PDB Short entry for 3LCD HEADER TRANSFERASE 10-JAN-10 3LCD TITLE INHIBITOR BOUND TO A DFG-IN STRUCTURE OF THE KINASE DOMAIN OF CSF-1R COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE COLONY-STIMULATING FACTOR 1 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: CSF-1-R, FMS PROTO-ONCOGENE, C-FMS; COMPND 6 EC: 2.7.10.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CSF-1R, CSF1R, FMS; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS KINASE CFMS CSF-1R CSF TYROSINE-KINASE COLONY STIMULATING FACTOR 1 KEYWDS 2 RECEPTOR, ATP-BINDING, DISULFIDE BOND, GLYCOPROTEIN, IMMUNOGLOBULIN KEYWDS 3 DOMAIN, KINASE, MEMBRANE, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, PROTO- KEYWDS 4 ONCOGENE, RECEPTOR, TRANSFERASE, TRANSMEMBRANE, TYROSINE-PROTEIN KEYWDS 5 KINASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KAMTEKAR,J.E.DAY,B.A.REITZ,K.J.MATHIS,M.J.MEYERS REVDAT 3 26-JUL-17 3LCD 1 SOURCE REMARK REVDAT 2 13-JUL-11 3LCD 1 VERSN REVDAT 1 02-MAR-10 3LCD 0 JRNL AUTH M.J.MEYERS,M.PELC,S.KAMTEKAR,J.DAY,G.I.PODA,M.K.HALL, JRNL AUTH 2 M.L.MICHENER,B.A.REITZ,K.J.MATHIS,B.S.PIERCE,M.D.PARIKH, JRNL AUTH 3 D.A.MISCHKE,S.A.LONG,J.J.PARLOW,D.R.ANDERSON,A.THORARENSEN JRNL TITL STRUCTURE-BASED DRUG DESIGN ENABLES CONVERSION OF A DFG-IN JRNL TITL 2 BINDING CSF-1R KINASE INHIBITOR TO A DFG-OUT BINDING MODE JRNL REF BIOORG.MED.CHEM.LETT. V. 20 1543 2010 JRNL REFN ISSN 0960-894X JRNL PMID 20137931 JRNL DOI 10.1016/J.BMCL.2010.01.078 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 12800 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 662 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 720 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2249 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 44.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.85000 REMARK 3 B22 (A**2) : 2.62000 REMARK 3 B33 (A**2) : -3.46000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.461 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.292 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.223 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.149 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2356 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1525 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3200 ; 1.173 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3735 ; 0.804 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 289 ; 5.871 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;36.032 ;24.804 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 379 ;15.870 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;21.934 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 349 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2645 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 458 ; 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): 1442 ; 0.412 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 588 ; 0.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2305 ; 0.783 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 914 ; 1.078 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 894 ; 1.782 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 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 : 2 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 560 A 665 REMARK 3 ORIGIN FOR THE GROUP (A): -17.8636 15.2414 -18.2073 REMARK 3 T TENSOR REMARK 3 T11: 0.1143 T22: 0.2014 REMARK 3 T33: 0.1161 T12: 0.0267 REMARK 3 T13: -0.0277 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.4613 L22: 4.0093 REMARK 3 L33: 3.8283 L12: 1.2006 REMARK 3 L13: 1.0483 L23: 1.5009 REMARK 3 S TENSOR REMARK 