1 2 0.500000 0.866025 0.000000 -30.20900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 52.32352 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 47.94867 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 MET A 1 REMARK 465 ARG A 157 REMARK 465 ALA A 158 REMARK 465 ASP A 159 REMARK 465 SER A 160 REMARK 465 LYS A 161 REMARK 465 ALA A 162 REMARK 465 ALA A 163 REMARK 465 ASN A 164 REMARK 465 SER A 165 REMARK 465 SER A 166 REMARK 465 LYS A 167 REMARK 465 SER A 168 REMARK 465 MET A 169 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 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 LEU A 39 48.43 -95.67 REMARK 500 ASN A 53 118.07 -33.89 REMARK 500 HIS A 195 -50.92 70.64 REMARK 500 ARG A 198 76.79 -119.22 REMARK 500 HIS A 220 -75.75 -148.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 198 0.08 SIDE CHAIN 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 MN A 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD1 REMARK 620 2 HIS A 10 NE2 110.6 REMARK 620 3 ASP A 41 OD2 90.8 103.4 REMARK 620 4 HIS A 197 NE2 92.2 87.8 166.6 REMARK 620 5 HOH A 428 O 108.5 139.2 87.0 79.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 ASN A 79 OD1 91.1 REMARK 620 3 HIS A 114 NE2 101.4 99.9 REMARK 620 4 HIS A 195 ND1 174.1 89.3 84.3 REMARK 620 5 HOH A 428 O 84.7 113.4 146.1 89.8 REMARK 620 N 1 2 3 4 DBREF 8QK5 A 1 240 UNP A6T5R0 LPXH_KLEP7 1 240 SEQADV 8QK5 GLU A 17 UNP A6T5R0 ALA 17 CONFLICT SEQADV 8QK5 HIS A 241 UNP A6T5R0 EXPRESSION TAG SEQADV 8QK5 HIS A 242 UNP A6T5R0 EXPRESSION TAG SEQADV 8QK5 HIS A 243 UNP A6T5R0 EXPRESSION TAG SEQADV 8QK5 HIS A 244 UNP A6T5R0 EXPRESSION TAG SEQADV 8QK5 HIS A 245 UNP A6T5R0 EXPRESSION TAG SEQADV 8QK5 HIS A 246 UNP A6T5R0 EXPRESSION TAG SEQRES 1 A 246 MET ALA THR LEU PHE ILE ALA ASP LEU HIS LEU GLN THR SEQRES 2 A 246 GLU GLU PRO GLU ILE THR ALA GLY PHE LEU ARG PHE LEU SEQRES 3 A 246 GLN GLY GLU ALA ARG GLN ALA ASP ALA LEU TYR ILE LEU SEQRES 4 A 246 GLY ASP LEU PHE GLU ALA TRP ILE GLY ASP ASP ASP PRO SEQRES 5 A 246 ASN PRO LEU HIS GLN GLN ILE ALA SER ALA ILE LYS ALA SEQRES 6 A 246 VAL VAL ASP ALA GLY VAL PRO CYS TYR PHE ILE HIS GLY SEQRES 7 A 246 ASN ARG ASP PHE LEU VAL GLY GLN ARG PHE ALA ARG GLN SEQRES 8 A 246 SER GLY MET ILE LEU LEU ALA GLU GLU GLU ARG LEU ASP SEQRES 9 A 246 LEU TYR GLY ARG GLU VAL LEU ILE MET HIS GLY ASP THR SEQRES 10 A 246 LEU CYS THR ASP ASP GLN GLY TYR LEU ALA PHE ARG ALA SEQRES 11 A 246 LYS VAL HIS THR PRO TRP ILE GLN ARG LEU PHE LEU ALA SEQRES 12 A 246 LEU PRO