HEADER TRANSFERASE 05-OCT-14 4V24 TITLE SPHINGOSINE KINASE 1 IN COMPLEX WITH PF-543 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOSINE KINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 EC: 2.7.1.91; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS TRANSFERASE, SPHK1, SPHINGOSINE, KINASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.ELKINS,J.WANG,F.SORRELL,C.TALLANT,D.WANG,L.SHRESTHA,C.BOUNTRA, AUTHOR 2 F.VON DELFT,S.KNAPP,A.EDWARDS REVDAT 4 10-JAN-24 4V24 1 REMARK REVDAT 3 24-JAN-18 4V24 1 AUTHOR REVDAT 2 31-DEC-14 4V24 1 JRNL REVDAT 1 15-OCT-14 4V24 0 JRNL AUTH J.WANG,S.KNAPP,N.J.PYNE,S.PYNE,J.M.ELKINS JRNL TITL CRYSTAL STRUCTURE OF SPHINGOSINE KINASE 1 WITH PF-543. JRNL REF ACS MED.CHEM.LETT. V. 5 1329 2014 JRNL REFN ISSN 1948-5875 JRNL PMID 25516793 JRNL DOI 10.1021/ML5004074 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 78214 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4053 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5710 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 303 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5403 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 476 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.52000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.535 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5671 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5491 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7723 ; 1.493 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12577 ; 0.900 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 717 ; 6.259 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;35.015 ;22.281 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 909 ;12.329 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;17.527 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 874 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6566 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1314 ; 0.003 ; 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): 2830 ; 1.747 ; 2.065 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2828 ; 1.747 ; 2.063 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3538 ; 2.715 ; 3.080 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2841 ; 2.454 ; 2.370 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 4V24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1290061871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PIXEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82290 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 43.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.96000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 3VZB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37.5% MPD, 0. 