HEADER SIGNALING PROTEIN 01-AUG-03 1Q47 TITLE STRUCTURE OF THE SEMAPHORIN 3A RECEPTOR-BINDING MODULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEMAPHORIN 3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SEMA-3A 65K (RESIDUES 26-520); COMPND 5 SYNONYM: SEMAPHORIN III, SEMA III, SEMAPHORIN D, SEMA D; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS BETA PROPELLER, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ANTIPENKO,J.-P.HIMANEN,K.VAN LEYEN,V.NARDI-DEI,J.LESNIAK, AUTHOR 2 W.A.BARTON,K.R.RAJASHANKAR,M.LU,C.HOEMME,A.PUSCHEL,D.NIKOLOV REVDAT 6 06-NOV-24 1Q47 1 HETSYN REVDAT 5 29-JUL-20 1Q47 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 01-FEB-17 1Q47 1 AUTHOR JRNL REVDAT 3 13-JUL-11 1Q47 1 VERSN REVDAT 2 24-FEB-09 1Q47 1 VERSN REVDAT 1 03-AUG-04 1Q47 0 JRNL AUTH A.ANTIPENKO,J.-P.HIMANEN,K.VAN LEYEN,V.NARDI-DEI,J.LESNIAK, JRNL AUTH 2 W.A.BARTON,K.R.RAJASHANKAR,M.LU,C.HOEMME,A.W.PUSCHEL, JRNL AUTH 3 D.B.NIKOLOV JRNL TITL STRUCTURE OF THE SEMAPHORIN-3A RECEPTOR BINDING MODULE. JRNL REF NEURON V. 39 589 2003 JRNL REFN ISSN 0896-6273 JRNL PMID 12925274 JRNL DOI 10.1016/S0896-6273(03)00502-6 REMARK 2 REMARK 2 RESOLUTION. 2.80 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 70534 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 7016 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7863 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Q47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000019894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-03 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 : APS REMARK 200 BEAMLINE : 8-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97, 0.964 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 277955 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, PEG 8000, HEPTYL-BETA-D REMARK 280 THIOGLUCOSIDE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 109.39550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.86650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 109.39550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.86650 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: THE BIOLOGICAL ASSEMBLY IS A DIMER WHICH IS FOUND IN THE REMARK 300 ASYMMETRIC UNIT. 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: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 PRO A 465 REMARK 465 LYS A 466 REMARK 465 GLU A 467 REMARK 465 THR A 468 REMARK 465 TRP A 469 REMARK 465 HIS A 470 REMARK 465 ASP A 471 REMARK 465 LEU A 472 REMARK 465 GLU A 473 REMARK 465 GLU A 474 REMARK 465 VAL A 475 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 ND2 ASN A 53 O1 NAG A 600 0.35 REMARK 500 CG