PDB Short entry for 4Q6R HEADER LYASE/LYASE INHIBITOR 23-APR-14 4Q6R TITLE CRYSTAL STRUCTURE OF HUMAN SPHINGOSINE-1-PHOSPHATE LYASE IN COMPLEX TITLE 2 WITH INHIBITOR 6-[(2R)-4-(4-BENZYL-7-CHLOROPHTHALAZIN-1-YL)-2- TITLE 3 METHYLPIPERAZIN-1-YL]PYRIDINE-3-CARBONITRILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOSINE-1-PHOSPHATE LYASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: S1PL, SP-LYASE 1, SPL 1, HSPL, SPHINGOSINE-1-PHOSPHATE COMPND 5 ALDOLASE; COMPND 6 EC: 4.1.2.27; COMPND 7 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: KIAA1252, SGPL1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PLP, PYRIDOXAL 5-PHOSPHATE-DEPENDENT ENZYMES, LYASE-LYASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.SRINIVAS REVDAT 4 06-DEC-23 4Q6R 1 REMARK REVDAT 3 20-SEP-23 4Q6R 1 REMARK SEQADV LINK REVDAT 2 23-JUL-14 4Q6R 1 JRNL REVDAT 1 21-MAY-14 4Q6R 0 JRNL AUTH S.WEILER,N.BRAENDLIN,C.BEERLI,C.BERGSDORF,A.SCHUBART, JRNL AUTH 2 H.SRINIVAS,B.OBERHAUSER,A.BILLICH JRNL TITL ORALLY ACTIVE 7-SUBSTITUTED JRNL TITL 2 (4-BENZYLPHTHALAZIN-1-YL) JRNL TITL 3 -2-METHYLPIPERAZIN-1-YL]NICOTINONITRILES AS ACTIVE-SITE JRNL TITL 4 INHIBITORS OF SPHINGOSINE 1-PHOSPHATE LYASE FOR THE JRNL TITL 5 TREATMENT OF MULTIPLE SCLEROSIS. JRNL REF J.MED.CHEM. V. 57 5074 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 24809814 JRNL DOI 10.1021/JM500338N REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.9.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45369 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2269 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.46 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3326 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2165 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3159 REMARK 3 BIN R VALUE (WORKING SET) : 0.2159 REMARK 3 BIN FREE R VALUE : 0.2288 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.02 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 167 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6907 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 344 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 16.52480 REMARK 3 B22 (A**2) : 17.36870 REMARK 3 B33 (A**2) : -33.89350 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.274 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.288 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.885 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 7161 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 9690 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : NULL ; NULL ; NULL REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.06 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.98 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.81 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4Q6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45426 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 24.