PDB Short entry for 1HCF HEADER TRANSFERASE/HORMONE 03-MAY-01 1HCF TITLE CRYSTAL STRUCTURE OF TRKB-D5 BOUND TO NEUROTROPHIN-4/5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTROPHIN-4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ACTIVE, FRAGMENT. PRO-REGION CLEAVED; COMPND 5 SYNONYM: NEUROTROPHIN-5, NEUROTROPHIN-4/5, NT-4/5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BDNF/NT-3 GROWTH FACTORS RECEPTOR; COMPND 8 CHAIN: X, Y; COMPND 9 FRAGMENT: EXTRACELLULAR DOMAIN 5 (RESIDUES 286 - 383); COMPND 10 SYNONYM: TRKB, GP145-TRKB; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 CELLULAR_LOCATION: PLASMA MEMBRANE; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS TRANSFERASE/HORMONE, COMPLEX(TRANSFERASE-GROWTH FACTOR), KEYWDS 2 NEUROTROPHIN-4/5, TRKB RECEPTOR, NGF-BETA SUPERFAMILY, KEYWDS 3 IMMUNOGLOBULIN DOMAIN, TRANSFERASE-HORMONE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BANFIELD,R.L.NAYLOR,A.G.S.ROBERTSON,S.J.ALLEN,D.DAWBARN,R.L.BRADY REVDAT 3 13-DEC-23 1HCF 1 REMARK REVDAT 2 24-FEB-09 1HCF 1 VERSN REVDAT 1 06-DEC-01 1HCF 0 JRNL AUTH M.J.BANFIELD,R.L.NAYLOR,A.G.S.ROBERTSON,S.J.ALLEN,D.DAWBARN, JRNL AUTH 2 R.L.BRADY JRNL TITL SPECIFICITY IN TRK-RECEPTOR:NEUROTROPHIN INTERACTION: THE JRNL TITL 2 CRYSTAL STRUCTURE OF TRKB-D5 IN COMPLEX WITH JRNL TITL 3 NEUROTROPHIN-4/5 JRNL REF STRUCTURE V. 9 1191 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11738045 JRNL DOI 10.1016/S0969-2126(01)00681-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.G.S.ROBERTSON,M.J.BANFIELD,S.J.ALLEN,J.A.DANDO, REMARK 1 AUTH 2 G.G.F.MASON,S.J.TYLER,G.S.BENNETT,S.D.BRAIN,A.R.CLARKE, REMARK 1 AUTH 3 R.L.BRADY,D.DAWBARN REMARK 1 TITL IDENTIFICATION AND STRUCTURE OF THE NERVE GROWTH FACTOR REMARK 1 TITL 2 BINDING SITE ON TRKA REMARK 1 REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 282 131 2001 REMARK 1 REFN ISSN 0006-291X REMARK 1 PMID 11263982 REMARK 1 DOI 10.1006/BBRC.2001.4462 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.WIESMANN,M.H.ULTSCH,S.H.BASS,A.M.DEVOS REMARK 1 TITL CRYSTAL STRUCTURE OF NERVE GROWTH FACTOR IN COMPLEX WITH THE REMARK 1 TITL 2 LIGAND-BINDING DOMAIN OF THE TRKA RECEPTOR REMARK 1 REF NATURE V. 401 184 1999 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 10490030 REMARK 1 DOI 10.1038/43705 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.H.ULTSCH,C.WIESMANN,L.C.SIMMONS,J.HENRICH,M.YANG,D.REILLY, REMARK 1 AUTH 2 S.H.BASS,A.M.DEVOS REMARK 1 TITL CRYSTAL STRUCTURES OF THE NEUROTROPHIN BINDING DOMAIN OF REMARK 1 TITL 2 TRKA, TRKB AND TRKC REMARK 1 REF J.MOL.BIOL. V. 290 149 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10388563 REMARK 1 DOI 10.1006/JMBI.1999.2816 