HEADER TRANSFERASE 25-MAR-24 8YTE TITLE CRYSTAL STRUCTURE OF TRKA D5 DOMAIN IN COMPLEX WITH MACROCYCLIC TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1,TRK1- COMPND 5 TRANSFORMING TYROSINE KINASE PROTEIN,TROPOMYOSIN-RELATED KINASE A, COMPND 6 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; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: MACROCYCLIC PEPTIDE; COMPND 12 CHAIN: B, D; COMPND 13 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE, CYCLIC PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR T.YAMADA,K.MIHARA,T.UEDA,D.YAMAUCHI,M.SHIMIZU,A.ANDO,K.MAYUMI, AUTHOR 2 Z.NAKATA,H.MIKAMIYAMA REVDAT 3 24-JUL-24 8YTE 1 JRNL REVDAT 2 17-JUL-24 8YTE 1 JRNL REVDAT 1 10-JUL-24 8YTE 0 JRNL AUTH T.YAMADA,K.MIHARA,T.UEDA,D.YAMAUCHI,M.SHIMIZU,A.ANDO, JRNL AUTH 2 K.MAYUMI,Z.NAKATA,H.MIKAMIYAMA JRNL TITL DISCOVERY AND HIT TO LEAD OPTIMIZATION OF MACROCYCLIC JRNL TITL 2 PEPTIDES AS NOVEL TROPOMYOSIN RECEPTOR KINASE A ANTAGONISTS. JRNL REF J.MED.CHEM. V. 67 11197 2024 JRNL REFN ISSN 0022-2623 JRNL PMID 38950284 JRNL DOI 10.1021/ACS.JMEDCHEM.4C00715 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12839 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 609 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) : 2.26 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 901 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1727 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -0.13000 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): 0.266 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.219 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1827 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1583 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2470 ; 1.235 ; 1.926 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3650 ; 0.703 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 220 ; 7.225 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;28.221 ;23.373 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 231 ;15.156 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;22.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 262 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2046 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 420 ; 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): 890 ; 1.506 ; 2.990 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 889 ; 1.504 ; 2.991 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1106 ; 2.582 ; 4.468 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1107 ; 2.581 ; 4.468 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 937 ; 1.416 ; 3.153 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 937 ; 1.415 ; 3.153 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1365 ; 2.249 ; 4.649 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1826 ; 4.020 ;33.594 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1817 ; 3.988 ;33.582 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 8YTE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13490 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.30200 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: 1WWA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, , 25% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, 0.2 M AMMONIUM ACETATE, VAPOR REMARK 280 DIFFUSION, 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 25.84000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.94450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.48600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.94450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.48600 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 2240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 ASN A 281 REMARK 465 ASP A 380 REMARK 465 ASN A 381 REMARK 465 PRO A 382 REMARK 465 ASN C 281 REMARK 465 VAL C 282 REMARK 465 ASN C 381 REMARK 465 PRO C 382 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 VAL A 282 CG1 CG2 REMARK 470 ASN A 338 CG OD1 ND2 REMARK 470 GLY B 0 N REMARK 470 HIS C 297 CG ND1 CD2 CE1 NE2 REMARK 470 ASN C 338 CG OD1 ND2 REMARK 470 GLN C 350 CG CD OE1 NE2 REMARK 470 MET C 379 CG SD CE REMARK 470 GLY D 0 N 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 CA GLY D 0 SG CYS D 13 1.64 REMARK 500 CA GLY B 0 SG CYS B 13 1.66 REMARK 500 O CYS D 13 N2 GM1 D 101 2.11 REMARK 500 O CYS B 13 N2 GM1 B 101 2.16 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 HIS A 297 -75.61 66.79 REMARK 500 GLN A 350 71.34 -156.58 REMARK 500 MET C 296 43.77 -147.35 REMARK 500 HIS C 297 -69.78 79.