HEADER SIGNALING PROTEIN 15-JUN-22 7Y4O TITLE RAT SEMAPHORIN 6D EXTRACELLULAR REGION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEMAPHORIN 6D; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ECTODOMAIN FRAGMENT; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SEMA6D; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: CHO-LEC 3.2.8.1 KEYWDS RECEPTOR LIGAND, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.TANAKA,M.NEYAZAKI,T.NOGI REVDAT 3 29-NOV-23 7Y4O 1 REMARK REVDAT 2 16-NOV-22 7Y4O 1 JRNL REVDAT 1 19-OCT-22 7Y4O 0 JRNL AUTH T.TANAKA,T.EKIMOTO,M.NAGATOMO,M.NEYAZAKI,E.SHIMOJI,T.YAMANE, JRNL AUTH 2 S.KANAGAWA,R.OI,E.MIHARA,J.TAKAGI,S.AKASHI,M.IKEGUCHI,T.NOGI JRNL TITL HYBRID IN VITRO/IN SILICO ANALYSIS OF LOW-AFFINITY JRNL TITL 2 PROTEIN-PROTEIN INTERACTIONS THAT REGULATE SIGNAL JRNL TITL 3 TRANSDUCTION BY SEMA6D. JRNL REF PROTEIN SCI. V. 31 E4452 2022 JRNL REFN ESSN 1469-896X JRNL PMID 36156831 JRNL DOI 10.1002/PRO.4452 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 163918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 8626 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7912 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.3726 REMARK 3 BIN FREE R VALUE SET COUNT : 429 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8515 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 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) : 63.46 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL 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 : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : FLAT BULK SOLVENT MODEL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7Y4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 169234 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69300 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: 3AFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 85.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 8.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12%(WT./VOL.) PEG3350, 100 MM CACL2, REMARK 280 400 MM SODIUM FORMATE AND 100 MM SODIUM ACETATE BUFFER (PH 4.5), REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 106.57350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 106.57350 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 95.70800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 106.57350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.85400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 106.57350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.56200 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 106.57350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 