HEADER TRANSFERASE 25-MAR-24 8YTD TITLE CRYSTAL STRUCTURE OF TRKA D5 DOMAIN IN COMPLEX WITH TWO DIFFERENT TITLE 2 MACROCYCLIC PEPTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A; 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; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: MACROCYCLIC PEPTIDE; COMPND 16 CHAIN: C; COMPND 17 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; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE 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 8YTD 1 JRNL REVDAT 2 17-JUL-24 8YTD 1 JRNL REVDAT 1 10-JUL-24 8YTD 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. 2.34 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) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 7979 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 429 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) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 573 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1037 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : -0.80000 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): 0.292 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.946 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1098 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 912 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1479 ; 1.369 ; 1.923 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2100 ; 0.752 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 130 ; 6.855 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;24.294 ;23.061 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 131 ;16.106 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;21.083 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 153 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1221 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 255 ; 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): 535 ; 1.607 ; 2.855 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 534 ; 1.602 ; 2.850 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 658 ; 2.743 ; 4.248 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 659 ; 2.741 ; 4.254 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 563 ; 1.739 ; 3.063 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 563 ; 1.738 ; 3.063 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 822 ; 2.679 ; 4.499 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1133 ; 4.739 ;32.831 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1127 ; 4.677 ;32.791 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 8YTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-20 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 : 8455 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.35100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% V/V ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 71.97950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.18700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.18700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.96925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.18700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.18700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.98975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.18700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.18700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 107.96925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.18700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.18700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.98975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 71.97950 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 522 LIES ON A SPECIAL POSITION. 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 ASN A 281 CG OD1 ND2 REMARK 470 VAL A 282 CG1 CG2 REMARK 470 ARG A 314 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 338 CG OD1 ND2 REMARK 470 GLN A 369 CG CD OE1 NE2 REMARK 470 ASN A 381 CG OD1 ND2 REMARK 470 GLY B 0 N REMARK 470 LYS C 2 CG CD CE NZ REMARK 470 CYS C 18 CA C O CB SG 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 B 0 SG CYS B 13 1.65 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 -79.18 72.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YTD A 281 382 UNP P04629 NTRK1_HUMAN 281 382 DBREF 8YTD B 0 14 PDB 8YTD 8YTD 0 14 DBREF 8YTD C 1 18 PDB 8YTD 8YTD 1 18 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 15 GLY PHE PHE LEU TYR PRO HIS GLY PHE TYR GLY ILE VAL SEQRES 2 B 15 CYS GM1 SEQRES 1 C 18 PHE LYS SER VAL SER TYR TRP GLY MEA GLY ARG LEU SER SEQRES 2 C 18 TYR TYR ASN HIS CYS HET GM1 B 14 5 HET MEA C 9 12 HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 4 HET EDO B 101 4 HETNAM GM1 AMINOMETHYLAMIDE HETNAM MEA N-METHYLPHENYLALANINE HETNAM EDO 1,2-ETHANEDIOL HETSYN GM1 GLYCINAMID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GM1 C2 H6 N2 O FORMUL 3 MEA C10 H13 N O2 FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 HOH *50(H2 O) HELIX 1 AA1 THR A 352 ASN A 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 ILE A 328 PHE A 332 -1 N PHE A 329 O ARG A 347 SHEET 1 AA3 6 GLY A 368 ALA A 376 0 SHEET 2 AA3 6 GLY A 357 ASN A 365 -1 N ALA A 363 O ALA A 370 SHEET 3 AA3 6 SER A 312 PHE A 317 -1 N ARG A 314 O LEU A 362 SHEET 4 AA3 6 SER A 320 ASN A 323 -1 O SER A 320 N PHE A 317 SHEET 5 AA3 6 LYS C 2 TYR C 6 1 O VAL C 4 N ASN A 323 SHEET 6 AA3 6 LEU C 12 ASN C 16 -1 O TYR C 15 N SER C 3 SSBOND 1 CYS A 300 CYS A 345 1555 1555 2.05 LINK C CYS B 13 N2 GM1 B 14 1555 1555 1.28 LINK C GLY C 8 N MEA C 9 1555 1555 1.31 LINK C MEA C 9 N GLY C 10 1555 1555 1.29 CISPEP 1 GLN A 308 PRO A 309 0 -1.07 CRYST1 50.374 50.374 143.959 90.00 90.00 90.00 P 43 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 0.019852 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019852 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006946 0.00000