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.C.ROBINSON,C.RADZIEJEWSKI,G.SPRAGGON,J.GREENWALD, REMARK 1 AUTH 2 M.R.KOSTURA,L.D.BURTNICK,D.I.STUART,S.CHOE,E.Y.JONES REMARK 1 TITL THE STRUCTURES OF NEUROTROPHIN 4 HOMODIMER AND THE REMARK 1 TITL 2 BRAIN-DERIVED NEUROTROPHIC FACTOR/NEUROTROPHIN 4 HETERODIMER REMARK 1 TITL 3 REVEAL A COMMON TRK BINDING SITE REMARK 1 REF PROTEIN SCI. V. 8 2589 1999 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 10631974 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15411 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 SET) : 0.218 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 761 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1430 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 84 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3419 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : -7.91000 REMARK 3 B33 (A**2) : 7.39000 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.33 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.546 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.997 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.728 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.120 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 40.14 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : SO4.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1290006161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15635 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1B98 (NEUROTROPHIN), 1WWB (TRK) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML COMPLEX IN 20MM TRIS, 150MM REMARK 280 NACL, PH 7.5, 100MM HEPES PH 7.5, 1.5M LISO4, PH 7.50 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 37.18600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.65900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.20300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.65900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.18600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.20300 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: COMPLEX OF HOMODIMERIC NEUROTROPHIN-4 AND REMARK 300 TWO CHAINSOF TRKB 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, X, Y 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 65 REMARK 465 ALA A 66 REMARK 465 GLU A 67 REMARK 465 GLU A 68 REMARK 465 GLY A 69 REMARK 465 GLY A 70 REMARK 465 GLY A 128 REMARK 465 ARG A 129 REMARK 465 ALA A 130 REMARK 465 GLY B 1 REMARK 465 VAL B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 GLY B 48 REMARK 465 GLY B 49 REMARK 465 ASN B 65 REMARK 465 ARG B 129 REMARK 465 ALA B 130 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 