106.57350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 95.70800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 106.57350 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 143.56200 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 106.57350 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 47.85400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 SER A 19 REMARK 465 SER A 20 REMARK 465 ARG A 21 REMARK 465 SER A 22 REMARK 465 ARG A 47 REMARK 465 PRO A 48 REMARK 465 SER A 49 REMARK 465 GLY A 50 REMARK 465 ASN A 51 REMARK 465 GLU A 52 REMARK 465 SER A 53 REMARK 465 GLN A 54 REMARK 465 ALA A 479 REMARK 465 GLU A 480 REMARK 465 SER A 481 REMARK 465 GLU A 482 REMARK 465 GLU A 483 REMARK 465 HIS A 569 REMARK 465 GLU A 570 REMARK 465 SER B 19 REMARK 465 SER B 20 REMARK 465 ARG B 21 REMARK 465 SER B 22 REMARK 465 ARG B 47 REMARK 465 PRO B 48 REMARK 465 SER B 49 REMARK 465 GLY B 50 REMARK 465 ASN B 51 REMARK 465 GLU B 52 REMARK 465 SER B 53 REMARK 465 GLN B 54 REMARK 465 GLU B 480 REMARK 465 SER B 481 REMARK 465 HIS B 569 REMARK 465 GLU B 570 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 GLN A 40 33.74 -87.76 REMARK 500 ARG A 45 -35.88 -131.52 REMARK 500 ARG A 66 -105.46 52.80 REMARK 500 ASP A 75 -9.25 62.59 REMARK 500 GLN A 87 -61.91 -122.42 REMARK 500 GLU A 89 139.97 -175.02 REMARK 500 TRP A 98 95.83 -163.26 REMARK 500 PHE A 125 83.85 -151.83 REMARK 500 ASN A 129 -156.72 -130.85 REMARK 500 ARG A 165 -41.61 -134.74 REMARK 500 THR A 187 -147.26 -170.74 REMARK 500 ASP A 195 69.49 -110.60 REMARK 500 MET A 202 172.52 60.81 REMARK 500 GLU A 220 62.35 39.75 REMARK 500 LEU A 247 -118.59 -97.77 REMARK 500 SER A 276 17.27 -148.43 REMARK 500 THR A 415 -52.28 -124.37 REMARK 500 ARG A 416 3.04 -65.95 REMARK 500 THR A 422 -82.34 -124.99 REMARK 500 GLN A 434 55.70 38.08 REMARK 500 SER A 459 -95.96 -159.51 REMARK 500 LEU A 460 -162.41 -105.85 REMARK 500 LEU A 465 99.83 -69.93 REMARK 500 CYS A 477 -106.89 -98.40 REMARK 500 ASP A 493 78.37 -117.84 REMARK 500 SER A 505 3.96 -161.73 REMARK 500 ARG A 514 27.47 -169.78 REMARK 500 LYS A 523 -70.27 -49.71 REMARK 500 THR A 545 53.31 -97.28 REMARK 500 GLU A 558 -70.87 -66.07 REMARK 500 ASP A 567 22.33 -71.85 REMARK 500 PRO B 24 -169.85 -68.32 REMARK 500 HIS B 36 -4.73 -58.93 REMARK 500 GLN B 40 33.28 -82.98 REMARK 500 ARG B 56 -150.19 -109.08 REMARK 500 ARG B 66 -113.23 50.95 REMARK 500 ASP B 75 -27.32 64.39 REMARK 500 THR B 88 -34.09 -131.75 REMARK 500 SER B 93 -80.68 -73.90 REMARK 500 TRP B 98 78.42 -157.11 REMARK 500 LYS B 111 25.20 -79.76 REMARK 500 ASP B 130 49.78 -89.14 REMARK 500 GLU B 131 -37.59 -159.16 