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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 <I/SIGMA(I)> 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: 1HBX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350 20%, TACSIMATE (BUFFERED) 8% REMARK 280 PEG, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+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 63.99250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 65.26600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 63.99250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 65.26600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 58 REMARK 465 PRO A 59 REMARK 465 GLY A 60 REMARK 465 SER A 61 REMARK 465 GLN A 62 REMARK 465 PRO A 63 REMARK 465 GLU A 64 REMARK 465 SER A 65 REMARK 465 LEU A 66 REMARK 465 TRP A 67 REMARK 465 SER A 68 REMARK 465 ARG A 69 REMARK 465 PHE A 70 REMARK 465 LYS A 71 REMARK 465 LYS A 72 REMARK 465 LYS A 73 REMARK 465 CYS A 74 REMARK 465 PHE A 75 REMARK 465 LYS A 76 REMARK 465 LEU A 77 REMARK 465 THR A 78 REMARK 465 ARG A 79 REMARK 465 LYS A 80 REMARK 465 MET A 81 REMARK 465 PRO A 82 REMARK 465 ILE A 83 REMARK 465 ILE A 84 REMARK 465 GLY A 85 REMARK 465 ARG A 86 REMARK 465 LYS A 87 REMARK 465 ILE A 88 REMARK 465 GLN A 89 REMARK 465 ASP A 90 REMARK 465 LYS A 91 REMARK 465 LEU A 92 REMARK 465 ASN A 93 REMARK 465 LYS A 94 REMARK 465 THR A 95 REMARK 465 LYS A 96 REMARK 465 ASP A 97 REMARK 465 ASP A 98 REMARK 465 ILE A 99 REMARK 465 SER A 100 REMARK 465 LYS A 101 REMARK 465 ASN A 102 REMARK 465 MET A 103 REMARK 465 SER A 104 REMARK 465 PHE A 105 REMARK 465 LEU A 106 REMARK 465 LYS A 107 REMARK 465 VAL A 108 REMARK 465 ASP A 109 REMARK 465 LYS A 110 REMARK 465 THR A 554 REMARK 465 VAL A 555 REMARK 465 THR A 556 REMARK 465 GLN A 557 REMARK 465 GLY A 558 REMARK 465 SER A 559 REMARK 465 GLN A 560 REMARK 465 MET A 561 REMARK 465 ASN A 562 REMARK 465 GLY A 563 REMARK 465 SER A 564 REMARK 465 PRO A 565 REMARK 465 LYS A 566 REMARK 465 PRO A 567 REMARK 465 HIS A 568 REMARK 465 GLY B 58 REMARK 465 PRO B 59 REMARK 465 GLY B 60 REMARK 465 SER B 61 REMARK 465 GLN B 62 REMARK 465 PRO B 63 REMARK 465 GLU B 64 REMARK 465 SER B 65 REMARK 465 LEU B 66 REMARK 465 TRP B 67 REMARK 465 SER B 68 REMARK 465 ARG B 69 REMARK 465 PHE B 70 REMARK 465 LYS B 71 REMARK 465 LYS B 72 REMARK 465 LYS B 73 REMARK 465 CYS B 74 REMARK 465 PHE B 75 REMARK 465 LYS B 76 REMARK 465 LEU B 77 REMARK 465 THR B 78 REMARK 465 ARG B 79 REMARK 465 LYS B 80 REMARK 465 MET B 81 REMARK 465 PRO B 82 REMARK 465 ILE B 83 REMARK 465 ILE B 84 REMARK 465 GLY B 85 REMARK 465 ARG B 86 REMARK 465 LYS B 87 REMARK 465 ILE B 88 REMARK 465 GLN B 89 REMARK 465 ASP B 90 REMARK 465 LYS B 91 REMARK 465 LEU B 92 REMARK 465 ASN B 93 REMARK 465 LYS B 94 REMARK 465 THR B 95 REMARK 465 LYS B 96 REMARK 465 ASP B 97 REMARK 465 ASP B 98 REMARK 465 ILE B 99 REMARK 