2 CB CG1 CG2 REMARK 470 ARG A 28 NE CZ NH1 NH2 REMARK 470 ARG A 36 NE CZ NH1 NH2 REMARK 470 LYS A 62 CD CE NZ REMARK 470 ARG A 83 NE CZ NH1 NH2 REMARK 470 ARG A 107 CD NE CZ NH1 NH2 REMARK 470 ARG B 53 CD NE CZ NH1 NH2 REMARK 470 LYS B 62 CD CE NZ REMARK 470 GLU X 371 CD OE1 OE2 REMARK 470 LYS Y 308 CG CD CE NZ 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 CYS X 345 CA - CB - SG ANGL. DEV. = 9.4 DEGREES REMARK 500 LEU X 346 N - CA - C ANGL. DEV. = -20.1 DEGREES REMARK 500 CYS Y 345 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 LEU Y 346 N - CA - C ANGL. DEV. = -17.9 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 VAL A 2 -84.93 -69.64 REMARK 500 SER A 3 -31.28 -150.49 REMARK 500 ALA A 46 -174.70 -59.63 REMARK 500 ALA A 47 -30.84 -38.42 REMARK 500 SER A 50 155.12 -30.81 REMARK 500 GLN A 105 -77.95 -63.97 REMARK 500 PRO B 45 170.25 -45.19 REMARK 500 PRO B 51 -143.97 -59.92 REMARK 500 LEU B 52 101.89 157.02 REMARK 500 GLU B 68 153.04 -46.04 REMARK 500 ARG B 126 -2.07 -156.22 REMARK 500 THR B 127 173.83 -46.72 REMARK 500 ASP X 298 -132.31 -118.06 REMARK 500 ASN X 320 59.69 36.42 REMARK 500 ASN X 338 -125.90 -93.52 REMARK 500 HIS X 339 -78.62 -75.94 REMARK 500 PHE Y 291 124.64 -172.71 REMARK 500 ASP Y 298 -124.92 -118.71 REMARK 500 PRO Y 311 -179.13 -62.67 REMARK 500 ASN Y 338 -94.27 -73.43 REMARK 500 GLU Y 366 -38.06 -37.45 REMARK 500 MET Y 379 148.10 -174.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WWB RELATED DB: PDB REMARK 900 LIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR REMARK 900 RELATED ID: 1B8M RELATED DB: PDB REMARK 900 BRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4 REMARK 900 RELATED ID: 1B98 RELATED DB: PDB REMARK 900 NEUROTROPHIN 4 (HOMODIMER) REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES NUMBERED X283, X284, X285 ARE REMARK 999 CLONING ARTEFACTS. THEY ARE DERIVED FROM REMARK 999 THE HIS-TAG SEQUENCE OF THE PET-15B PLASMID, REMARK 999 AND DO NOT CORRESPOND TO THE NATIVE TRKB REMARK 999 RESIDUES 283, 284 AND 285. REMARK 999 REMARK 999 RESIDUES NUMBERED Y283, Y284, Y285 ARE REMARK 999 CLONING ARTEFACTS. THEY ARE DERIVED FROM REMARK 999 THE HIS-TAG SEQUENCE OF THE PET-15B PLASMID, REMARK 999 AND DO NOT CORRESPOND TO THE NATIVE TRKB REMARK 999 RESIDUES 283, 284 AND 285. DBREF 1HCF A 1 130 UNP P34130 NT5_HUMAN 81 210 DBREF 1HCF B 1 130 UNP P34130 NT5_HUMAN 81 210 DBREF 1HCF X 283 285 PDB 1HCF 1HCF 283 285 DBREF 1HCF X 286 383 UNP Q16620 TRKB_HUMAN 286 383 DBREF 1HCF Y 283 285 PDB 1HCF 1HCF 283 285 DBREF 1HCF Y 286 383 UNP Q16620 TRKB_HUMAN 286 383 SEQRES 1 A 130 GLY VAL SER GLU THR ALA PRO ALA SER ARG ARG GLY GLU SEQRES 2 A 130 LEU ALA VAL CYS ASP ALA VAL SER GLY