1 M BISTRIS PH 5.5 AND REMARK 280 0.1 M AMMONIUM ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.27450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 SER A 79 REMARK 465 MET A 80 REMARK 465 GLU A 81 REMARK 465 PRO A 82 REMARK 465 ARG A 83 REMARK 465 VAL A 84 REMARK 465 GLU A 85 REMARK 465 VAL A 86 REMARK 465 MET A 87 REMARK 465 ASP A 88 REMARK 465 PRO A 89 REMARK 465 ALA A 90 REMARK 465 GLY A 91 REMARK 465 GLY A 92 REMARK 465 PRO A 312 REMARK 465 VAL A 313 REMARK 465 VAL A 314 REMARK 465 VAL A 315 REMARK 465 GLN A 316 REMARK 465 GLN A 317 REMARK 465 SER B 79 REMARK 465 MET B 80 REMARK 465 GLU B 81 REMARK 465 PRO B 82 REMARK 465 ARG B 83 REMARK 465 VAL B 84 REMARK 465 GLU B 85 REMARK 465 VAL B 86 REMARK 465 MET B 87 REMARK 465 ASP B 88 REMARK 465 PRO B 89 REMARK 465 ALA B 90 REMARK 465 GLY B 91 REMARK 465 GLY B 92 REMARK 465 SER B 198 REMARK 465 GLY B 199 REMARK 465 PRO B 312 REMARK 465 VAL B 313 REMARK 465 VAL B 314 REMARK 465 VAL B 315 REMARK 465 GLN B 316 REMARK 465 GLN B 317 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 ARG A 94 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 110 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 115 CD CE NZ REMARK 470 ARG A 143 CD NE CZ NH1 NH2 REMARK 470 ARG A 293 CG CD NE CZ NH1 NH2 REMARK 470 SER A 311 OG REMARK 470 GLU A 341 CD OE1 OE2 REMARK 470 LYS A 421 CG CD CE NZ REMARK 470 ARG B 94 CD NE CZ NH1 NH2 REMARK 470 ARG B 110 CD NE CZ NH1 NH2 REMARK 470 LYS B 115 CD CE NZ REMARK 470 GLU B 130 CD OE1 OE2 REMARK 470 ARG B 143 CD NE CZ NH1 NH2 REMARK 470 ARG B 293 NE CZ NH1 NH2 REMARK 470 SER B 311 OG REMARK 470 GLU B 341 CD OE1 OE2 REMARK 470 LYS B 394 CE NZ REMARK 470 LYS B 421 CG CD CE NZ 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 A 2052 O HOH A 2057 1.94 REMARK 500 O GLY A 166 O HOH A 2051 2.01 REMARK 500 O HOH A 2072 O HOH A 2073 2.01 REMARK 500 O HOH B 2064 O HOH B 2071 2.05 REMARK 500 O GLY B 166 O HOH B 2065 2.06 REMARK 500 OD1 ASP A 340 O HOH A 2179 2.10 REMARK 500 O PRO B 309 O HOH B 2175 2.11 REMARK 500 O HOH B 2108 O HOH B 2121 2.17 REMARK 500 O ALA A 287 NH1 ARG A 382 2.18 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 144 -1.98 70.87 REMARK 500 SER A 165 -163.68 -175.41 REMARK 500 SER A 165 -155.74 -179.67 REMARK 500 ASN A 200 99.27 173.38 REMARK 500 ASN A 217 -126.54 52.32 REMARK 500 LEU A 253 -56.10 -131.17 REMARK 500 ASP A 321 75.69 -106.99 REMARK 500 ASN B 144 -10.74 80.01 REMARK 500 SER B 165 -157.49 -179.85 REMARK 500 SER B 165 -164.08 -174.67 REMARK 500 ALA B 196 14.22 -153.98 REMARK 500 ASN B 217 -128.44 52.03 REMARK 500 LEU B 253 -56.44 -132.54 REMARK 500 ASP B 321 74.07 -107.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 (R)-(1-(4-((3-METHYL-5-((PHENYLSULFONYL)METHYL)PHENOXY)METHYL)BENZYL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GYR A 1450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GYR B 1450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1451 DBREF 4V24 A 87 449 UNP Q9NYA1 SPHK1_HUMAN 1 363 DBREF 4V24 B 87 449 UNP Q9NYA1 SPHK1_HUMAN 1 363 SEQADV 4V24 SER A 79 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 MET A 80 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 GLU A 81 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 PRO A 82 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 ARG A 83 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 VAL A 84 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 GLU A 85 