REMARK 500 TYR B 155 81.02 -63.61 REMARK 500 ASP B 156 49.35 -99.74 REMARK 500 ALA B 164 7.70 59.00 REMARK 500 THR B 187 -150.79 -164.12 REMARK 500 SER B 194 -37.30 -133.24 REMARK 500 SER B 201 -159.57 -152.91 REMARK 500 LEU B 247 -153.78 -81.88 REMARK 500 REMARK 500 THIS ENTRY HAS 66 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF1 7Y4O A 22 570 UNP A0A0G2JZC4_RAT DBREF2 7Y4O A A0A0G2JZC4 22 570 DBREF1 7Y4O B 22 570 UNP A0A0G2JZC4_RAT DBREF2 7Y4O B A0A0G2JZC4 22 570 SEQADV 7Y4O SER A 19 UNP A0A0G2JZC EXPRESSION TAG SEQADV 7Y4O SER A 20 UNP A0A0G2JZC EXPRESSION TAG SEQADV 7Y4O ARG A 21 UNP A0A0G2JZC EXPRESSION TAG SEQADV 7Y4O GLY A 332 UNP A0A0G2JZC SER 332 ENGINEERED MUTATION SEQADV 7Y4O SER B 19 UNP A0A0G2JZC EXPRESSION TAG SEQADV 7Y4O SER B 20 UNP A0A0G2JZC EXPRESSION TAG SEQADV 7Y4O ARG B 21 UNP A0A0G2JZC EXPRESSION TAG SEQADV 7Y4O GLY B 332 UNP A0A0G2JZC SER 332 ENGINEERED MUTATION SEQRES 1 A 552 SER SER ARG SER PHE PRO GLU ASP ASP GLU PRO LEU ASN SEQRES 2 A 552 THR VAL ASP TYR HIS TYR SER ARG GLN TYR PRO VAL PHE SEQRES 3 A 552 ARG GLY ARG PRO SER GLY ASN GLU SER GLN HIS ARG LEU SEQRES 4 A 552 ASP PHE GLN LEU MET LEU LYS ILE ARG ASP THR LEU TYR SEQRES 5 A 552 ILE ALA GLY ARG ASP GLN VAL TYR THR VAL ASN LEU ASN SEQRES 6 A 552 ASP ILE PRO GLN THR GLU VAL ILE PRO SER LYS LYS LEU SEQRES 7 A 552 THR TRP ARG SER ARG GLN GLN ASP ARG GLU ASN CYS ALA SEQRES 8 A 552 MET LYS GLY LYS HIS LYS ASP GLU CYS HIS ASN PHE ILE SEQRES 9 A 552 LYS VAL PHE VAL PRO ARG ASN ASP GLU MET VAL PHE VAL SEQRES 10 A 552 CYS GLY THR ASN ALA PHE ASN PRO MET CYS ARG TYR TYR SEQRES 11 A 552 ARG LEU SER THR LEU GLU TYR ASP GLY GLU GLU ILE SER SEQRES 12 A 552 GLY LEU ALA ARG CYS PRO PHE ASP ALA ARG GLN THR ASN SEQRES 13 A 552 VAL ALA LEU PHE ALA ASP GLY LYS LEU TYR SER ALA THR SEQRES 14 A 552 VAL ALA ASP PHE LEU ALA SER ASP ALA VAL ILE TYR ARG SEQRES 15 A 552 SER MET GLY ASP GLY SER ALA LEU ARG THR ILE LYS TYR SEQRES 16 A 552 ASP SER LYS TRP ILE LYS GLU PRO HIS PHE LEU HIS ALA SEQRES 17 A 552 ILE GLU TYR GLY ASN TYR VAL TYR PHE PHE PHE ARG GLU SEQRES 18 A 552 ILE ALA VAL GLU HIS ASN ASN LEU GLY LYS ALA VAL TYR SEQRES 19 A 552 SER ARG VAL ALA ARG ILE CYS LYS ASN ASP MET GLY GLY SEQRES 20 A 552 SER GLN ARG VAL LEU GLU LYS HIS TRP THR SER PHE LEU SEQRES 21 A 552 LYS ALA ARG LEU ASN CYS SER VAL PRO GLY ASP SER PHE SEQRES 22 A 552 PHE TYR PHE ASP VAL LEU GLN SER ILE THR ASP ILE ILE SEQRES 23 A 552 GLN ILE ASN GLY ILE PRO THR VAL ILE GLY VAL PHE THR SEQRES 24 A 552 THR GLN LEU ASN SER ILE PRO GLY SER ALA VAL CYS ALA SEQRES 25 A 552 PHE GLY MET ASP ASP ILE GLU LYS VAL PHE LYS GLY ARG SEQRES 26 A 552 PHE LYS GLU GLN LYS THR PRO