ASN A 125 C7 NAG A 601 0.52 REMARK 500 OD1 ASN B 125 O1 NAG B 601 0.57 REMARK 500 ND2 ASN A 125 N2 NAG A 601 0.66 REMARK 500 CG ASN B 125 O1 NAG B 601 0.87 REMARK 500 ND2 ASN B 125 C1 NAG B 601 0.97 REMARK 500 CG ASN B 125 C1 NAG B 601 1.01 REMARK 500 CG ASN A 125 O7 NAG A 601 1.09 REMARK 500 ND2 ASN A 125 C2 NAG A 601 1.12 REMARK 500 CB ASN A 125 C7 NAG A 601 1.14 REMARK 500 ND2 ASN B 125 O5 NAG B 601 1.15 REMARK 500 CG ASN A 125 N2 NAG A 601 1.17 REMARK 500 ND2 ASN B 53 O1 NAG B 600 1.22 REMARK 500 OD1 ASN A 125 O7 NAG A 601 1.28 REMARK 500 CB ASN A 125 O7 NAG A 601 1.28 REMARK 500 CB ASN A 125 C8 NAG A 601 1.29 REMARK 500 ND2 ASN A 125 C7 NAG A 601 1.36 REMARK 500 ND2 ASN A 53 C1 NAG A 600 1.47 REMARK 500 CG ASN A 53 O1 NAG A 600 1.61 REMARK 500 OD1 ASN B 125 C1 NAG B 601 1.65 REMARK 500 OD1 ASN A 125 C7 NAG A 601 1.73 REMARK 500 ND2 ASN B 125 O1 NAG B 601 1.79 REMARK 500 OD1 ASN A 125 N2 NAG A 601 1.88 REMARK 500 CA ASN A 125 O7 NAG A 601 1.92 REMARK 500 ND2 ASN A 125 C3 NAG A 601 1.94 REMARK 500 CG ASN B 53 O1 NAG B 600 1.95 REMARK 500 ND2 ASN B 53 O7 NAG B 600 2.01 REMARK 500 CG ASN A 125 C8 NAG A 601 2.04 REMARK 500 ND2 ASN B 125 C5 NAG B 601 2.14 REMARK 500 ND2 ASN A 125 C1 NAG A 601 2.17 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 ASN A 28 -1.82 -140.78 REMARK 500 LYS A 33 79.12 -110.60 REMARK 500 GLU A 41 46.38 -83.89 REMARK 500 SER A 42 13.34 -172.06 REMARK 500 ASN A 49 2.03 -57.02 REMARK 500 SER A 55 -158.02 177.60 REMARK 500 SER A 56 52.64 37.82 REMARK 500 ASP A 75 19.04 42.00 REMARK 500 ILE A 85 7.29 -64.72 REMARK 500 VAL A 95 136.77 81.95 REMARK 500 GLU A 113 -44.89 -138.60 REMARK 500 TYR A 124 -79.90 -118.57 REMARK 500 HIS A 138 66.17 -166.79 REMARK 500 VAL A 146 17.79 -150.31 REMARK 500 PRO A 150 6.62 -69.83 REMARK 500 ASN A 153 70.45 33.11 REMARK 500 PHE A 155 52.50 -158.05 REMARK 500 GLN A 158 86.25 -60.20 REMARK 500 ASP A 159 -143.33 -68.08 REMARK 500 SER A 160 -156.27 54.47 REMARK 500 HIS A 161 -92.06 21.35 REMARK 500 PHE A 162 115.79 76.12 REMARK 500 LEU A 180 117.57 -171.14 REMARK 500 THR A 190 -157.22 -155.86 REMARK 500 LEU A 205 -178.50 65.67 REMARK 500 HIS A 207 -38.44 32.58 REMARK 500 ASP A 217 84.98 -152.36 REMARK 500 SER A 218 -19.79 -46.69 REMARK 500 ILE A 227 -39.78 -136.51 REMARK 500 SER A 228 156.78 177.73 REMARK 500 SER A 235 -166.74 -101.72 REMARK 500 ASP A 253 70.97 -155.84 REMARK 500 SER A 257 -150.86 -60.95 REMARK 500 SER A 278 126.00 62.54 REMARK 500 ASN A 299 25.09 -70.61 REMARK 500 ASN A 315 101.82 -56.81 REMARK 500 ASN A 321 58.88 -145.23 REMARK 500 THR A 385 -126.63 -121.27 REMARK 500 ALA A 403 -59.90 76.42 REMARK 500 ASN A 417 4.52 85.44 