TRP VAL THR ASP SEQRES 3 A 130 ARG ARG THR ALA VAL ASP LEU ARG GLY ARG GLU VAL GLU SEQRES 4 A 130 VAL LEU GLY GLU VAL PRO ALA ALA GLY GLY SER PRO LEU SEQRES 5 A 130 ARG GLN TYR PHE PHE GLU THR ARG CYS LYS ALA ASP ASN SEQRES 6 A 130 ALA GLU GLU GLY GLY PRO GLY ALA GLY GLY GLY GLY CYS SEQRES 7 A 130 ARG GLY VAL ASP ARG ARG HIS TRP VAL SER GLU CYS LYS SEQRES 8 A 130 ALA LYS GLN SER TYR VAL ARG ALA LEU THR ALA ASP ALA SEQRES 9 A 130 GLN GLY ARG VAL GLY TRP ARG TRP ILE ARG ILE ASP THR SEQRES 10 A 130 ALA CYS VAL CYS THR LEU LEU SER ARG THR GLY ARG ALA SEQRES 1 B 130 GLY VAL SER GLU THR ALA PRO ALA SER ARG ARG GLY GLU SEQRES 2 B 130 LEU ALA VAL CYS ASP ALA VAL SER GLY TRP VAL THR ASP SEQRES 3 B 130 ARG ARG THR ALA VAL ASP LEU ARG GLY ARG GLU VAL GLU SEQRES 4 B 130 VAL LEU GLY GLU VAL PRO ALA ALA GLY GLY SER PRO LEU SEQRES 5 B 130 ARG GLN TYR PHE PHE GLU THR ARG CYS LYS ALA ASP ASN SEQRES 6 B 130 ALA GLU GLU GLY GLY PRO GLY ALA GLY GLY GLY GLY CYS SEQRES 7 B 130 ARG GLY VAL ASP ARG ARG HIS TRP VAL SER GLU CYS LYS SEQRES 8 B 130 ALA LYS GLN SER TYR VAL ARG ALA LEU THR ALA ASP ALA SEQRES 9 B 130 GLN GLY ARG VAL GLY TRP ARG TRP ILE ARG ILE ASP THR SEQRES 10 B 130 ALA CYS VAL CYS THR LEU LEU SER ARG THR GLY ARG ALA SEQRES 1 X 101 SER HIS MET ALA PRO THR ILE THR PHE LEU GLU SER PRO SEQRES 2 X 101 THR SER ASP HIS HIS TRP CYS ILE PRO PHE THR VAL LYS SEQRES 3 X 101 GLY ASN PRO LYS PRO ALA LEU GLN TRP PHE TYR ASN GLY SEQRES 4 X 101 ALA ILE LEU ASN GLU SER LYS TYR ILE CYS THR LYS ILE SEQRES 5 X 101 HIS VAL THR ASN HIS THR GLU TYR HIS GLY CYS LEU GLN SEQRES 6 X 101 LEU ASP ASN PRO THR HIS MET ASN ASN GLY ASP TYR THR SEQRES 7 X 101 LEU ILE ALA LYS ASN GLU TYR GLY LYS ASP GLU LYS GLN SEQRES 8 X 101 ILE SER ALA HIS PHE MET GLY TRP PRO GLY SEQRES 1 Y 101 SER HIS MET ALA PRO THR ILE THR PHE LEU GLU SER PRO SEQRES 2 Y 101 THR SER ASP HIS HIS TRP CYS ILE PRO PHE THR VAL LYS SEQRES 3 Y 101 GLY ASN PRO LYS PRO ALA LEU GLN TRP PHE TYR ASN GLY SEQRES 4 Y 101 ALA ILE LEU ASN GLU SER LYS TYR ILE CYS THR LYS ILE SEQRES 5 Y 101 HIS VAL THR ASN HIS THR GLU TYR HIS GLY CYS LEU GLN SEQRES 6 Y 101 LEU ASP ASN PRO THR HIS MET ASN ASN GLY ASP TYR THR SEQRES 7 Y 101 LEU ILE ALA LYS ASN GLU TYR GLY LYS ASP GLU LYS GLN SEQRES 8 Y 101 ILE SER ALA HIS PHE MET GLY TRP PRO GLY HET SO4 A1128 5 HET SO4 B1129 5 HET SO4 B1130 5 HET SO4 B1131 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 HOH *60(H2 O) HELIX 1 1 PRO A 7 ARG A 11 5 5 HELIX 2 1 PRO B 7 ARG B 11 5 5 HELIX 3 2 HIS X 353 ASN X 356 5 4 HELIX 4 3 HIS Y 353 ASN Y 356 5 4 SHEET 1 AA 2 ASP A 18 THR A 25 0 SHEET 2 AA 2 PHE A 56 CYS A 61 -1 O PHE A 56 N VAL A 24 SHEET 1 AB 4 ARG A 28 VAL A 31 0 SHEET 2 AB 4 ARG A 36 