ASP SER VAL TRP THR ALA SEQRES 27 A 552 VAL PRO GLU ASP LYS VAL PRO LYS PRO ARG PRO GLY CYS SEQRES 28 A 552 CYS ALA LYS HIS GLY LEU ALA GLU ALA TYR LYS THR SER SEQRES 29 A 552 ILE ASP PHE PRO ASP ASP THR LEU SER PHE ILE LYS SER SEQRES 30 A 552 HIS PRO LEU MET ASP SER ALA VAL PRO PRO ILE ALA ASP SEQRES 31 A 552 GLU PRO TRP PHE THR LYS THR ARG VAL ARG TYR ARG LEU SEQRES 32 A 552 THR ALA ILE GLU VAL ASP ARG SER ALA GLY PRO TYR GLN SEQRES 33 A 552 ASN TYR THR VAL ILE PHE VAL GLY SER GLU ALA GLY VAL SEQRES 34 A 552 VAL LEU LYS VAL LEU ALA LYS THR SER PRO PHE SER LEU SEQRES 35 A 552 ASN ASP SER VAL LEU LEU GLU GLU ILE GLU ALA TYR ASN SEQRES 36 A 552 PRO ALA LYS CYS SER ALA GLU SER GLU GLU ASP ARG LYS SEQRES 37 A 552 VAL VAL SER LEU GLN LEU ASP ARG ASP HIS HIS ALA LEU SEQRES 38 A 552 TYR VAL ALA PHE SER SER CYS VAL VAL ARG ILE PRO LEU SEQRES 39 A 552 SER ARG CYS GLU ARG TYR GLY SER CYS LYS LYS SER CYS SEQRES 40 A 552 ILE ALA SER ARG ASP PRO TYR CYS GLY TRP LEU SER GLN SEQRES 41 A 552 GLY VAL CYS GLU ARG VAL THR LEU GLY MET LEU ALA GLY SEQRES 42 A 552 GLY TYR GLU GLN ASP THR GLU TYR GLY ASN THR ALA HIS SEQRES 43 A 552 LEU GLY ASP CYS HIS GLU SEQRES 1 B 552 SER SER ARG SER PHE PRO GLU ASP ASP GLU PRO LEU ASN SEQRES 2 B 552 THR VAL ASP TYR HIS TYR SER ARG GLN TYR PRO VAL PHE SEQRES 3 B 552 ARG GLY ARG PRO SER GLY ASN GLU SER GLN HIS ARG LEU SEQRES 4 B 552 ASP PHE GLN LEU MET LEU LYS ILE ARG ASP THR LEU TYR SEQRES 5 B 552 ILE ALA GLY ARG ASP GLN VAL TYR THR VAL ASN LEU ASN SEQRES 6 B 552 ASP ILE PRO GLN THR GLU VAL ILE PRO SER LYS LYS LEU SEQRES 7 B 552 THR TRP ARG SER ARG GLN GLN ASP ARG GLU ASN CYS ALA SEQRES 8 B 552 MET LYS GLY LYS HIS LYS ASP GLU CYS HIS ASN PHE ILE SEQRES 9 B 552 LYS VAL PHE VAL PRO ARG ASN ASP GLU MET VAL PHE VAL SEQRES 10 B 552 CYS GLY THR ASN ALA PHE ASN PRO MET CYS ARG TYR TYR SEQRES 11 B 552 ARG LEU SER THR LEU GLU TYR ASP GLY GLU GLU ILE SER SEQRES 12 B 552 GLY LEU ALA ARG CYS PRO PHE ASP ALA ARG GLN THR ASN SEQRES 13 B 552 VAL ALA LEU PHE ALA ASP GLY LYS LEU TYR SER ALA THR SEQRES 14 B 552 VAL ALA ASP PHE LEU ALA SER ASP ALA VAL ILE TYR ARG SEQRES 15 B 552 SER MET GLY ASP GLY SER ALA LEU ARG THR ILE LYS TYR SEQRES 16 B 552 ASP SER LYS TRP ILE LYS GLU PRO HIS PHE LEU HIS ALA SEQRES 17 B 552 ILE GLU TYR GLY ASN TYR VAL TYR PHE PHE PHE ARG GLU SEQRES 18 B 552 ILE ALA VAL GLU HIS ASN ASN LEU GLY LYS ALA VAL TYR SEQRES 19 B 552 SER ARG VAL ALA ARG ILE CYS LYS ASN ASP MET GLY GLY SEQRES 20 B 552 SER GLN ARG VAL LEU GLU LYS HIS TRP THR SER PHE LEU SEQRES 21 B 552 LYS ALA ARG LEU ASN CYS SER VAL PRO GLY ASP SER PHE SEQRES 22 B 552 PHE TYR PHE ASP VAL LEU GLN SER ILE THR ASP ILE ILE