465 SER B 100 REMARK 465 LYS B 101 REMARK 465 ASN B 102 REMARK 465 MET B 103 REMARK 465 SER B 104 REMARK 465 PHE B 105 REMARK 465 LEU B 106 REMARK 465 LYS B 107 REMARK 465 VAL B 108 REMARK 465 ASP B 109 REMARK 465 THR B 554 REMARK 465 VAL B 555 REMARK 465 THR B 556 REMARK 465 GLN B 557 REMARK 465 GLY B 558 REMARK 465 SER B 559 REMARK 465 GLN B 560 REMARK 465 MET B 561 REMARK 465 ASN B 562 REMARK 465 GLY B 563 REMARK 465 SER B 564 REMARK 465 PRO B 565 REMARK 465 LYS B 566 REMARK 465 PRO B 567 REMARK 465 HIS B 568 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 PHE A 139 -54.43 -23.51 REMARK 500 THR A 148 -65.95 63.23 REMARK 500 SER A 151 -65.31 -131.21 REMARK 500 PRO A 172 0.05 -65.42 REMARK 500 HIS A 174 75.37 -118.02 REMARK 500 PHE A 178 69.76 -119.35 REMARK 500 PHE A 337 -7.83 -142.70 REMARK 500 ASP A 338 -155.24 -106.34 REMARK 500 LLP A 353 -109.38 -94.51 REMARK 500 THR A 391 -167.00 -121.32 REMARK 500 LEU A 448 -141.48 -119.60 REMARK 500 THR B 148 -60.08 61.13 REMARK 500 SER B 151 -71.53 -133.13 REMARK 500 PRO B 172 0.53 -65.81 REMARK 500 HIS B 174 75.32 -118.46 REMARK 500 PHE B 178 69.47 -118.40 REMARK 500 PHE B 337 -8.06 -142.05 REMARK 500 ASP B 338 -156.16 -106.57 REMARK 500 LLP B 353 -110.65 -92.64 REMARK 500 THR B 391 -166.34 -120.41 REMARK 500 LEU B 448 -143.31 -121.26 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 SIN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 30J A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 30J B 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HBX RELATED DB: PDB REMARK 900 RELATED ID: 3MC6 RELATED DB: PDB DBREF 4Q6R A 62 568 UNP O95470 SGPL1_HUMAN 62 568 DBREF 4Q6R B 62 568 UNP O95470 SGPL1_HUMAN 62 568 SEQADV 4Q6R GLY A 58 UNP O95470 EXPRESSION TAG SEQADV 4Q6R PRO A 59 UNP O95470 EXPRESSION TAG SEQADV 4Q6R GLY A 60 UNP O95470 EXPRESSION TAG SEQADV 4Q6R SER A 61 UNP O95470 EXPRESSION TAG SEQADV 4Q6R GLY B 58 UNP O95470 EXPRESSION TAG SEQADV 4Q6R PRO B 59 UNP O95470 EXPRESSION TAG SEQADV 4Q6R GLY B 60 UNP O95470 EXPRESSION TAG SEQADV 4Q6R SER B 61 UNP O95470 EXPRESSION TAG SEQRES 1 A 511 GLY PRO GLY SER GLN PRO GLU SER LEU TRP SER ARG PHE SEQRES 2 A 511 LYS LYS LYS CYS PHE LYS LEU THR ARG LYS MET PRO ILE SEQRES 3 A 511 ILE GLY ARG LYS ILE GLN ASP LYS LEU ASN LYS THR LYS SEQRES 4 A 511 ASP ASP ILE SER LYS ASN MET SER PHE LEU LYS VAL ASP SEQRES 5 A 511 LYS GLU TYR VAL LYS ALA LEU PRO SER GLN GLY LEU SER SEQRES 6 A 511 SER SER ALA VAL LEU GLU LYS LEU LYS GLU TYR SER SER SEQRES 7 A 511 MET ASP ALA PHE TRP GLN GLU GLY ARG ALA SER GLY THR SEQRES 8 A 511 VAL TYR SER GLY GLU GLU LYS LEU THR GLU LEU LEU VAL SEQRES 9 A 511 LYS ALA TYR GLY ASP PHE ALA TRP SER ASN PRO LEU HIS SEQRES 10 A 511 PRO ASP ILE PHE PRO GLY LEU ARG LYS ILE GLU ALA GLU SEQRES 11 A 511 ILE VAL ARG ILE ALA CYS SER LEU PHE ASN GLY GLY PRO SEQRES 12 A 511 ASP SER CYS GLY CYS VAL THR SER GLY GLY THR GLU