HEADER TRANSFERASE/TRANSFERASE INHIBITOR 26-OCT-16 5H3Q TITLE CRYSTAL STRUCTURE OF TRKA KINASE WITH LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRKA KINASE,NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1, COMPND 5 TRK1-TRANSFORMING TYROSINE KINASE PROTEIN,TROPOMYOSIN-RELATED KINASE COMPND 6 A,TYROSINE KINASE RECEPTOR,TYROSINE KINASE RECEPTOR A,TRK-A,GP140TRK, COMPND 7 P140-TRKA; COMPND 8 EC: 2.7.10.1; COMPND 9 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: NTRK1, MTC, TRK, TRKA; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS TRKA INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.NORITAKA REVDAT 4 08-NOV-23 5H3Q 1 REMARK REVDAT 3 26-FEB-20 5H3Q 1 REMARK REVDAT 2 08-MAR-17 5H3Q 1 JRNL REVDAT 1 22-FEB-17 5H3Q 0 JRNL AUTH N.FURUYA,T.MOMOSE,K.KATSUNO,N.FUSHIMI,H.MURANAKA,C.HANDA, JRNL AUTH 2 T.OZAWA,T.KINOSHITA JRNL TITL THE JUXTAMEMBRANE REGION OF TRKA KINASE IS CRITICAL FOR JRNL TITL 2 INHIBITOR SELECTIVITY JRNL REF BIOORG. MED. CHEM. LETT. V. 27 1233 2017 JRNL REFN ESSN 1464-3405 JRNL PMID 28159414 JRNL DOI 10.1016/J.BMCL.2017.01.056 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 32367 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1704 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2285 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.3850 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.4240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2387 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.93000 REMARK 3 B22 (A**2) : -0.98000 REMARK 3 B33 (A**2) : -1.95000 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): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.599 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2518 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2382 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3412 ; 2.137 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5449 ; 1.287 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ; 6.628 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;36.233 ;22.931 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 403 ;15.441 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.033 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 364 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2838 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 615 ; 0.002 ; 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): 1216 ; 3.943 ; 4.147 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1217 ; 3.942 ; 4.149 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1519 ; 5.561 ; 6.191 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5H3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-14 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32612 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 49.