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 345 LEU A 346 147.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YTE A 281 382 UNP P04629 NTRK1_HUMAN 281 382 DBREF 8YTE B 0 13 PDB 8YTE 8YTE 0 13 DBREF 8YTE C 281 382 UNP P04629 NTRK1_HUMAN 281 382 DBREF 8YTE D 0 13 PDB 8YTE 8YTE 0 13 SEQRES 1 A 102 ASN VAL SER PHE PRO ALA SER VAL GLN LEU HIS THR ALA SEQRES 2 A 102 VAL GLU MET HIS HIS TRP CYS ILE PRO PHE SER VAL ASP SEQRES 3 A 102 GLY GLN PRO ALA PRO SER LEU ARG TRP LEU PHE ASN GLY SEQRES 4 A 102 SER VAL LEU ASN GLU THR SER PHE ILE PHE THR GLU PHE SEQRES 5 A 102 LEU GLU PRO ALA ALA ASN GLU THR VAL ARG HIS GLY CYS SEQRES 6 A 102 LEU ARG LEU ASN GLN PRO THR HIS VAL ASN ASN GLY ASN SEQRES 7 A 102 TYR THR LEU LEU ALA ALA ASN PRO PHE GLY GLN ALA SER SEQRES 8 A 102 ALA SER ILE MET ALA ALA PHE MET ASP ASN PRO SEQRES 1 B 14 GLY PHE PHE LEU TYR PRO HIS GLY PHE TYR GLY ILE VAL SEQRES 2 B 14 CYS SEQRES 1 C 102 ASN VAL SER PHE PRO ALA SER VAL GLN LEU HIS THR ALA SEQRES 2 C 102 VAL GLU MET HIS HIS TRP CYS ILE PRO PHE SER VAL ASP SEQRES 3 C 102 GLY GLN PRO ALA PRO SER LEU ARG TRP LEU PHE ASN GLY SEQRES 4 C 102 SER VAL LEU ASN GLU THR SER PHE ILE PHE THR GLU PHE SEQRES 5 C 102 LEU GLU PRO ALA ALA ASN GLU THR VAL ARG HIS GLY CYS SEQRES 6 C 102 LEU ARG LEU ASN GLN PRO THR HIS VAL ASN ASN GLY ASN SEQRES 7 C 102 TYR THR LEU LEU ALA ALA ASN PRO PHE GLY GLN ALA SER SEQRES 8 C 102 ALA SER ILE MET ALA ALA PHE MET ASP ASN PRO SEQRES 1 D 14 GLY PHE PHE LEU TYR PRO HIS GLY PHE TYR GLY ILE VAL SEQRES 2 D 14 CYS HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 4 HET GM1 B 101 5 HET EDO B 102 4 HET EDO C 401 4 HET EDO C 402 4 HET EDO C 403 4 HET EDO C 404 4 HET GM1 D 101 5 HET EDO D 102 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM GM1 AMINOMETHYLAMIDE HETSYN EDO ETHYLENE GLYCOL HETSYN GM1 GLYCINAMID FORMUL 5 EDO 9(C2 H6 O2) FORMUL 8 GM1 2(C2 H6 N2 O) FORMUL 16 HOH *91(H2 O) HELIX 1 AA1 THR A 352 ASN A 356 5 5 HELIX 2 AA2 THR C 352 ASN C 356 5 5 SHEET 1 AA1 3 PHE A 284 LEU A 290 0 SHEET 2 AA1 3 TRP A 299 GLN A 308 -1 O GLN A 308 N PHE A 284 SHEET 3 AA1 3 VAL A 294 GLU A 295 -1 N VAL A 294 O CYS A 300 SHEET 1 AA2 4 PHE A 284 LEU A 290 0 SHEET 2 AA2 4 TRP A 299 GLN A 308 -1 O GLN A 308 N PHE A 284 SHEET 3 AA2 4 ARG A 342 LEU A 348 -1 O ARG A 342 N VAL A 305 SHEET 4 AA2 4 PHE A 329 PHE A 332 -1 N PHE A 329 O ARG A 347 SHEET 1 AA3 4 SER A 320 VAL A 321 0 SHEET 2 AA3 4 SER A 312 PHE A 317 -1 N PHE A 317 O SER A 320 SHEET 3 AA3 4 GLY A 357 ASN A 365 -1 O LEU A 362 N ARG A 314 SHEET 4 AA3 4 GLY A 368 ALA A 376 -1 O ALA A 370 N ALA A 363 SHEET 1 AA4 3 PHE C 284 LEU C 290 0 SHEET 2 AA4 3 TRP C 299 GLN C 308 -1 O ASP C 306 N SER C 287 SHEET 3 AA4 3 VAL C 294 GLU C 295 -1 N VAL C 294 O CYS C 300 SHEET 1 AA5 4 PHE C 284 LEU C 290 0 SHEET 2 AA5 4 TRP C 299 GLN C 308 -1 O ASP C 306 N SER C 287 SHEET 3 AA5 4 ARG C 342 LEU C 348 -1 O ARG C 342 N VAL C 305 SHEET 4 AA5 4 ILE C 328 PHE C 332 -1 N PHE C 329 O ARG C 347 SHEET 1 AA6 4 SER C 320 VAL C 321 0 SHEET 2 AA6 4 SER C 312 PHE C 317 -1 N PHE C 317 O SER C 320 SHEET 3 AA6 4 GLY C 357 ASN C 365 -1 O LEU C 362 N ARG C 314 SHEET 4 AA6 4 GLY C 368 ALA C 376 -1 O ILE C 374 N TYR C 359 SSBOND 1 CYS A 300 CYS A 345 1555 1555 2.05 SSBOND 2 CYS C 300 CYS C 345 1555 1555 2.05 LINK C CYS B 13 N2 GM1 B 101 1555 1555 1.28 LINK C CYS D 13 N2 GM1 D 101 1555 1555 1.27 CISPEP 1 GLN A 308 PRO A 309 0 -1.49 CISPEP 2 GLN C 308 PRO C 309 0 -1.81 CRYST1 51.680 66.972 79.889 90.00 90.00 90.00 P 21 21 21 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 0.019350 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012517 0.00000