SER SEQRES 13 A 511 ILE LEU MET ALA CYS LYS ALA TYR ARG ASP LEU ALA PHE SEQRES 14 A 511 GLU LYS GLY ILE LYS THR PRO GLU ILE VAL ALA PRO GLN SEQRES 15 A 511 SER ALA HIS ALA ALA PHE ASN LYS ALA ALA SER TYR PHE SEQRES 16 A 511 GLY MET LYS ILE VAL ARG VAL PRO LEU THR LYS MET MET SEQRES 17 A 511 GLU VAL ASP VAL ARG ALA MET ARG ARG ALA ILE SER ARG SEQRES 18 A 511 ASN THR ALA MET LEU VAL CYS SER THR PRO GLN PHE PRO SEQRES 19 A 511 HIS GLY VAL ILE ASP PRO VAL PRO GLU VAL ALA LYS LEU SEQRES 20 A 511 ALA VAL LYS TYR LYS ILE PRO LEU HIS VAL ASP ALA CYS SEQRES 21 A 511 LEU GLY GLY PHE LEU ILE VAL PHE MET GLU LYS ALA GLY SEQRES 22 A 511 TYR PRO LEU GLU HIS PRO PHE ASP PHE ARG VAL LYS GLY SEQRES 23 A 511 VAL THR SER ILE SER ALA ASP THR HIS LLP TYR GLY TYR SEQRES 24 A 511 ALA PRO LYS GLY SER SER LEU VAL LEU TYR SER ASP LYS SEQRES 25 A 511 LYS TYR ARG ASN TYR GLN PHE PHE VAL ASP THR ASP TRP SEQRES 26 A 511 GLN GLY GLY ILE TYR ALA SER PRO THR ILE ALA GLY SER SEQRES 27 A 511 ARG PRO GLY GLY ILE SER ALA ALA CYS TRP ALA ALA LEU SEQRES 28 A 511 MET HIS PHE GLY GLU ASN GLY TYR VAL GLU ALA THR LYS SEQRES 29 A 511 GLN ILE ILE LYS THR ALA ARG PHE LEU LYS SER GLU LEU SEQRES 30 A 511 GLU ASN ILE LYS GLY ILE PHE VAL PHE GLY ASN PRO GLN SEQRES 31 A 511 LEU SER VAL ILE ALA LEU GLY SER ARG ASP PHE ASP ILE SEQRES 32 A 511 TYR ARG LEU SER ASN LEU MET THR ALA LYS GLY TRP ASN SEQRES 33 A 511 LEU ASN GLN LEU GLN PHE PRO PRO SER ILE HIS PHE CYS SEQRES 34 A 511 ILE THR LEU LEU HIS ALA ARG LYS ARG VAL ALA ILE GLN SEQRES 35 A 511 PHE LEU LYS ASP ILE ARG GLU SER VAL THR GLN ILE MET SEQRES 36 A 511 LYS ASN PRO LYS ALA LYS THR THR GLY MET GLY ALA ILE SEQRES 37 A 511 TYR GLY MET ALA GLN THR THR VAL ASP ARG ASN MET VAL SEQRES 38 A 511 ALA GLU LEU SER SER VAL PHE LEU ASP SER LEU TYR SER SEQRES 39 A 511 THR ASP THR VAL THR GLN GLY SER GLN MET ASN GLY SER SEQRES 40 A 511 PRO LYS PRO HIS SEQRES 1 B 511 GLY PRO GLY SER GLN PRO GLU SER LEU TRP SER ARG PHE SEQRES 2 B 511 LYS LYS LYS CYS PHE LYS LEU THR ARG LYS MET PRO ILE SEQRES 3 B 511 ILE GLY ARG LYS ILE GLN ASP LYS LEU ASN LYS THR LYS SEQRES 4 B 511 ASP ASP ILE SER LYS ASN MET SER PHE LEU LYS VAL ASP SEQRES 5 B 511 LYS GLU TYR VAL LYS ALA LEU PRO SER GLN GLY LEU SER SEQRES 6 B 511 SER SER ALA VAL LEU GLU LYS LEU LYS GLU TYR SER SER SEQRES 7 B 511 MET ASP ALA PHE TRP GLN GLU GLY ARG ALA SER GLY THR SEQRES 8 B 511 VAL TYR SER GLY GLU GLU LYS LEU THR GLU LEU LEU VAL SEQRES 9 B 511 LYS ALA TYR GLY ASP PHE ALA TRP SER ASN PRO LEU HIS SEQRES 10 B 511 PRO ASP ILE PHE PRO GLY LEU ARG LYS ILE GLU ALA GLU SEQRES 11 B 511 ILE VAL ARG ILE ALA CYS SER LEU PHE ASN GLY GLY PRO SEQRES 12 B 511 ASP SER CYS GLY CYS VAL THR SER GLY GLY THR GLU SER SEQRES 13 B 511 ILE LEU MET ALA CYS LYS ALA TYR ARG ASP LEU ALA PHE SEQRES 14 B 511 GLU LYS GLY ILE LYS THR PRO GLU ILE VAL ALA PRO GLN SEQRES 15 B 511 SER ALA HIS ALA ALA PHE ASN LYS ALA ALA SER TYR PHE