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.68800 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: MOLREP REMARK 200 STARTING MODEL: 4F0I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M SODIUM TARTRATE, 100MM TRIS-HCL REMARK 280 PH 8.5, 5 MM DTT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 70.42250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 78.59750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 70.42250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 78.59750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 70.42250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 78.59750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 70.42250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 78.59750 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 473 REMARK 465 SER A 474 REMARK 465 SER A 475 REMARK 465 LEU A 476 REMARK 465 SER A 477 REMARK 465 PRO A 478 REMARK 465 THR A 479 REMARK 465 GLU A 480 REMARK 465 GLY A 481 REMARK 465 LYS A 482 REMARK 465 GLY A 483 REMARK 465 LEU A 532 REMARK 465 LEU A 533 REMARK 465 PRO A 534 REMARK 465 GLU A 535 REMARK 465 GLN A 536 REMARK 465 ASP A 537 REMARK 465 ALA A 549 REMARK 465 SER A 550 REMARK 465 GLU A 551 REMARK 465 SER A 552 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 547 CG CD CE NZ REMARK 470 ARG A 554 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 593 CZ NH1 NH2 REMARK 470 LEU A 610 CG CD1 CD2 REMARK 470 ARG A 702 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 703 CG CD CE NZ REMARK 470 LYS A 775 CG CD CE NZ REMARK 470 GLY A 796 CA C O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A 620 N GLY A 620 CA 0.124 REMARK 500 SER A 632 CB SER A 632 OG -0.086 REMARK 500 REMARK 500 REMARK: NULL 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 GLY A 620 C - N - CA ANGL. DEV. = -18.3 DEGREES REMARK 500 THR A 741 CA - CB - CG2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 766 CG - CD - NE ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 766 NE - CZ - NH2 ANGL. DEV. = -4.1 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 LYS A 609 -79.04 -59.19 REMARK 500 ARG A 649 -12.71 77.47 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 NA A1004 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 708 OG REMARK 620 2 ASP A 709 OD1 122.6 REMARK 620 3 HOH A1142 O 103.2 113.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7HF A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTT A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTT A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1004 DBREF 5H3Q A 473 796 UNP P04629 NTRK1_HUMAN 473 796 SEQRES 1 A 324 GLY SER SER LEU SER PRO THR GLU GLY LYS GLY SER GLY SEQRES 2 A 324 LEU GLN GLY HIS ILE ILE GLU ASN PRO GLN TYR PHE SER SEQRES 3 A 324 ASP ALA CYS VAL HIS HIS ILE LYS ARG ARG ASP ILE VAL SEQRES 4 A 324 LEU LYS TRP GLU LEU GLY GLU GLY ALA PHE GLY LYS VAL SEQRES 5 A 324 PHE LEU ALA GLU CYS HIS ASN LEU LEU PRO GLU GLN ASP SEQRES 6 A 324 LYS MET LEU VAL ALA VAL LYS ALA LEU LYS GLU ALA SER SEQRES 7 A 324 GLU SER ALA ARG GLN ASP PHE GLN ARG GLU ALA GLU LEU SEQRES 8 A 324 LEU THR MET LEU GLN HIS GLN HIS ILE VAL ARG PHE PHE SEQRES 9 A 324 GLY VAL CYS THR GLU GLY ARG PRO LEU LEU MET VAL PHE SEQRES 10 A 324 GLU TYR MET ARG HIS GLY ASP LEU ASN ARG PHE LEU ARG SEQRES 11 A 324 SER HIS GLY PRO ASP ALA LYS LEU LEU ALA GLY GLY GLU SEQRES 12 A 324 ASP VAL ALA PRO GLY PRO LEU GLY LEU GLY GLN LEU LEU SEQRES 13 A 324 ALA VAL ALA SER GLN VAL ALA ALA GLY MET VAL TYR LEU SEQRES 14 A 324 ALA GLY LEU HIS PHE VAL HIS ARG ASP LEU ALA THR ARG SEQRES 15 A 324 ASN CYS LEU VAL GLY GLN