LEU PHE ILE ARG HIS ARG ILE ALA ALA ARG MET SEQRES 13 A 246 ARG ALA ASP SER LYS ALA ALA ASN SER SER LYS SER MET SEQRES 14 A 246 GLU ILE MET ASP VAL ASN PRO GLN ALA VAL VAL ASP ALA SEQRES 15 A 246 MET GLU ARG HIS HIS VAL GLN TRP LEU ILE HIS GLY HIS SEQRES 16 A 246 THR HIS ARG PRO ALA VAL HIS GLU LEU GLN ALA ASN GLY SEQRES 17 A 246 GLN PRO ALA TRP ARG VAL VAL LEU GLY ALA TRP HIS SER SEQRES 18 A 246 GLU GLY SER MET VAL LYS VAL THR PRO ASP ASP VAL GLU SEQRES 19 A 246 LEU ILE HIS PHE PRO PHE HIS HIS HIS HIS HIS HIS HET MN A 301 1 HET MN A 302 1 HET VN6 A 303 46 HETNAM MN MANGANESE (II) ION HETNAM VN6 5-[[3-(AMINOMETHYL)AZETIDIN-1-YL]METHYL]-N-[4-[4-(4- HETNAM 2 VN6 CYANO-6-METHYL-PYRIMIDIN-2-YL)PIPERAZIN-1- HETNAM 3 VN6 YL]SULFONYLPHENYL]-2-[METHYL(METHYLSULFONYL) HETNAM 4 VN6 AMINO]BENZAMIDE FORMUL 2 MN 2(MN 2+) FORMUL 4 VN6 C30 H37 N9 O5 S2 FORMUL 5 HOH *48(H2 O) HELIX 1 AA1 GLU A 15 GLY A 28 1 14 HELIX 2 AA2 GLU A 29 ALA A 33 5 5 HELIX 3 AA3 ASN A 53 ALA A 69 1 17 HELIX 4 AA4 GLY A 85 GLY A 93 1 9 HELIX 5 AA5 GLY A 115 CYS A 119 5 5 HELIX 6 AA6 ASP A 122 HIS A 133 1 12 HELIX 7 AA7 THR A 134 LEU A 144 1 11 HELIX 8 AA8 PRO A 145 MET A 156 1 12 HELIX 9 AA9 ASN A 175 HIS A 186 1 12 SHEET 1 AA1 6 ILE A 95 LEU A 96 0 SHEET 2 AA1 6 CYS A 73 PHE A 75 1 N CYS A 73 O ILE A 95 SHEET 3 AA1 6 ALA A 35 ILE A 38 1 N ILE A 38 O TYR A 74 SHEET 4 AA1 6 THR A 3 ILE A 6 1 N LEU A 4 O TYR A 37 SHEET 5 AA1 6 GLU A 222 VAL A 228 -1 O VAL A 228 N THR A 3 SHEET 6 AA1 6 VAL A 233 PRO A 239 -1 O ILE A 236 N MET A 225 SHEET 1 AA2 5 GLU A 100 LEU A 105 0 SHEET 2 AA2 5 ARG A 108 MET A 113 -1 O ARG A 108 N LEU A 105 SHEET 3 AA2 5 TRP A 190 HIS A 193 1 O TRP A 190 N LEU A 111 SHEET 4 AA2 5 GLN A 209 VAL A 215 1 O VAL A 214 N LEU A 191 SHEET 5 AA2 5 ALA A 200 ALA A 206 -1 N ALA A 200 O VAL A 215 LINK OD1 ASP A 8 MN MN A 301 1555 1555 2.13 LINK NE2 HIS A 10 MN MN A 301 1555 1555 2.24 LINK OD2 ASP A 41 MN MN A 301 1555 1555 2.21 LINK OD2 ASP A 41 MN MN A 302 1555 1555 2.22 LINK OD1 ASN A 79 MN MN A 302 1555 1555 2.12 LINK NE2 HIS A 114 MN MN A 302 1555 1555 2.29 LINK ND1 HIS A 195 MN MN A 302 1555 1555 2.32 LINK NE2 HIS A 197 MN MN A 301 1555 1555 2.24 LINK MN MN A 301 O HOH A 428 1555 1555 2.14 LINK MN MN A 302 O HOH A 428 1555 1555 2.22 CRYST1 60.418 60.418 287.692 90.00 90.00 120.00 P 61 2 2 12 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 0.016551 0.009556 0.000000 0.00000 SCALE2 0.000000 0.019112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003476 0.00000