REMARK 500 THR A 425 -38.39 -133.60 REMARK 500 ALA A 441 -162.83 -119.38 REMARK 500 VAL A 455 31.66 -141.13 REMARK 500 THR A 457 146.65 -178.17 REMARK 500 LYS A 497 5.33 -69.45 REMARK 500 GLN A 498 -4.02 -143.59 REMARK 500 HIS A 515 -73.74 -134.95 REMARK 500 ARG A 516 68.34 60.12 REMARK 500 ASN B 53 46.62 -104.21 REMARK 500 SER B 55 -174.01 178.70 REMARK 500 REMARK 500 THIS ENTRY HAS 99 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 57 0.08 SIDE CHAIN REMARK 500 TYR A 429 0.07 SIDE CHAIN REMARK 500 TYR B 375 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1Q47 A 26 520 UNP O08665 SEM3A_MOUSE 26 520 DBREF 1Q47 B 26 520 UNP O08665 SEM3A_MOUSE 26 520 SEQRES 1 A 495 LYS ASN ASN VAL PRO ARG LEU LYS LEU SER TYR LYS GLU SEQRES 2 A 495 MET LEU GLU SER ASN ASN VAL ILE THR PHE ASN GLY LEU SEQRES 3 A 495 ALA ASN SER SER SER TYR HIS THR PHE LEU LEU ASP GLU SEQRES 4 A 495 GLU ARG SER ARG LEU TYR VAL GLY ALA LYS ASP HIS ILE SEQRES 5 A 495 PHE SER PHE ASN LEU VAL ASN ILE LYS ASP PHE GLN LYS SEQRES 6 A 495 ILE VAL TRP PRO VAL SER TYR THR ARG ARG ASP GLU CYS SEQRES 7 A 495 LYS TRP ALA GLY LYS ASP ILE LEU LYS GLU CYS ALA ASN SEQRES 8 A 495 PHE ILE LYS VAL LEU GLU ALA TYR ASN GLN THR HIS LEU SEQRES 9 A 495 TYR ALA CYS GLY THR GLY ALA PHE HIS PRO ILE CYS THR SEQRES 10 A 495 TYR ILE GLU VAL GLY HIS HIS PRO GLU ASP ASN ILE PHE SEQRES 11 A 495 LYS LEU GLN ASP SER HIS PHE GLU ASN GLY ARG GLY LYS SEQRES 12 A 495 SER PRO TYR ASP PRO LYS LEU LEU THR ALA SER LEU LEU SEQRES 13 A 495 ILE ASP GLY GLU LEU TYR SER GLY THR ALA ALA ASP PHE SEQRES 14 A 495 MET GLY ARG ASP PHE ALA ILE PHE ARG THR LEU GLY HIS SEQRES 15 A 495 HIS HIS PRO ILE ARG THR GLU GLN HIS ASP SER ARG TRP SEQRES 16 A 495 LEU ASN ASP PRO ARG PHE ILE SER ALA HIS LEU ILE PRO SEQRES 17 A 495 GLU SER ASP ASN PRO GLU ASP ASP LYS VAL TYR PHE PHE SEQRES 18 A 495 PHE ARG GLU ASN ALA ILE ASP GLY GLU HIS SER GLY LYS SEQRES 19 A 495 ALA THR HIS ALA ARG ILE GLY GLN ILE CYS LYS ASN ASP SEQRES 20 A 495 PHE GLY GLY HIS ARG SER LEU VAL ASN LYS TRP THR THR SEQRES 21 A 495 PHE LEU LYS ALA ARG LEU ILE CYS SER VAL PRO GLY PRO SEQRES 22 A 495 ASN GLY ILE ASP THR HIS PHE ASP GLU LEU GLN ASP VAL SEQRES 23 A 495 PHE LEU MET ASN SER LYS ASP PRO LYS ASN PRO ILE VAL SEQRES 24 A 495 TYR GLY VAL PHE THR THR SER SER ASN ILE PHE LYS GLY SEQRES 25 A 495 SER ALA VAL CYS MET TYR SER MET SER ASP VAL ARG ARG SEQRES 26 A 495 VAL PHE LEU GLY PRO TYR ALA HIS ARG ASP GLY PRO ASN SEQRES 27 A 495 TYR GLN TRP VAL PRO TYR GLN GLY ARG VAL PRO TYR PRO SEQRES 28 A 495 ARG PRO GLY THR CYS PRO SER LYS THR PHE GLY GLY PHE SEQRES 29 A 495 ASP SER THR LYS ASP LEU PRO ASP ASP VAL ILE THR PHE SEQRES 30 A 