HEADER SIGNALING PROTEIN 02-JAN-08 3BUK TITLE CRYSTAL STRUCTURE OF THE NEUROTROPHIN-3 AND P75NTR SYMMETRICAL COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTROPHIN-3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NT-3, NEUROTROPHIC FACTOR, HDNF, NERVE GROWTH FACTOR 2, NGF- COMPND 5 2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: ECTODOMAIN; COMPND 11 SYNONYM: LOW-AFFINITY NERVE GROWTH FACTOR RECEPTOR, NGF RECEPTOR, COMPND 12 GP80-LNGFR, LOW AFFINITY NEUROTROPHIN RECEPTOR P75NTR; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: NT-3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 8 ORGANISM_COMMON: RAT; SOURCE 9 GENE: NGFR, TNFRSF16; SOURCE 10 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 11 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 14 EXPRESSION_SYSTEM_VECTOR: PFASTBAC1 KEYWDS LIGAND-RECEPTOR COMPLEX, BETA-SHEET, NEUROTROPHIN-3, P75NTR, CLEAVAGE KEYWDS 2 ON PAIR OF BASIC RESIDUES, GLYCOPROTEIN, GROWTH FACTOR, SECRETED, KEYWDS 3 APOPTOSIS, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, MEMBRANE, KEYWDS 4 NEUROGENESIS, TRANSMEMBRANE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.JIANG,Y.GONG,P.CAO,H.J.YU REVDAT 8 30-OCT-24 3BUK 1 REMARK REVDAT 7 01-NOV-23 3BUK 1 REMARK REVDAT 6 10-NOV-21 3BUK 1 SEQADV HETSYN REVDAT 5 29-JUL-20 3BUK 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE REVDAT 4 13-JUL-11 3BUK 1 VERSN REVDAT 3 24-FEB-09 3BUK 1 VERSN REVDAT 2 26-AUG-08 3BUK 1 JRNL REVDAT 1 15-JUL-08 3BUK 0 JRNL AUTH Y.GONG,P.CAO,H.J.YU,T.JIANG JRNL TITL CRYSTAL STRUCTURE OF THE NEUROTROPHIN-3 AND P75NTR JRNL TITL 2 SYMMETRICAL COMPLEX. JRNL REF NATURE V. 454 789 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18596692 JRNL DOI 10.1038/NATURE07089 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 22069 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1190 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1682 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.4750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4080 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : -1.46000 REMARK 3 B12 (A**2) : 0.49000 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): 0.552 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.339 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4218 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5754 ; 1.725 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 8.952 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;41.964 ;25.104 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 666 ;22.348 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;22.814 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3222 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1736 ; 0.250 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2844 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 233 ; 0.151 ; 0.200 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): 34 ; 0.242 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.076 ; 0.200 