GLY LEU VAL VAL LYS ILE GLY SEQRES 16 A 324 ASP PHE GLY MET SER ARG ASP ILE TYR SER THR ASP TYR SEQRES 17 A 324 TYR ARG VAL GLY GLY ARG THR MET LEU PRO ILE ARG TRP SEQRES 18 A 324 MET PRO PRO GLU SER ILE LEU TYR ARG LYS PHE THR THR SEQRES 19 A 324 GLU SER ASP VAL TRP SER PHE GLY VAL VAL LEU TRP GLU SEQRES 20 A 324 ILE PHE THR TYR GLY LYS GLN PRO TRP TYR GLN LEU SER SEQRES 21 A 324 ASN THR GLU ALA ILE ASP CYS ILE THR GLN GLY ARG GLU SEQRES 22 A 324 LEU GLU ARG PRO ARG ALA CYS PRO PRO GLU VAL TYR ALA SEQRES 23 A 324 ILE MET ARG GLY CYS TRP GLN ARG GLU PRO GLN GLN ARG SEQRES 24 A 324 HIS SER ILE LYS ASP VAL HIS ALA ARG LEU GLN ALA LEU SEQRES 25 A 324 ALA GLN ALA PRO PRO VAL TYR LEU ASP VAL LEU GLY HET 7HF A1001 36 HET DTT A1002 8 HET DTT A1003 8 HET NA A1004 1 HETNAM 7HF 1-[(3S,4R)-4-[3,4-BIS(FLUORANYL)PHENYL]-1-(2- HETNAM 2 7HF METHOXYETHYL)PYRROLIDIN-3-YL]-3-(5-ETHOXY-4-METHYL-2- HETNAM 3 7HF PHENYL-PYRAZOL-3-YL)UREA HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM NA SODIUM ION HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 2 7HF C26 H31 F2 N5 O3 FORMUL 3 DTT 2(C4 H10 O2 S2) FORMUL 5 NA NA 1+ FORMUL 6 HOH *94(H2 O) HELIX 1 AA1 HIS A 489 ASN A 493 5 5 HELIX 2 AA2 LYS A 506 ARG A 508 5 3 HELIX 3 AA3 ARG A 554 THR A 565 1 12 HELIX 4 AA4 LEU A 597 HIS A 604 1 8 HELIX 5 AA5 GLY A 623 LEU A 644 1 22 HELIX 6 AA6 ALA A 652 ARG A 654 5 3 HELIX 7 AA7 MET A 671 TYR A 676 1 6 HELIX 8 AA8 SER A 677 TYR A 680 5 4 HELIX 9 AA9 PRO A 690 MET A 694 5 5 HELIX 10 AB1 PRO A 695 ARG A 702 1 8 HELIX 11 AB2 THR A 705 THR A 722 1 18 HELIX 12 AB3 SER A 732 GLY A 743 1 12 HELIX 13 AB4 PRO A 753 TRP A 764 1 12 HELIX 14 AB5 GLU A 767 ARG A 771 5 5 HELIX 15 AB6 SER A 773 GLN A 786 1 14 HELIX 16 AB7 PRO A 788 ASP A 793 1 6 SHEET 1 AA1 5 ILE A 510 GLY A 519 0 SHEET 2 AA1 5 GLY A 522 CYS A 529 -1 O LEU A 526 N TRP A 514 SHEET 3 AA1 5 MET A 539 LEU A 546 -1 O ALA A 545 N LYS A 523 SHEET 4 AA1 5 LEU A 586 GLU A 590 -1 O PHE A 589 N ALA A 542 SHEET 5 AA1 5 PHE A 575 CYS A 579 -1 N PHE A 576 O VAL A 588 SHEET 1 AA2 3 GLY A 595 ASP A 596 0 SHEET 2 AA2 3 CYS A 656 GLY A 659 -1 O VAL A 658 N GLY A 595 SHEET 3 AA2 3 VAL A 663 ILE A 666 -1 O VAL A 663 N GLY A 659 SHEET 1 AA3 2 TYR A 681 ARG A 682 0 SHEET 2 AA3 2 MET A 688 LEU A 689 -1 O LEU A 689 N TYR A 681 LINK SG CYS A 579 S1 DTT A1002 1555 1555 2.16 LINK SG CYS A 739 S1 DTT A1003 1555 1555 2.16 LINK OG SER A 708 NA NA A1004 1555 1555 2.87 LINK OD1 ASP A 709 NA NA A1004 1555 1555 2.77 LINK NA NA A1004 O HOH A1142 1555 1555 2.73 CISPEP 1 ARG A 583 PRO A 584 0 -11.44 SITE 1 AC1 17 LEU A 486 GLY A 488 HIS A 489 ILE A 490 SITE 2 AC1 17 ASN A 493 LYS A 544 GLU A 560 VAL A 573 SITE 3 AC1 17 MET A 587 PHE A 589 VAL A 647 HIS A 648 SITE 4 AC1 17 GLY A 667 ASP A 668 GLY A 670 HOH A1156 SITE 5 AC1 17 HOH A1162 SITE 1 AC2 7 ARG A 507 CYS A 579 THR A 580 GLU A 581 SITE 2 AC2 7 GLY A 582 ARG A 583 PRO A 584 SITE 1 AC3 5 TYR A 701 ASP A 738 CYS A 739 GLN A 742 SITE 2 AC3 5 ARG A 744 SITE 1 AC4 5 ARG A 649 PHE A 704 SER A 708 ASP A 709 SITE 2 AC4 5 HOH A1142 CRYST1 140.845 157.195 52.306 90.00 90.00 90.00 C 2 2 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 0.007100 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019118 0.00000