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 VAL A 86 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 SER B 79 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 MET B 80 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 GLU B 81 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 PRO B 82 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 ARG B 83 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 VAL B 84 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 GLU B 85 UNP Q9NYA1 EXPRESSION TAG SEQADV 4V24 VAL B 86 UNP Q9NYA1 EXPRESSION TAG SEQRES 1 A 371 SER MET GLU PRO ARG VAL GLU VAL MET ASP PRO ALA GLY SEQRES 2 A 371 GLY PRO ARG GLY VAL LEU PRO ARG PRO CYS ARG VAL LEU SEQRES 3 A 371 VAL LEU LEU ASN PRO ARG GLY GLY LYS GLY LYS ALA LEU SEQRES 4 A 371 GLN LEU PHE ARG SER HIS VAL GLN PRO LEU LEU ALA GLU SEQRES 5 A 371 ALA GLU ILE SER PHE THR LEU MET LEU THR GLU ARG ARG SEQRES 6 A 371 ASN HIS ALA ARG GLU LEU VAL ARG SER GLU GLU LEU GLY SEQRES 7 A 371 ARG TRP ASP ALA LEU VAL VAL MET SER GLY ASP GLY LEU SEQRES 8 A 371 MET HIS GLU VAL VAL ASN GLY LEU MET GLU ARG PRO ASP SEQRES 9 A 371 TRP GLU THR ALA ILE GLN LYS PRO LEU CYS SER LEU PRO SEQRES 10 A 371 ALA GLY SER GLY ASN ALA LEU ALA ALA SER LEU ASN HIS SEQRES 11 A 371 TYR ALA GLY TYR GLU GLN VAL THR ASN GLU ASP LEU LEU SEQRES 12 A 371 THR ASN CYS THR LEU LEU LEU CYS ARG ARG LEU LEU SER SEQRES 13 A 371 PRO MET ASN LEU LEU SER LEU HIS THR ALA SER GLY LEU SEQRES 14 A 371 ARG LEU PHE SER VAL LEU SER LEU ALA TRP GLY PHE ILE SEQRES 15 A 371 ALA ASP VAL ASP LEU GLU SER GLU LYS TYR ARG ARG LEU SEQRES 16 A 371 GLY GLU MET ARG PHE THR LEU GLY THR PHE LEU ARG LEU SEQRES 17 A 371 ALA ALA LEU ARG THR TYR ARG GLY ARG LEU ALA TYR LEU SEQRES 18 A 371 PRO VAL GLY ARG VAL GLY SER LYS THR PRO ALA SER PRO SEQRES 19 A 371 VAL VAL VAL GLN GLN GLY PRO VAL ASP ALA HIS LEU VAL SEQRES 20 A 371 PRO LEU GLU GLU PRO VAL PRO SER HIS TRP THR VAL VAL SEQRES 21 A 371 PRO ASP GLU ASP PHE VAL LEU VAL LEU ALA LEU LEU HIS SEQRES 22 A 371 SER HIS LEU GLY SER GLU MET PHE ALA ALA PRO MET GLY SEQRES 23 A 371 ARG CYS ALA ALA GLY VAL MET HIS LEU PHE TYR VAL ARG SEQRES 24 A 371 ALA GLY VAL SER ARG ALA MET LEU LEU ARG LEU PHE LEU SEQRES 25 A 371 ALA MET GLU LYS GLY ARG HIS MET GLU TYR GLU CYS PRO SEQRES 26 A 371 TYR LEU VAL TYR VAL PRO VAL VAL ALA PHE ARG LEU GLU SEQRES 27 A 371 PRO LYS ASP GLY LYS GLY VAL PHE ALA VAL ASP GLY GLU SEQRES 28 A 371 LEU MET VAL SER GLU ALA VAL GLN GLY GLN VAL HIS PRO SEQRES 29 A 371 ASN TYR PHE TRP MET VAL SER SEQRES 1 B 371 SER MET GLU PRO ARG VAL GLU VAL MET ASP PRO ALA GLY SEQRES 2 B 371 GLY PRO ARG GLY VAL LEU PRO ARG PRO CYS ARG VAL LEU SEQRES 3 B 371 VAL LEU LEU ASN PRO ARG GLY GLY LYS GLY LYS ALA LEU SEQRES 4 B 371 GLN LEU PHE ARG SER HIS VAL GLN PRO LEU LEU ALA GLU SEQRES 5 B 371 ALA GLU ILE SER PHE THR LEU MET LEU THR GLU ARG ARG SEQRES 6 B 371 ASN HIS ALA ARG GLU LEU VAL ARG SER GLU GLU LEU GLY SEQRES 7 B 371 ARG TRP ASP ALA LEU VAL VAL MET SER GLY ASP GLY LEU SEQRES 8 B 371 MET HIS GLU VAL VAL ASN GLY LEU MET GLU ARG PRO ASP SEQRES 9 B 371 TRP GLU THR ALA ILE GLN LYS PRO LEU CYS