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): 2686 ; 1.473 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4334 ; 2.617 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1532 ; 2.053 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1420 ; 2.942 ; 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 : 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 3BUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0030 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23326 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1NT3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9M LITHIUM SULFATE, 0.05M NA REMARK 280 CITRATE, 0.7M AMMONIUM SULFATE, PH 5.0, EVAPORATION, TEMPERATURE REMARK 280 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 62.90000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.31533 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.36667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 62.90000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 36.31533 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.36667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 62.90000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 36.31533 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.36667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.63066 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 88.73333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 72.63066 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 88.73333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 72.63066 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 88.73333 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 TYR A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 HIS A 4 REMARK 465 ILE A 116 REMARK 465 GLY A 117 REMARK 465 ARG A 118 REMARK 465 THR A 119 REMARK 465 TYR B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 HIS B 4 REMARK 465 ILE B 116 REMARK 465 GLY B 117 REMARK 465 ARG B 118 REMARK 465 THR B 119 REMARK 465 LYS C 1 REMARK 465 GLU C 2 REMARK 465 HIS C 162 REMARK 465 HIS C 163 REMARK 465 HIS C 164 REMARK 465 HIS C 165 REMARK 465 HIS C 166 REMARK 465 HIS C 167 REMARK 465 LYS D 1 REMARK 465 GLU D 2 REMARK 465 HIS D 162 REMARK 465 HIS D 163 REMARK 465 HIS D 164 REMARK 465 HIS D 165 REMARK 465 HIS D 166 REMARK 465 HIS D 167 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 5 CG CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS B 5 CG CD CE NZ REMARK 470 LYS B 64 CG CD CE NZ REMARK 470 LYS C 17 CG CD CE NZ REMARK 470 LYS D 17 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 HIS A 7 -157.05 -138.97 REMARK 500 ASN A 45 -96.27 -86.79 REMARK 500 LYS A 64 -74.88 -14.58 REMARK 500 ASP A 71 87.35 -62.79 REMARK 500 ASN A 94 11.26 57.88 REMARK 500 SER B 6 -135.20 -109.87 REMARK 500 ARG B 8 -78.00 -149.34 REMARK 500 THR B 43 -148.30 -115.75 REMARK 500 ASN B 45 74.58 -179.70 REMARK 500 LYS B 64 -75.94 -14.27 REMARK 500 ASP B 71 84.62 -69.06 REMARK 500 CYS C 4 80.74 -165.21 REMARK 