SEQRES 16 B 511 GLY MET LYS ILE VAL ARG VAL PRO LEU THR LYS MET MET SEQRES 17 B 511 GLU VAL ASP VAL ARG ALA MET ARG ARG ALA ILE SER ARG SEQRES 18 B 511 ASN THR ALA MET LEU VAL CYS SER THR PRO GLN PHE PRO SEQRES 19 B 511 HIS GLY VAL ILE ASP PRO VAL PRO GLU VAL ALA LYS LEU SEQRES 20 B 511 ALA VAL LYS TYR LYS ILE PRO LEU HIS VAL ASP ALA CYS SEQRES 21 B 511 LEU GLY GLY PHE LEU ILE VAL PHE MET GLU LYS ALA GLY SEQRES 22 B 511 TYR PRO LEU GLU HIS PRO PHE ASP PHE ARG VAL LYS GLY SEQRES 23 B 511 VAL THR SER ILE SER ALA ASP THR HIS LLP TYR GLY TYR SEQRES 24 B 511 ALA PRO LYS GLY SER SER LEU VAL LEU TYR SER ASP LYS SEQRES 25 B 511 LYS TYR ARG ASN TYR GLN PHE PHE VAL ASP THR ASP TRP SEQRES 26 B 511 GLN GLY GLY ILE TYR ALA SER PRO THR ILE ALA GLY SER SEQRES 27 B 511 ARG PRO GLY GLY ILE SER ALA ALA CYS TRP ALA ALA LEU SEQRES 28 B 511 MET HIS PHE GLY GLU ASN GLY TYR VAL GLU ALA THR LYS SEQRES 29 B 511 GLN ILE ILE LYS THR ALA ARG PHE LEU LYS SER GLU LEU SEQRES 30 B 511 GLU ASN ILE LYS GLY ILE PHE VAL PHE GLY ASN PRO GLN SEQRES 31 B 511 LEU SER VAL ILE ALA LEU GLY SER ARG ASP PHE ASP ILE SEQRES 32 B 511 TYR ARG LEU SER ASN LEU MET THR ALA LYS GLY TRP ASN SEQRES 33 B 511 LEU ASN GLN LEU GLN PHE PRO PRO SER ILE HIS PHE CYS SEQRES 34 B 511 ILE THR LEU LEU HIS ALA ARG LYS ARG VAL ALA ILE GLN SEQRES 35 B 511 PHE LEU LYS ASP ILE ARG GLU SER VAL THR GLN ILE MET SEQRES 36 B 511 LYS ASN PRO LYS ALA LYS THR THR GLY MET GLY ALA ILE SEQRES 37 B 511 TYR GLY MET ALA GLN THR THR VAL ASP ARG ASN MET VAL SEQRES 38 B 511 ALA GLU LEU SER SER VAL PHE LEU ASP SER LEU TYR SER SEQRES 39 B 511 THR ASP THR VAL THR GLN GLY SER GLN MET ASN GLY SER SEQRES 40 B 511 PRO LYS PRO HIS MODRES 4Q6R LLP A 353 LYS MODRES 4Q6R LLP B 353 LYS HET LLP A 353 24 HET LLP B 353 24 HET SIN A 901 8 HET GOL A 902 6 HET 30J A 903 33 HET PO4 B 601 5 HET 30J B 602 33 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM SIN SUCCINIC ACID HETNAM GOL GLYCEROL HETNAM 30J 6-[(2R)-4-(4-BENZYL-7-CHLOROPHTHALAZIN-1-YL)-2- HETNAM 2 30J METHYLPIPERAZIN-1-YL]PYRIDINE-3-CARBONITRILE HETNAM PO4 PHOSPHATE ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 SIN C4 H6 O4 FORMUL 4 GOL C3 H8 O3 FORMUL 5 30J 2(C26 H23 CL N6) FORMUL 6 PO4 O4 P 3- FORMUL 8 HOH *344(H2 O) HELIX 1 1 SER A 122 SER A 135 1 14 HELIX 2 2 MET A 136 GLY A 143 5 8 HELIX 3 3 GLU A 153 ASP A 166 1 14 HELIX 4 4 PHE A 178 PHE A 196 1 19 HELIX 5 5 GLY A 209 LYS A 228 1 20 HELIX 6 6 ALA A 243 GLY A 253 1 11 HELIX 7 7 ASP A 268 ARG A 274 1 7 HELIX 8 8 PRO A 297 LYS A 309 1 13 HELIX 9 9 GLY A 319 VAL A 324 1 6 HELIX 10 10 ASP A 368 ASN A 373 1 6 HELIX 11 11 PRO A 397 GLU A 435 1 39 HELIX 12 12 ILE A 460 LYS A 470 1 11 HELIX 13 13 THR A 488 ARG A 495 1 8 HELIX 14 14 VAL A 496 ASN A 514 1 19 HELIX 15 15 THR A 520 THR A 532 1 13 HELIX 16 16 ASP A 534 TYR A 550 1 17 HELIX 17 17 SER B 122 MET B 136 1 15 HELIX 18 18 PHE B 139 GLY B 143 5 5 HELIX 19 19 GLU