SER LEU PRO SEQRES 10 B 371 ALA GLY SER GLY ASN ALA LEU ALA ALA SER LEU ASN HIS SEQRES 11 B 371 TYR ALA GLY TYR GLU GLN VAL THR ASN GLU ASP LEU LEU SEQRES 12 B 371 THR ASN CYS THR LEU LEU LEU CYS ARG ARG LEU LEU SER SEQRES 13 B 371 PRO MET ASN LEU LEU SER LEU HIS THR ALA SER GLY LEU SEQRES 14 B 371 ARG LEU PHE SER VAL LEU SER LEU ALA TRP GLY PHE ILE SEQRES 15 B 371 ALA ASP VAL ASP LEU GLU SER GLU LYS TYR ARG ARG LEU SEQRES 16 B 371 GLY GLU MET ARG PHE THR LEU GLY THR PHE LEU ARG LEU SEQRES 17 B 371 ALA ALA LEU ARG THR TYR ARG GLY ARG LEU ALA TYR LEU SEQRES 18 B 371 PRO VAL GLY ARG VAL GLY SER LYS THR PRO ALA SER PRO SEQRES 19 B 371 VAL VAL VAL GLN GLN GLY PRO VAL ASP ALA HIS LEU VAL SEQRES 20 B 371 PRO LEU GLU GLU PRO VAL PRO SER HIS TRP THR VAL VAL SEQRES 21 B 371 PRO ASP GLU ASP PHE VAL LEU VAL LEU ALA LEU LEU HIS SEQRES 22 B 371 SER HIS LEU GLY SER GLU MET PHE ALA ALA PRO MET GLY SEQRES 23 B 371 ARG CYS ALA ALA GLY VAL MET HIS LEU PHE TYR VAL ARG SEQRES 24 B 371 ALA GLY VAL SER ARG ALA MET LEU LEU ARG LEU PHE LEU SEQRES 25 B 371 ALA MET GLU LYS GLY ARG HIS MET GLU TYR GLU CYS PRO SEQRES 26 B 371 TYR LEU VAL TYR VAL PRO VAL VAL ALA PHE ARG LEU GLU SEQRES 27 B 371 PRO LYS ASP GLY LYS GLY VAL PHE ALA VAL ASP GLY GLU SEQRES 28 B 371 LEU MET VAL SER GLU ALA VAL GLN GLY GLN VAL HIS PRO SEQRES 29 B 371 ASN TYR PHE TRP MET VAL SER HET GYR A1450 33 HET ACT A1451 4 HET GYR B1450 33 HETNAM GYR {(2R)-1-[4-({3-METHYL-5-[(PHENYLSULFONYL) HETNAM 2 GYR METHYL]PHENOXY}METHYL)BENZYL]PYRROLIDIN-2-YL}METHANOL HETNAM ACT ACETATE ION HETSYN GYR PF-543 FORMUL 3 GYR 2(C27 H31 N O4 S) FORMUL 4 ACT C2 H3 O2 1- FORMUL 6 HOH *476(H2 O) HELIX 1 1 LYS A 115 VAL A 124 1 10 HELIX 2 2 VAL A 124 ALA A 131 1 8 HELIX 3 3 ASN A 144 GLU A 153 1 10 HELIX 4 4 GLY A 166 GLU A 179 1 14 HELIX 5 5 ASP A 182 ILE A 187 1 6 HELIX 6 6 ASN A 200 ALA A 210 1 11 HELIX 7 7 THR A 216 ARG A 231 1 16 HELIX 8 8 PHE A 259 GLU A 268 1 10 HELIX 9 9 LYS A 269 GLU A 275 5 7 HELIX 10 10 MET A 276 ALA A 288 1 13 HELIX 11 11 VAL A 301 GLY A 305 1 5 HELIX 12 12 SER A 381 MET A 392 1 12 HELIX 13 13 GLU A 393 GLY A 395 5 3 HELIX 14 14 ARG A 396 GLU A 401 5 6 HELIX 15 15 LYS B 115 VAL B 124 1 10 HELIX 16 16 VAL B 124 ALA B 131 1 8 HELIX 17 17 ASN B 144 SER B 152 1 9 HELIX 18 18 GLY B 166 GLU B 179 1 14 HELIX 19 19 ASP B 182 ILE B 187 1 6 HELIX 20 20 ASN B 200 ALA B 210 1 11 HELIX 21 21 THR B 216 ARG B 231 1 16 HELIX 22 22 PHE B 259 GLU B 268 1 10 HELIX 23 23 LYS B 269 GLU B 275 5 7 HELIX 24 24 MET B 276 ALA B 288 1 13 HELIX 25 25 VAL B 301 GLY B 305 1 5 HELIX 26 26 SER B 381 GLU B 393 1 13 HELIX 27 27 ARG B 396 GLU B 401 5 6 SHEET 1 AA 2 GLY A 95 VAL A 96 0 SHEET 2 AA 2 LEU A 232 THR A 243 -1 O LEU A 233 N GLY A 95 SHEET 1 AB 2 ARG A 248 SER A 251 0 SHEET 2 AB 2 LEU A 232 THR A 243 -1 O LEU A 239 N SER A 251 SHEET 1 AC 2 THR A 336 VAL A 337 0 SHEET 2 AC 2 TYR A 292 PRO A 300 -1 O TYR A 298 N THR A 336 SHEET 1 AD 9 GLU A 429 VAL A 432 0 SHEET 2 AD 9 VAL A 423 VAL A 426 -1 O PHE A 424 N MET A 431 SHEET 3 AD 9 SER A 254 GLY A 258 -1 O ALA A 256 N ALA A 425 SHEET 4 AD 9 ASP A 342 LEU A 349 -1 O VAL A 346 N TRP