500 THR C 6 -11.19 -148.20 REMARK 500 LEU C 8 10.81 -147.45 REMARK 500 THR C 10 -99.65 -92.86 REMARK 500 HIS C 11 -75.75 -58.70 REMARK 500 CYS C 15 -85.73 -22.29 REMARK 500 PRO C 28 -177.01 -67.69 REMARK 500 CYS C 29 98.86 -67.76 REMARK 500 GLU C 90 28.70 -62.53 REMARK 500 THR C 91 -176.73 -176.23 REMARK 500 VAL C 107 -70.87 -116.35 REMARK 500 GLN C 111 -60.96 -143.69 REMARK 500 ASP C 112 -94.69 -108.89 REMARK 500 ASP C 144 -46.16 -27.96 REMARK 500 LEU C 149 -81.95 -77.07 REMARK 500 CYS D 4 61.78 -159.02 REMARK 500 SER D 5 -64.45 -15.52 REMARK 500 LEU D 8 21.85 -155.85 REMARK 500 THR D 10 -99.88 -89.43 REMARK 500 CYS D 15 -76.15 -26.43 REMARK 500 SER D 42 -6.17 75.59 REMARK 500 ALA D 82 -179.04 -62.46 REMARK 500 HIS D 93 -134.23 -95.02 REMARK 500 GLN D 111 -89.25 -97.16 REMARK 500 ASP D 112 -57.09 -129.56 REMARK 500 ASP D 144 -53.48 -13.19 REMARK 500 LEU D 149 -77.97 -84.24 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 GLY B 44 ASN B 45 138.09 REMARK 500 ASN B 45 SER B 46 137.60 REMARK 500 TYR C 9 THR C 10 -132.66 REMARK 500 TYR D 9 THR D 10 -136.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NT3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH P75. DBREF 3BUK A 1 119 UNP P20783 NT3_HUMAN 139 257 DBREF 3BUK B 1 119 UNP P20783 NT3_HUMAN 139 257 DBREF 3BUK C 1 161 UNP P07174 TNR16_RAT 29 189 DBREF 3BUK D 1 161 UNP P07174 TNR16_RAT 29 189 SEQADV 3BUK SER C 42 UNP P07174 ASN 70 ENGINEERED MUTATION SEQADV 3BUK HIS C 162 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS C 163 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS C 164 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS C 165 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS C 166 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS C 167 UNP P07174 EXPRESSION TAG SEQADV 3BUK SER D 42 UNP P07174 ASN 70 ENGINEERED MUTATION SEQADV 3BUK HIS D 162 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS D 163 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS D 164 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS D 165 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS D 166 UNP P07174 EXPRESSION TAG SEQADV 3BUK HIS D 167 UNP P07174 EXPRESSION TAG SEQRES 1 A 119 TYR ALA GLU HIS LYS SER HIS ARG GLY GLU TYR SER VAL SEQRES 2 A 119 CYS ASP SER GLU SER LEU TRP VAL THR ASP LYS SER SER SEQRES 3 A 119 ALA ILE ASP ILE ARG GLY HIS GLN VAL THR VAL LEU GLY SEQRES 4 A 119 GLU ILE LYS THR GLY ASN SER PRO VAL LYS GLN TYR PHE SEQRES 5 A 119 TYR GLU THR ARG CYS LYS GLU ALA ARG PRO VAL LYS ASN SEQRES 6 A 119 GLY CYS ARG GLY ILE ASP ASP LYS HIS TRP ASN SER GLN SEQRES 7 A 119 CYS LYS THR SER GLN THR TYR VAL ARG ALA LEU THR SER SEQRES 8 A 119 GLU ASN ASN LYS LEU VAL GLY TRP ARG TRP ILE ARG ILE SEQRES 9 A 119 ASP THR SER CYS VAL CYS ALA LEU SER ARG LYS ILE GLY SEQRES 10 A 119 ARG THR SEQRES 1 B 119 TYR ALA GLU HIS LYS SER HIS ARG GLY GLU TYR SER VAL SEQRES 2 B 119 CYS ASP SER GLU SER LEU TRP VAL THR ASP LYS SER SER SEQRES 3 B 119 ALA ILE ASP ILE ARG GLY HIS GLN VAL THR VAL LEU GLY