495 ALA ARG SER HIS PRO ALA MET TYR ASN PRO VAL PHE PRO SEQRES 31 A 495 ILE ASN ASN ARG PRO ILE MET ILE LYS THR ASP VAL ASN SEQRES 32 A 495 TYR GLN PHE THR GLN ILE VAL VAL ASP ARG VAL ASP ALA SEQRES 33 A 495 GLU ASP GLY GLN TYR ASP VAL MET PHE ILE GLY THR ASP SEQRES 34 A 495 VAL GLY THR VAL LEU LYS VAL VAL SER VAL PRO LYS GLU SEQRES 35 A 495 THR TRP HIS ASP LEU GLU GLU VAL LEU LEU GLU GLU MET SEQRES 36 A 495 THR VAL PHE ARG GLU PRO THR THR ILE SER ALA MET GLU SEQRES 37 A 495 LEU SER THR LYS GLN GLN GLN LEU TYR ILE GLY SER THR SEQRES 38 A 495 ALA GLY VAL ALA GLN LEU PRO LEU HIS ARG CYS ASP ILE SEQRES 39 A 495 TYR SEQRES 1 B 495 LYS ASN ASN VAL PRO ARG LEU LYS LEU SER TYR LYS GLU SEQRES 2 B 495 MET LEU GLU SER ASN ASN VAL ILE THR PHE ASN GLY LEU SEQRES 3 B 495 ALA ASN SER SER SER TYR HIS THR PHE LEU LEU ASP GLU SEQRES 4 B 495 GLU ARG SER ARG LEU TYR VAL GLY ALA LYS ASP HIS ILE SEQRES 5 B 495 PHE SER PHE ASN LEU VAL ASN ILE LYS ASP PHE GLN LYS SEQRES 6 B 495 ILE VAL TRP PRO VAL SER TYR THR ARG ARG ASP GLU CYS SEQRES 7 B 495 LYS TRP ALA GLY LYS ASP ILE LEU LYS GLU CYS ALA ASN SEQRES 8 B 495 PHE ILE LYS VAL LEU GLU ALA TYR ASN GLN THR HIS LEU SEQRES 9 B 495 TYR ALA CYS GLY THR GLY ALA PHE HIS PRO ILE CYS THR SEQRES 10 B 495 TYR ILE GLU VAL GLY HIS HIS PRO GLU ASP ASN ILE PHE SEQRES 11 B 495 LYS LEU GLN ASP SER HIS PHE GLU ASN GLY ARG GLY LYS SEQRES 12 B 495 SER PRO TYR ASP PRO LYS LEU LEU THR ALA SER LEU LEU SEQRES 13 B 495 ILE ASP GLY GLU LEU TYR SER GLY THR ALA ALA ASP PHE SEQRES 14 B 495 MET GLY ARG ASP PHE ALA ILE PHE ARG THR LEU GLY HIS SEQRES 15 B 495 HIS HIS PRO ILE ARG THR GLU GLN HIS ASP SER ARG TRP SEQRES 16 B 495 LEU ASN ASP PRO ARG PHE ILE SER ALA HIS LEU ILE PRO SEQRES 17 B 495 GLU SER ASP ASN PRO GLU ASP ASP LYS VAL TYR PHE PHE SEQRES 18 B 495 PHE ARG GLU ASN ALA ILE ASP GLY GLU HIS SER GLY LYS SEQRES 19 B 495 ALA THR HIS ALA ARG ILE GLY GLN ILE CYS LYS ASN ASP SEQRES 20 B 495 PHE GLY GLY HIS ARG SER LEU VAL ASN LYS TRP THR THR SEQRES 21 B 495 PHE LEU LYS ALA ARG LEU ILE CYS SER VAL PRO GLY PRO SEQRES 22 B 495 ASN GLY ILE ASP THR HIS PHE ASP GLU LEU GLN ASP VAL SEQRES 23 B 495 PHE LEU MET ASN SER LYS ASP PRO LYS ASN PRO ILE VAL SEQRES 24 B 495 TYR GLY VAL PHE THR THR SER SER ASN ILE PHE LYS GLY SEQRES 25 B 495 SER ALA VAL CYS MET TYR SER MET SER ASP VAL ARG ARG SEQRES 26 B 495 VAL PHE LEU GLY PRO TYR ALA HIS ARG ASP GLY PRO ASN SEQRES 27 B 495 TYR GLN TRP VAL PRO TYR GLN GLY ARG VAL PRO TYR PRO SEQRES 28 B 495 ARG PRO GLY THR CYS PRO SER LYS THR PHE GLY GLY PHE SEQRES 29 B 495 ASP SER THR LYS ASP LEU PRO ASP ASP VAL ILE THR PHE SEQRES 30 B 495 ALA ARG SER HIS PRO ALA MET TYR ASN PRO VAL