3 S11: -0.0911 S12: 0.0517 S13: 0.2421 REMARK 3 S21: -0.2627 S22: -0.0338 S23: 0.3366 REMARK 3 S31: -0.2122 S32: -0.0896 S33: 0.1249 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 666 A 930 REMARK 3 ORIGIN FOR THE GROUP (A): -25.4038 0.0035 0.1204 REMARK 3 T TENSOR REMARK 3 T11: 0.0545 T22: 0.0657 REMARK 3 T33: 0.0268 T12: 0.0190 REMARK 3 T13: -0.0269 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 3.2779 L22: 2.3065 REMARK 3 L33: 4.1515 L12: 0.4900 REMARK 3 L13: -1.1742 L23: 0.3519 REMARK 3 S TENSOR REMARK 3 S11: -0.0284 S12: -0.0076 S13: -0.0472 REMARK 3 S21: -0.0115 S22: -0.0414 S23: 0.1252 REMARK 3 S31: 0.2026 S32: 0.0840 S33: 0.0698 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3LCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-09 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07804 REMARK 200 MONOCHROMATOR : DIAMOND [111] REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 5.650 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EQUAL VOLUMES OF PROTEIN:LIGAND (10 REMARK 280 MG/ML PROTEIN, 1 MM LIGAND, 200 MM NACL, 50 MM POTASSIUM REMARK 280 DIHYDROGEN PHOSPHATE PH 7.5, 5% GLYCEROL, 0.25 MM TCEP) AND WELL REMARK 280 SOLUTION (0.1 M SODIUM ACETATE PH 5.5, 0.2 M LITHIUM SULFATE, 5 REMARK 280 MM DTT, 1.5% GLYCEROL, 10-25% PEG 3350) WERE MIXED AND SET UP., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.82450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.51200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.06250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.51200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.82450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.06250 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 300 REMARK: THE KINASE DOMAIN FRAGMENT IS MONOMERIC 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 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 535 REMARK 465 VAL A 536 REMARK 465 ASP A 537 REMARK 465 TYR A 538 REMARK 465 LYS A 539 REMARK 465 TYR A 540 REMARK 465 LYS A 541 REMARK 465 GLN A 542 REMARK 465 LYS A 543 REMARK 465 PRO A 544 REMARK 465 LYS A 545 REMARK 465 TYR A 546 REMARK 465 GLN A 547 REMARK 465 VAL A 548 REMARK 465 ARG A 549 REMARK 465 TRP A 550 REMARK 465 LYS A 551 REMARK 465 ILE A 552 REMARK 465 ILE A 553 REMARK 465 GLU A 554 REMARK 465 SER A 555 REMARK 465 TYR A 556 REMARK 465 GLU A 557 REMARK 465 LYS A 744 REMARK 465 GLU A 745 REMARK 465 ASP A 746 REMARK 465 GLY A 747 REMARK 465 ARG A 748 REMARK 465 ASN A 805 REMARK 465 ASP A 806 REMARK 465 ALA A 914 REMARK 465 GLN A 915 REMARK 465 GLU A 916 REMARK 465 ASP A 917 REMARK 465 ARG A 918 REMARK 465 ARG A 919 REMARK 465 GLU A 920 REMARK 465 ARG A 921 REMARK 465 ASP A 922 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 PHE A 563 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE A 593 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 619 CG CD CE NZ REMARK 470 ARG A 753 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 812 CG CD CE NZ REMARK 470 LYS A 864 CG CD CE NZ 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 ASP A 778 45.93 -147.46 REMARK 500 ASP A 796 85.48 58.72 REMARK 500 PHE A 797 30.97 -99.90 REMARK 500 ASN A 814 -15.42 78.95 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 SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BDY A 923 DBREF 3LCD A 538 681 UNP P07333 CSF1R_HUMAN 538 681 DBREF 3LCD A 741 919 UNP P07333 CSF1R_HUMAN 741 919 SEQADV 3LCD GLY A 535 UNP P07333 EXPRESSION TAG SEQADV 3LCD VAL A 536 UNP P07333 EXPRESSION TAG SEQADV 3LCD ASP A 537 UNP P07333 EXPRESSION TAG SEQRES 1 A 329 GLY VAL ASP TYR LYS TYR LYS GLN LYS PRO LYS TYR GLN