SEQRES 4 B 119 GLU ILE LYS THR GLY ASN SER PRO VAL LYS GLN TYR PHE SEQRES 5 B 119 TYR GLU THR ARG CYS LYS GLU ALA ARG PRO VAL LYS ASN SEQRES 6 B 119 GLY CYS ARG GLY ILE ASP ASP LYS HIS TRP ASN SER GLN SEQRES 7 B 119 CYS LYS THR SER GLN THR TYR VAL ARG ALA LEU THR SER SEQRES 8 B 119 GLU ASN ASN LYS LEU VAL GLY TRP ARG TRP ILE ARG ILE SEQRES 9 B 119 ASP THR SER CYS VAL CYS ALA LEU SER ARG LYS ILE GLY SEQRES 10 B 119 ARG THR SEQRES 1 C 167 LYS GLU THR CYS SER THR GLY LEU TYR THR HIS SER GLY SEQRES 2 C 167 GLU CYS CYS LYS ALA CYS ASN LEU GLY GLU GLY VAL ALA SEQRES 3 C 167 GLN PRO CYS GLY ALA ASN GLN THR VAL CYS GLU PRO CYS SEQRES 4 C 167 LEU ASP SER VAL THR PHE SER ASP VAL VAL SER ALA THR SEQRES 5 C 167 GLU PRO CYS LYS PRO CYS THR GLU CYS LEU GLY LEU GLN SEQRES 6 C 167 SER MET SER ALA PRO CYS VAL GLU ALA ASP ASP ALA VAL SEQRES 7 C 167 CYS ARG CYS ALA TYR GLY TYR TYR GLN ASP GLU GLU THR SEQRES 8 C 167 GLY HIS CYS GLU ALA CYS SER VAL CYS GLU VAL GLY SER SEQRES 9 C 167 GLY LEU VAL PHE SER CYS GLN ASP LYS GLN ASN THR VAL SEQRES 10 C 167 CYS GLU GLU CYS PRO GLU GLY THR TYR SER ASP GLU ALA SEQRES 11 C 167 ASN HIS VAL ASP PRO CYS LEU PRO CYS THR VAL CYS GLU SEQRES 12 C 167 ASP THR GLU ARG GLN LEU ARG GLU CYS THR PRO TRP ALA SEQRES 13 C 167 ASP ALA GLU CYS GLU HIS HIS HIS HIS HIS HIS SEQRES 1 D 167 LYS GLU THR CYS SER THR GLY LEU TYR THR HIS SER GLY SEQRES 2 D 167 GLU CYS CYS LYS ALA CYS ASN LEU GLY GLU GLY VAL ALA SEQRES 3 D 167 GLN PRO CYS GLY ALA ASN GLN THR VAL CYS GLU PRO CYS SEQRES 4 D 167 LEU ASP SER VAL THR PHE SER ASP VAL VAL SER ALA THR SEQRES 5 D 167 GLU PRO CYS LYS PRO CYS THR GLU CYS LEU GLY LEU GLN SEQRES 6 D 167 SER MET SER ALA PRO CYS VAL GLU ALA ASP ASP ALA VAL SEQRES 7 D 167 CYS ARG CYS ALA TYR GLY TYR TYR GLN ASP GLU GLU THR SEQRES 8 D 167 GLY HIS CYS GLU ALA CYS SER VAL CYS GLU VAL GLY SER SEQRES 9 D 167 GLY LEU VAL PHE SER CYS GLN ASP LYS GLN ASN THR VAL SEQRES 10 D 167 CYS GLU GLU CYS PRO GLU GLY THR TYR SER ASP GLU ALA SEQRES 11 D 167 ASN HIS VAL ASP PRO CYS LEU PRO CYS THR VAL CYS GLU SEQRES 12 D 167 ASP THR GLU ARG GLN LEU ARG GLU CYS THR PRO TRP ALA SEQRES 13 D 167 ASP ALA GLU CYS GLU HIS HIS HIS HIS HIS HIS MODRES 3BUK ASN C 32 ASN GLYCOSYLATION SITE MODRES 3BUK ASN D 32 ASN GLYCOSYLATION SITE HET NAG C 168 14 HET NAG D 168 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 5 NAG 2(C8 H15 N O6) FORMUL 7 HOH *143(H2 O) SHEET 1 A 5 GLU A 10 SER A 12 0 SHEET 2 A 5 GLY B 98 ARG B 114 -1 O LEU B 112 N TYR A 11 SHEET 3 A 5 TRP B 75 SER B 91 -1 N VAL B 86 O ILE B 102 SHEET 4 A 5 GLN B 34 VAL B 37 -1 N THR B 36 O SER B 91 SHEET 5 A 5 SER B 26 ILE B 28 -1 N ALA B 27 O VAL B 35 SHEET 1 B 2 SER A 16 VAL A 21 0 SHEET 2 B 2 PHE A 52 CYS A 57 -1 O ARG A 56 N GLU A 17 SHEET 1 C 5 SER A 26 ILE A 28 0 SHEET 2 C 5 GLN A 34 VAL A 37 -1 O VAL A 35 N ALA A 27 SHEET 3 C 5 TRP A 75 SER A 91 -1 O SER A 91 N THR A 36 SHEET 4 C 5 GLY A 98 ARG A 114 -1 O VAL A 109 N LYS A 80 SHEET 5 C 5 GLU B 10 SER B 12 -1 O TYR B 11 N LEU A 112 SHEET 1 D 2 GLU A 40 ILE A 41 0 SHEET 