PHE PRO SEQRES 31 B 495 ILE ASN ASN ARG PRO ILE MET ILE LYS THR ASP VAL ASN SEQRES 32 B 495 TYR GLN PHE THR GLN ILE VAL VAL ASP ARG VAL ASP ALA SEQRES 33 B 495 GLU ASP GLY GLN TYR ASP VAL MET PHE ILE GLY THR ASP SEQRES 34 B 495 VAL GLY THR VAL LEU LYS VAL VAL SER VAL PRO LYS GLU SEQRES 35 B 495 THR TRP HIS ASP LEU GLU GLU VAL LEU LEU GLU GLU MET SEQRES 36 B 495 THR VAL PHE ARG GLU PRO THR THR ILE SER ALA MET GLU SEQRES 37 B 495 LEU SER THR LYS GLN GLN GLN LEU TYR ILE GLY SER THR SEQRES 38 B 495 ALA GLY VAL ALA GLN LEU PRO LEU HIS ARG CYS ASP ILE SEQRES 39 B 495 TYR MODRES 1Q47 ASN A 53 ASN GLYCOSYLATION SITE MODRES 1Q47 ASN A 125 ASN GLYCOSYLATION SITE MODRES 1Q47 ASN B 53 ASN GLYCOSYLATION SITE MODRES 1Q47 ASN B 125 ASN GLYCOSYLATION SITE HET NAG A 600 15 HET NAG A 601 15 HET NAG B 600 15 HET NAG B 601 15 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 3 NAG 4(C8 H15 N O6) HELIX 1 1 SER A 35 GLU A 41 1 7 HELIX 2 2 SER A 96 ALA A 106 1 11 HELIX 3 3 ASN A 237 ASP A 240 5 4 HELIX 4 4 SER A 344 LEU A 353 1 10 HELIX 5 5 SER A 391 LEU A 395 5 5 HELIX 6 6 PRO A 396 SER A 405 1 10 HELIX 7 7 PRO A 415 ARG A 419 5 5 HELIX 8 8 SER B 35 GLU B 41 1 7 HELIX 9 9 SER B 96 ALA B 106 1 11 HELIX 10 10 ASN B 237 GLU B 239 5 3 HELIX 11 11 SER B 344 LEU B 353 1 10 HELIX 12 12 SER B 391 LEU B 395 5 5 HELIX 13 13 ASP B 397 PHE B 402 1 6 HELIX 14 14 PRO B 415 ARG B 419 5 5 SHEET 1 A 4 ILE A 46 PHE A 48 0 SHEET 2 A 4 VAL A 509 PRO A 513 -1 O GLN A 511 N ILE A 46 SHEET 3 A 4 GLN A 500 GLY A 504 -1 N LEU A 501 O LEU A 512 SHEET 4 A 4 ALA A 491 SER A 495 -1 N ALA A 491 O GLY A 504 SHEET 1 B 4 THR A 59 ASP A 63 0 SHEET 2 B 4 ARG A 68 ALA A 73 -1 O TYR A 70 N LEU A 61 SHEET 3 B 4 HIS A 76 ASN A 81 -1 O PHE A 80 N LEU A 69 SHEET 4 B 4 PHE A 88 VAL A 92 -1 O GLN A 89 N SER A 79 SHEET 1 C 4 ILE A 118 ALA A 123 0 SHEET 2 C 4 HIS A 128 GLY A 133 -1 O TYR A 130 N GLU A 122 SHEET 3 C 4 ILE A 140 GLU A 145 -1 O ILE A 144 N LEU A 129 SHEET 4 C 4 LYS A 156 ASN A 164 -1 O GLU A 163 N CYS A 141 SHEET 1 D 4 ALA A 178 ILE A 182 0 SHEET 2 D 4 GLU A 185 ALA A 191 -1 O TYR A 187 N LEU A 180 SHEET 3 D 4 PHE A 199 LEU A 205 -1 O PHE A 202 N SER A 188 SHEET 4 D 4 ILE A 211 ARG A 212 -1 O ILE A 211 N ARG A 203 SHEET 1 E 4 ARG A 225 ILE A 232 0 SHEET 2 E 4 LYS A 242 ASN A 250 -1 O TYR A 244 N HIS A 230 SHEET 3 E 4 THR A 261 CYS A 269 -1 O ILE A 268 N VAL A 243 SHEET 4 E 4 LEU A 287 ARG A 290 -1 O ALA A 289 N ILE A 265 SHEET 1 F 2 SER A 294 VAL A 295 0 SHEET 2 F 2 THR A 303 HIS A 304 -1 O THR A 303 N VAL A 295 SHEET 1 G 4 GLU A 307 MET A 314 0 SHEET 2 G 4 ILE A 323 THR A 329 -1 O ILE A 323 N MET A 314 SHEET 3 G 4 SER A 338 TYR A 343 -1 O ALA