SEQRES 2 A 329 VAL ARG TRP LYS ILE ILE GLU SER TYR GLU GLY ASN SER SEQRES 3 A 329 TYR THR PHE ILE ASP PRO THR GLN LEU PRO TYR ASN GLU SEQRES 4 A 329 LYS TRP GLU PHE PRO ARG ASN ASN LEU GLN PHE GLY LYS SEQRES 5 A 329 THR LEU GLY ALA GLY ALA PHE GLY LYS VAL VAL GLU ALA SEQRES 6 A 329 THR ALA PHE GLY LEU GLY LYS GLU ASP ALA VAL LEU LYS SEQRES 7 A 329 VAL ALA VAL LYS MET LEU LYS SER THR ALA HIS ALA ASP SEQRES 8 A 329 GLU LYS GLU ALA LEU MET SER GLU LEU LYS ILE MET SER SEQRES 9 A 329 HIS LEU GLY GLN HIS GLU ASN ILE VAL ASN LEU LEU GLY SEQRES 10 A 329 ALA CYS THR HIS GLY GLY PRO VAL LEU VAL ILE THR GLU SEQRES 11 A 329 TYR CYS CYS TYR GLY ASP LEU LEU ASN PHE LEU ARG ARG SEQRES 12 A 329 LYS ALA GLU ALA ASP LEU ASP LYS GLU ASP GLY ARG PRO SEQRES 13 A 329 LEU GLU LEU ARG ASP LEU LEU HIS PHE SER SER GLN VAL SEQRES 14 A 329 ALA GLN GLY MET ALA PHE LEU ALA SER LYS ASN CYS ILE SEQRES 15 A 329 HIS ARG ASP VAL ALA ALA ARG ASN VAL LEU LEU THR ASN SEQRES 16 A 329 GLY HIS VAL ALA LYS ILE GLY ASP PHE GLY LEU ALA ARG SEQRES 17 A 329 ASP ILE MET ASN ASP SER ASN TYR ILE VAL LYS GLY ASN SEQRES 18 A 329 ALA ARG LEU PRO VAL LYS TRP MET ALA PRO GLU SER ILE SEQRES 19 A 329 PHE ASP CYS VAL TYR THR VAL GLN SER ASP VAL TRP SER SEQRES 20 A 329 TYR GLY ILE LEU LEU TRP GLU ILE PHE SER LEU GLY LEU SEQRES 21 A 329 ASN PRO TYR PRO GLY ILE LEU VAL ASN SER LYS PHE TYR SEQRES 22 A 329 LYS LEU VAL LYS ASP GLY TYR GLN MET ALA GLN PRO ALA SEQRES 23 A 329 PHE ALA PRO LYS ASN ILE TYR SER ILE MET GLN ALA CYS SEQRES 24 A 329 TRP ALA LEU GLU PRO THR HIS ARG PRO THR PHE GLN GLN SEQRES 25 A 329 ILE CYS SER PHE LEU GLN GLU GLN ALA GLN GLU ASP ARG SEQRES 26 A 329 ARG GLU ARG ASP HET SO4 A 1 5 HET SO4 A 2 5 HET BDY A 923 36 HETNAM SO4 SULFATE ION HETNAM BDY N~3~-(2,6-DICHLOROBENZYL)-5-(4-{[(2R)-2-(PYRROLIDIN-1- HETNAM 2 BDY YLMETHYL)PYRROLIDIN-1-YL]CARBONYL}PHENYL)PYRAZINE-2,3- HETNAM 3 BDY DIAMINE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 BDY C27 H30 CL2 N6 O FORMUL 5 HOH *44(H2 O) HELIX 1 1 ASP A 565 LEU A 569 5 5 HELIX 2 2 ASN A 572 GLU A 576 5 5 HELIX 3 3 PRO A 578 ASN A 580 5 3 HELIX 4 4 HIS A 623 GLY A 641 1 19 HELIX 5 5 ASP A 670 ASP A 743 1 15 HELIX 6 6 GLU A 751 SER A 771 1 21 HELIX 7 7 ALA A 780 ARG A 782 5 3 HELIX 8 8 ASN A 788 HIS A 790 5 3 HELIX 9 9 PRO A 818 MET A 822 5 5 HELIX 10 10 ALA A 823 ASP A 829 1 7 HELIX 11 11 THR A 833 SER A 850 1 18 HELIX 12 12 ASN A 862 ASP A 871 1 10 HELIX 13 13 PRO A 882 TRP A 893 1 12 HELIX 14 14 GLU A 896 ARG A 900 5 5 HELIX 15 15 THR A 902 GLN A 913 1 12 SHEET 1 A 5 LEU A 582 ALA A 590 0 SHEET 2 A 5 GLY A 594 PHE A 602 -1 O GLU A 598 N GLY A 585 SHEET 3 A 5 VAL A 610 LEU A 618 -1 O LEU A 611 N ALA A 601 SHEET 4 A 5 LEU A 660 GLU A 664 -1 O THR A 663 N ALA A 614 SHEET 5 A 5 LEU A 649 CYS A 653 -1 N LEU A 650 O ILE A 662 SHEET 1 B 2 CYS A 774 ILE A 775 0 SHEET 2 B 2 ARG A 801 ASP A 802 -1 O ARG A 801 N ILE A 775 SHEET 1 C 2 VAL A 784 LEU A 786 0 SHEET 2 C 2 ALA A 792 ILE A 794 -1 O LYS A 793 N LEU A 785 SHEET 1 D 2 TYR A 809 ILE A 810 0 SHEET 2 D 2 VAL A 831 TYR A 832 -1 O TYR A 832 N TYR A 809 LINK C ALA A 681 N ASP A 741 1555 1555 1.33 SITE 1 AC1 3 TYR A 668 ASN A 788 GLY A 789 SITE 1 AC2 7 ARG A 777 ARG A 801 TYR A 809 VAL A 811 SITE 2 AC2 7 LYS A 812 GLY A 813 ALA A 815 SITE 1 AC3 14 HOH A 14 HOH A 47 HOH A 65 LEU A 588 SITE 2 AC3 14 VAL A 596 ALA A 614 GLU A 664 TYR A 665 SITE 3 AC3 14 CYS A 666 TYR A 668 GLY A 669 ARG A 782 SITE 4 AC3 14 LEU A 785 ASP A 796 CRYST1 57.649 74.125 91.024 90.00 90.00 90.00 P 21 21 21 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 0.017346 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010986 0.00000