A 257 SHEET 5 AD 9 MET A 371 ARG A 377 1 O HIS A 372 N LEU A 349 SHEET 6 AD 9 LEU A 405 PRO A 417 1 O VAL A 406 N TYR A 375 SHEET 7 AD 9 VAL A 436 VAL A 448 -1 O VAL A 436 N LEU A 415 SHEET 8 AD 9 LEU A 232 THR A 243 -1 O SER A 234 N MET A 447 SHEET 9 AD 9 ARG A 248 SER A 251 -1 O LEU A 249 N LEU A 241 SHEET 1 AE 6 GLU A 429 VAL A 432 0 SHEET 2 AE 6 VAL A 423 VAL A 426 -1 O PHE A 424 N MET A 431 SHEET 3 AE 6 SER A 254 GLY A 258 -1 O ALA A 256 N ALA A 425 SHEET 4 AE 6 ASP A 342 LEU A 349 -1 O VAL A 346 N TRP A 257 SHEET 5 AE 6 TYR A 292 PRO A 300 -1 O TYR A 292 N PHE A 343 SHEET 6 AE 6 THR A 336 VAL A 337 -1 O THR A 336 N TYR A 298 SHEET 1 AF 4 ILE A 133 LEU A 139 0 SHEET 2 AF 4 CYS A 101 LEU A 107 1 O CYS A 101 N SER A 134 SHEET 3 AF 4 ALA A 160 SER A 165 1 O ALA A 160 N LEU A 104 SHEET 4 AF 4 LEU A 191 PRO A 195 1 O CYS A 192 N VAL A 163 SHEET 1 BA 2 GLY B 95 VAL B 96 0 SHEET 2 BA 2 LEU B 232 THR B 243 1 O LEU B 233 N GLY B 95 SHEET 1 BB 2 ARG B 248 SER B 251 0 SHEET 2 BB 2 LEU B 232 THR B 243 -1 O LEU B 239 N SER B 251 SHEET 1 BC 2 THR B 336 VAL B 337 0 SHEET 2 BC 2 TYR B 292 PRO B 300 -1 O TYR B 298 N THR B 336 SHEET 1 BD 9 GLU B 429 VAL B 432 0 SHEET 2 BD 9 VAL B 423 VAL B 426 -1 O PHE B 424 N MET B 431 SHEET 3 BD 9 SER B 254 GLY B 258 -1 O ALA B 256 N ALA B 425 SHEET 4 BD 9 ASP B 342 LEU B 349 -1 O VAL B 346 N TRP B 257 SHEET 5 BD 9 MET B 371 ARG B 377 1 O HIS B 372 N LEU B 349 SHEET 6 BD 9 LEU B 405 PRO B 417 1 O VAL B 406 N TYR B 375 SHEET 7 BD 9 VAL B 436 VAL B 448 -1 O VAL B 436 N LEU B 415 SHEET 8 BD 9 LEU B 232 THR B 243 -1 O SER B 234 N MET B 447 SHEET 9 BD 9 ARG B 248 SER B 251 -1 O LEU B 249 N LEU B 241 SHEET 1 BE 6 GLU B 429 VAL B 432 0 SHEET 2 BE 6 VAL B 423 VAL B 426 -1 O PHE B 424 N MET B 431 SHEET 3 BE 6 SER B 254 GLY B 258 -1 O ALA B 256 N ALA B 425 SHEET 4 BE 6 ASP B 342 LEU B 349 -1 O VAL B 346 N TRP B 257 SHEET 5 BE 6 TYR B 292 PRO B 300 -1 O TYR B 292 N PHE B 343 SHEET 6 BE 6 THR B 336 VAL B 337 -1 O THR B 336 N TYR B 298 SHEET 1 BF 4 ILE B 133 LEU B 139 0 SHEET 2 BF 4 CYS B 101 LEU B 107 1 O CYS B 101 N SER B 134 SHEET 3 BF 4 ALA B 160 SER B 165 1 O ALA B 160 N LEU B 104 SHEET 4 BF 4 LEU B 191 PRO B 195 1 O CYS B 192 N VAL B 163 CISPEP 1 ARG A 99 PRO A 100 0 -12.78 CISPEP 2 GLY A 318 PRO A 319 0 -0.57 CISPEP 3 ARG B 99 PRO B 100 0 -11.43 CISPEP 4 GLY B 318 PRO B 319 0 0.68 SITE 1 AC1 12 PHE A 259 ILE A 260 VAL A 263 ASP A 264 SITE 2 AC1 12 THR A 282 MET A 358 ALA A 360 PHE A 374 SITE 3 AC1 12 LEU A 388 HIS A 397 LEU A 405 HOH A2123 SITE 1 AC2 14 PHE B 259 ILE B 260 VAL B 263 ASP B 264 SITE 2 AC2 14 THR B 282 LEU B 347 MET B 358 ALA B 360 SITE 3 AC2 14 PHE B 374 LEU B 388 MET B 392 HIS B 397 SITE 4 AC2 14 LEU B 405 HOH B2140 SITE 1 AC3 1 HOH A2229 CRYST1 86.570 60.549 89.592 90.00 107.17 90.00 P 1 21 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 0.011551 0.000000 0.003569 0.00000 SCALE2 0.000000 0.016516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011682 0.00000 MTRIX1 1 -0.338530 -0.006760 0.940930 -1.40937 1 MTRIX2 1 0.003470 -0.999980 -0.005940 12.97121 1 MTRIX3 1 0.940950 0.001260 0.338540 -2.04934 1