A 339 N PHE A 328 SHEET 4 G 4 MET A 422 LYS A 424 -1 O LYS A 424 N SER A 338 SHEET 1 H 2 ALA A 357 HIS A 358 0 SHEET 2 H 2 VAL A 367 PRO A 368 -1 O VAL A 367 N HIS A 358 SHEET 1 I 4 PHE A 431 ASP A 440 0 SHEET 2 I 4 GLN A 445 THR A 453 -1 O PHE A 450 N VAL A 435 SHEET 3 I 4 VAL A 458 VAL A 462 -1 O VAL A 461 N MET A 449 SHEET 4 I 4 GLU A 478 MET A 480 -1 O GLU A 478 N LYS A 460 SHEET 1 J 5 LEU B 32 LEU B 34 0 SHEET 2 J 5 VAL B 475 THR B 481 1 O GLU B 479 N LEU B 34 SHEET 3 J 5 THR B 457 VAL B 462 -1 N VAL B 458 O MET B 480 SHEET 4 J 5 GLY B 444 THR B 453 -1 N MET B 449 O VAL B 461 SHEET 5 J 5 PHE B 431 ALA B 441 -1 N VAL B 435 O PHE B 450 SHEET 1 K 4 ILE B 46 PHE B 48 0 SHEET 2 K 4 GLY B 508 PRO B 513 -1 O VAL B 509 N PHE B 48 SHEET 3 K 4 GLN B 500 SER B 505 -1 N LEU B 501 O LEU B 512 SHEET 4 K 4 ALA B 491 LEU B 494 -1 N GLU B 493 O TYR B 502 SHEET 1 L 4 THR B 59 ASP B 63 0 SHEET 2 L 4 ARG B 68 GLY B 72 -1 O TYR B 70 N LEU B 61 SHEET 3 L 4 HIS B 76 ASN B 81 -1 O PHE B 80 N LEU B 69 SHEET 4 L 4 PHE B 88 VAL B 92 -1 O ILE B 91 N ILE B 77 SHEET 1 M 4 ASN B 116 ALA B 123 0 SHEET 2 M 4 HIS B 128 GLY B 135 -1 O TYR B 130 N GLU B 122 SHEET 3 M 4 ILE B 140 GLU B 145 -1 O THR B 142 N ALA B 131 SHEET 4 M 4 LYS B 156 ASN B 164 -1 O GLU B 163 N CYS B 141 SHEET 1 N 3 ALA B 178 ILE B 182 0 SHEET 2 N 3 GLU B 185 ALA B 191 -1 O TYR B 187 N LEU B 180 SHEET 3 N 3 PHE B 199 LEU B 205 -1 O PHE B 202 N SER B 188 SHEET 1 O 4 ARG B 225 PRO B 233 0 SHEET 2 O 4 ASP B 241 ASN B 250 -1 O PHE B 246 N SER B 228 SHEET 3 O 4 THR B 261 CYS B 269 -1 O ILE B 268 N VAL B 243 SHEET 4 O 4 LEU B 287 LEU B 291 -1 O LEU B 287 N GLN B 267 SHEET 1 P 2 SER B 294 VAL B 295 0 SHEET 2 P 2 THR B 303 HIS B 304 -1 O THR B 303 N VAL B 295 SHEET 1 Q 4 GLU B 307 MET B 314 0 SHEET 2 Q 4 ILE B 323 THR B 329 -1 O ILE B 323 N MET B 314 SHEET 3 Q 4 SER B 338 TYR B 343 -1 O ALA B 339 N PHE B 328 SHEET 4 Q 4 MET B 422 LYS B 424 -1 O LYS B 424 N SER B 338 SHEET 1 R 2 ALA B 357 HIS B 358 0 SHEET 2 R 2 VAL B 367 PRO B 368 -1 O VAL B 367 N HIS B 358 SSBOND 1 CYS A 103 CYS A 114 1555 1555 2.05 SSBOND 2 CYS A 132 CYS A 141 1555 1555 2.06 SSBOND 3 CYS A 269 CYS A 381 1555 1555 2.04 SSBOND 4 CYS A 293 CYS A 341 1555 1555 2.06 SSBOND 5 CYS B 103 CYS B 114 1555 1555 2.05 SSBOND 6 CYS B 269 CYS B 381 1555 1555 2.05 SSBOND 7 CYS B 293 CYS B 341 1555 1555 2.05 CISPEP 1 TYR A 375 PRO A 376 0 -0.45 CISPEP 2 TYR B 375 PRO B 376 0 0.02 CRYST1 218.791 59.733 122.715 90.00 109.01 90.00 C 1 2 1 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 0.004571 0.000000 0.001574 0.00000 SCALE2 0.000000 0.016741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008619 0.00000