2 D 2 VAL A 48 LYS A 49 -1 O VAL A 48 N ILE A 41 SHEET 1 E 2 SER B 16 VAL B 21 0 SHEET 2 E 2 PHE B 52 CYS B 57 -1 O ARG B 56 N GLU B 17 SHEET 1 F 2 GLU B 40 ILE B 41 0 SHEET 2 F 2 VAL B 48 LYS B 49 -1 O VAL B 48 N ILE B 41 SHEET 1 G 2 GLU C 23 GLN C 27 0 SHEET 2 G 2 VAL C 35 PRO C 38 -1 O VAL C 35 N GLN C 27 SHEET 1 H 2 THR C 44 PHE C 45 0 SHEET 2 H 2 LYS C 56 PRO C 57 -1 O LYS C 56 N PHE C 45 SHEET 1 I 2 GLN C 65 ALA C 69 0 SHEET 2 I 2 VAL C 78 CYS C 81 -1 O ARG C 80 N SER C 66 SHEET 1 J 2 TYR C 85 GLN C 87 0 SHEET 2 J 2 CYS C 94 ALA C 96 -1 O GLU C 95 N TYR C 86 SHEET 1 K 2 SER C 104 PHE C 108 0 SHEET 2 K 2 VAL C 117 GLU C 120 -1 O VAL C 117 N PHE C 108 SHEET 1 L 2 THR C 125 TYR C 126 0 SHEET 2 L 2 LEU C 137 PRO C 138 -1 O LEU C 137 N TYR C 126 SHEET 1 M 2 GLU D 23 GLN D 27 0 SHEET 2 M 2 VAL D 35 PRO D 38 -1 O VAL D 35 N GLN D 27 SHEET 1 N 2 THR D 44 PHE D 45 0 SHEET 2 N 2 LYS D 56 PRO D 57 -1 O LYS D 56 N PHE D 45 SHEET 1 O 2 GLN D 65 ALA D 69 0 SHEET 2 O 2 VAL D 78 CYS D 81 -1 O VAL D 78 N ALA D 69 SHEET 1 P 2 TYR D 85 GLN D 87 0 SHEET 2 P 2 CYS D 94 ALA D 96 -1 O GLU D 95 N TYR D 86 SHEET 1 Q 2 SER D 104 PHE D 108 0 SHEET 2 Q 2 VAL D 117 GLU D 120 -1 O VAL D 117 N VAL D 107 SHEET 1 R 2 THR D 125 TYR D 126 0 SHEET 2 R 2 LEU D 137 PRO D 138 -1 O LEU D 137 N TYR D 126 SHEET 1 S 2 ARG D 147 GLN D 148 0 SHEET 2 S 2 CYS D 160 GLU D 161 -1 O GLU D 161 N ARG D 147 SSBOND 1 CYS A 14 CYS A 79 1555 1555 2.02 SSBOND 2 CYS A 57 CYS A 108 1555 1555 2.02 SSBOND 3 CYS A 67 CYS A 110 1555 1555 2.03 SSBOND 4 CYS B 14 CYS B 79 1555 1555 2.03 SSBOND 5 CYS B 57 CYS B 108 1555 1555 2.03 SSBOND 6 CYS B 67 CYS B 110 1555 1555 2.04 SSBOND 7 CYS C 4 CYS C 15 1555 1555 2.17 SSBOND 8 CYS C 16 CYS C 29 1555 1555 2.05 SSBOND 9 CYS C 19 CYS C 36 1555 1555 2.06 SSBOND 10 CYS C 39 CYS C 55 1555 1555 2.08 SSBOND 11 CYS C 58 CYS C 71 1555 1555 2.03 SSBOND 12 CYS C 61 CYS C 79 1555 1555 2.02 SSBOND 13 CYS C 81 CYS C 94 1555 1555 1.96 SSBOND 14 CYS C 97 CYS C 110 1555 1555 2.01 SSBOND 15 CYS C 100 CYS C 118 1555 1555 2.08 SSBOND 16 CYS C 121 CYS C 136 1555 1555 2.04 SSBOND 17 CYS C 139 CYS C 152 1555 1555 2.02 SSBOND 18 CYS C 142 CYS C 160 1555 1555 2.01 SSBOND 19 CYS D 4 CYS D 15 1555 1555 2.14 SSBOND 20 CYS D 16 CYS D 29 1555 1555 2.05 SSBOND 21 CYS D 19 CYS D 36 1555 1555 2.07 SSBOND 22 CYS D 39 CYS D 55 1555 1555 2.06 SSBOND 23 CYS D 58 CYS D 71 1555 1555 2.05 SSBOND 24 CYS D 61 CYS D 79 1555 1555 2.01 SSBOND 25 CYS D 81 CYS D 94 1555 1555 1.96 SSBOND 26 CYS D 97 CYS D 110 1555 1555 1.99 SSBOND 27 CYS D 100 CYS D 118 1555 1555 2.07 SSBOND 28 CYS D 121 CYS D 136 1555 1555 2.03 SSBOND 29 CYS D 139 CYS D 152 1555 1555 2.02 SSBOND 30 CYS D 142 CYS D 160 1555 1555 2.02 LINK ND2 ASN C 32 C1 NAG C 168 1555 1555 1.46 LINK ND2 ASN D 32 C1 NAG D 168 1555 1555 1.45 CRYST1 125.800 125.800 133.100 90.00 90.00 120.00 H 3 18 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 0.007947 0.004588 0.000000 0.00000 SCALE2 0.000000 0.009177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007513 0.00000