VAL A 40 -1 O VAL A 38 N ALA A 30 SHEET 3 AB 4 VAL A 87 ALA A 102 -1 O ALA A 102 N GLU A 39 SHEET 4 AB 4 ARG A 107 SER A 125 -1 O GLY A 109 N THR A 101 SHEET 1 AC 2 GLY A 42 ALA A 46 0 SHEET 2 AC 2 SER A 50 ARG A 53 -1 O LEU A 52 N VAL A 44 SHEET 1 BA 2 ASP B 18 THR B 25 0 SHEET 2 BA 2 PHE B 56 CYS B 61 -1 O PHE B 56 N VAL B 24 SHEET 1 BB 4 ARG B 28 VAL B 31 0 SHEET 2 BB 4 ARG B 36 VAL B 40 -1 O VAL B 38 N ALA B 30 SHEET 3 BB 4 VAL B 87 ALA B 102 -1 O ALA B 102 N GLU B 39 SHEET 4 BB 4 ARG B 107 SER B 125 -1 O GLY B 109 N THR B 101 SHEET 1 BC 2 GLY B 42 ALA B 46 0 SHEET 2 BC 2 SER B 50 ARG B 53 -1 O LEU B 52 N VAL B 44 SHEET 1 XX 4 ALA X 322 ASN X 325 0 SHEET 2 XX 4 ALA X 314 TYR X 319 -1 N TYR X 319 O ALA X 322 SHEET 3 XX 4 GLY X 357 LYS X 364 -1 N LYS X 364 O ALA X 314 SHEET 4 XX 4 GLY X 368 HIS X 377 -1 N ALA X 376 O GLY X 357 SHEET 1 XY 4 MET X 285 GLU X 293 0 SHEET 2 XY 4 TRP X 301 GLY X 309 -1 N LYS X 308 O THR X 288 SHEET 3 XY 4 GLU X 341 ASP X 349 -1 N LEU X 348 O TRP X 301 SHEET 4 XY 4 CYS X 331 ASN X 338 -1 N VAL X 336 O HIS X 343 SHEET 1 XZ 4 PRO X 295 SER X 297 0 SHEET 2 XZ 4 TRP X 301 GLY X 309 -1 N ILE X 303 O THR X 296 SHEET 3 XZ 4 GLU X 341 ASP X 349 -1 N LEU X 348 O TRP X 301 SHEET 4 XZ 4 CYS X 331 ASN X 338 -1 N VAL X 336 O HIS X 343 SHEET 1 YX 4 ALA Y 322 ASN Y 325 0 SHEET 2 YX 4 ALA Y 314 TYR Y 319 -1 N TYR Y 319 O ALA Y 322 SHEET 3 YX 4 GLY Y 357 LYS Y 364 -1 N LYS Y 364 O ALA Y 314 SHEET 4 YX 4 GLY Y 368 HIS Y 377 -1 N ALA Y 376 O GLY Y 357 SHEET 1 YY 4 MET Y 285 GLU Y 293 0 SHEET 2 YY 4 TRP Y 301 GLY Y 309 -1 N LYS Y 308 O THR Y 288 SHEET 3 YY 4 GLU Y 341 ASP Y 349 -1 N LEU Y 348 O TRP Y 301 SHEET 4 YY 4 CYS Y 331 ASN Y 338 -1 N VAL Y 336 O HIS Y 343 SHEET 1 YZ 4 PRO Y 295 SER Y 297 0 SHEET 2 YZ 4 TRP Y 301 GLY Y 309 -1 N ILE Y 303 O THR Y 296 SHEET 3 YZ 4 GLU Y 341 ASP Y 349 -1 N LEU Y 348 O TRP Y 301 SHEET 4 YZ 4 CYS Y 331 ASN Y 338 -1 N VAL Y 336 O HIS Y 343 SSBOND 1 CYS A 17 CYS A 90 1555 1555 2.04 SSBOND 2 CYS A 61 CYS A 119 1555 1555 2.04 SSBOND 3 CYS A 78 CYS A 121 1555 1555 2.03 SSBOND 4 CYS B 17 CYS B 90 1555 1555 2.03 SSBOND 5 CYS B 61 CYS B 119 1555 1555 2.04 SSBOND 6 CYS B 78 CYS B 121 1555 1555 2.04 SSBOND 7 CYS X 302 CYS X 345 1555 1555 2.04 SSBOND 8 CYS Y 302 CYS Y 345 1555 1555 2.04 CISPEP 1 ASN X 310 PRO X 311 0 0.03 CISPEP 2 ASN Y 310 PRO Y 311 0 -0.02 SITE 1 AC1 1 ARG A 11 SITE 1 AC2 6 ARG B 34 ARG B 36 HIS B 85 ARG B 111 SITE 2 AC2 6 HOH B2007 HOH B2015 SITE 1 AC3 3 ALA B 8 ARG B 11 HOH B2018 SITE 1 AC4 3 ARG A 84 ARG B 34 HOH B2019 CRYST1 74.372 80.406 91.318 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 0.013446 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010951 0.00000