B 153 PHE B 167 1 15 HELIX 20 20 PHE B 178 PHE B 196 1 19 HELIX 21 21 GLY B 209 LYS B 228 1 20 HELIX 22 22 ALA B 243 GLY B 253 1 11 HELIX 23 23 ASP B 268 ILE B 276 1 9 HELIX 24 24 PRO B 297 LYS B 309 1 13 HELIX 25 25 GLY B 319 VAL B 324 1 6 HELIX 26 26 ASP B 368 ASN B 373 1 6 HELIX 27 27 PRO B 397 GLU B 435 1 39 HELIX 28 28 ILE B 460 LYS B 470 1 11 HELIX 29 29 THR B 488 LYS B 494 1 7 HELIX 30 30 VAL B 496 ASN B 514 1 19 HELIX 31 31 THR B 520 THR B 532 1 13 HELIX 32 32 ASP B 534 TYR B 550 1 17 SHEET 1 A 7 CYS A 203 THR A 207 0 SHEET 2 A 7 SER A 362 TYR A 366 -1 O TYR A 366 N CYS A 203 SHEET 3 A 7 VAL A 344 ALA A 349 -1 N ILE A 347 O LEU A 365 SHEET 4 A 7 LEU A 312 ALA A 316 1 N VAL A 314 O SER A 346 SHEET 5 A 7 THR A 280 SER A 286 1 N CYS A 285 O ASP A 315 SHEET 6 A 7 GLU A 234 PRO A 238 1 N GLU A 234 O ALA A 281 SHEET 7 A 7 LYS A 255 VAL A 259 1 O LYS A 255 N ILE A 235 SHEET 1 B 2 PHE A 377 ASP A 379 0 SHEET 2 B 2 TYR A 387 SER A 389 -1 O TYR A 387 N ASP A 379 SHEET 1 C 4 PHE A 441 VAL A 442 0 SHEET 2 C 4 VAL A 450 GLY A 454 -1 O GLY A 454 N PHE A 441 SHEET 3 C 4 SER A 482 CYS A 486 -1 O ILE A 483 N LEU A 453 SHEET 4 C 4 ASN A 475 LEU A 477 -1 N LEU A 477 O SER A 482 SHEET 1 D 7 CYS B 203 THR B 207 0 SHEET 2 D 7 SER B 362 TYR B 366 -1 O TYR B 366 N CYS B 203 SHEET 3 D 7 VAL B 344 ALA B 349 -1 N ILE B 347 O LEU B 365 SHEET 4 D 7 LEU B 312 ALA B 316 1 N VAL B 314 O SER B 346 SHEET 5 D 7 THR B 280 SER B 286 1 N CYS B 285 O ASP B 315 SHEET 6 D 7 GLU B 234 PRO B 238 1 N GLU B 234 O ALA B 281 SHEET 7 D 7 LYS B 255 VAL B 259 1 O LYS B 255 N ILE B 235 SHEET 1 E 2 PHE B 377 ASP B 379 0 SHEET 2 E 2 TYR B 387 SER B 389 -1 O TYR B 387 N ASP B 379 SHEET 1 F 4 PHE B 441 VAL B 442 0 SHEET 2 F 4 VAL B 450 GLY B 454 -1 O GLY B 454 N PHE B 441 SHEET 3 F 4 SER B 482 CYS B 486 -1 O ILE B 483 N LEU B 453 SHEET 4 F 4 ASN B 475 LEU B 477 -1 N LEU B 477 O SER B 482 LINK C HIS A 352 N LLP A 353 1555 1555 1.34 LINK C LLP A 353 N TYR A 354 1555 1555 1.35 LINK C HIS B 352 N LLP B 353 1555 1555 1.35 LINK C LLP B 353 N TYR B 354 1555 1555 1.35 CISPEP 1 THR A 287 PRO A 288 0 -0.82 CISPEP 2 PHE A 479 PRO A 480 0 7.56 CISPEP 3 THR B 287 PRO B 288 0 -1.09 CISPEP 4 PHE B 479 PRO B 480 0 6.74 SITE 1 AC1 10 THR A 148 TYR A 150 HIS A 242 PHE A 290 SITE 2 AC1 10 LLP A 353 HOH A1176 HOH A1177 HIS B 174 SITE 3 AC1 10 TYR B 387 30J B 602 SITE 1 AC2 5 ARG A 462 ASN A 465 LYS A 518 THR A 519 SITE 2 AC2 5 THR A 520 SITE 1 AC3 10 LEU A 173 PRO A 175 ILE A 386 TYR A 387 SITE 2 AC3 10 ALA A 388 MET B 528 VAL B 538 LEU B 541 SITE 3 AC3 10 SER B 542 PHE B 545 SITE 1 AC4 6 ASN A 171 HIS A 174 THR B 148 TYR B 150 SITE 2 AC4 6 LLP B 353 HOH B 854 SITE 1 AC5 10 ILE A 525 VAL A 538 LEU A 541 SER A 542 SITE 2 AC5 10 PHE A 545 SIN A 901 LEU B 173 ILE B 386 SITE 3 AC5 10 TYR B 387 ALA B 388 CRYST1 127.985 130.532 68.224 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014658 0.00000