SEQRES 23 B 552 GLN ILE ASN GLY ILE PRO THR VAL ILE GLY VAL PHE THR SEQRES 24 B 552 THR GLN LEU ASN SER ILE PRO GLY SER ALA VAL CYS ALA SEQRES 25 B 552 PHE GLY MET ASP ASP ILE GLU LYS VAL PHE LYS GLY ARG SEQRES 26 B 552 PHE LYS GLU GLN LYS THR PRO ASP SER VAL TRP THR ALA SEQRES 27 B 552 VAL PRO GLU ASP LYS VAL PRO LYS PRO ARG PRO GLY CYS SEQRES 28 B 552 CYS ALA LYS HIS GLY LEU ALA GLU ALA TYR LYS THR SER SEQRES 29 B 552 ILE ASP PHE PRO ASP ASP THR LEU SER PHE ILE LYS SER SEQRES 30 B 552 HIS PRO LEU MET ASP SER ALA VAL PRO PRO ILE ALA ASP SEQRES 31 B 552 GLU PRO TRP PHE THR LYS THR ARG VAL ARG TYR ARG LEU SEQRES 32 B 552 THR ALA ILE GLU VAL ASP ARG SER ALA GLY PRO TYR GLN SEQRES 33 B 552 ASN TYR THR VAL ILE PHE VAL GLY SER GLU ALA GLY VAL SEQRES 34 B 552 VAL LEU LYS VAL LEU ALA LYS THR SER PRO PHE SER LEU SEQRES 35 B 552 ASN ASP SER VAL LEU LEU GLU GLU ILE GLU ALA TYR ASN SEQRES 36 B 552 PRO ALA LYS CYS SER ALA GLU SER GLU GLU ASP ARG LYS SEQRES 37 B 552 VAL VAL SER LEU GLN LEU ASP ARG ASP HIS HIS ALA LEU SEQRES 38 B 552 TYR VAL ALA PHE SER SER CYS VAL VAL ARG ILE PRO LEU SEQRES 39 B 552 SER ARG CYS GLU ARG TYR GLY SER CYS LYS LYS SER CYS SEQRES 40 B 552 ILE ALA SER ARG ASP PRO TYR CYS GLY TRP LEU SER GLN SEQRES 41 B 552 GLY VAL CYS GLU ARG VAL THR LEU GLY MET LEU ALA GLY SEQRES 42 B 552 GLY TYR GLU GLN ASP THR GLU TYR GLY ASN THR ALA HIS SEQRES 43 B 552 LEU GLY ASP CYS HIS GLU HET NAG A 601 14 HET NAG B 601 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 3 NAG 2(C8 H15 N O6) HELIX 1 AA1 ASP A 34 ARG A 39 1 6 HELIX 2 AA2 ARG A 101 LYS A 111 1 11 HELIX 3 AA3 MET A 333 LYS A 341 1 9 HELIX 4 AA4 PRO A 358 VAL A 362 5 5 HELIX 5 AA5 HIS A 373 GLU A 377 5 5 HELIX 6 AA6 PRO A 386 SER A 391 1 6 HELIX 7 AA7 ARG A 514 GLY A 519 1 6 HELIX 8 AA8 CYS A 521 ALA A 527 1 7 HELIX 9 AA9 LEU A 549 TYR A 553 5 5 HELIX 10 AB1 ASP B 34 ARG B 39 1 6 HELIX 11 AB2 ARG B 101 LYS B 111 1 11 HELIX 12 AB3 MET B 333 LYS B 341 1 9 HELIX 13 AB4 ASP B 387 LYS B 394 1 8 HELIX 14 AB5 ARG B 514 TYR B 518 5 5 HELIX 15 AB6 CYS B 521 ARG B 529 1 9 HELIX 16 AB7 LEU B 549 TYR B 553 5 5 SHEET 1 AA1 5 ASN A 31 VAL A 33 0 SHEET 2 AA1 5 VAL A 464 GLU A 470 1 O GLU A 470 N VAL A 33 SHEET 3 AA1 5 VAL A 447 LEU A 452 -1 N LEU A 452 O VAL A 464 SHEET 4 AA1 5 TYR A 436 VAL A 441 -1 N ILE A 439 O VAL A 451 SHEET 5 AA1 5 ILE A 424 ALA A 430 -1 N GLU A 425 O PHE A 440 SHEET 1 AA2 4 VAL A 43 PHE A 44 0 SHEET 2 AA2 4 VAL A 507 PRO A 511 -1 O VAL A 507 N PHE A 44 SHEET 3 AA2 4 ALA A 498 ALA A 502 -1 N LEU A 499 O ILE A 510 SHEET 4 AA2 4 LEU A 490 ASP A 493 -1 N ASP A 493 O ALA A 498 SHEET 1 AA3 4 LEU A 61 ILE A 65 0 SHEET 2 AA3 4 THR A 68 ALA A 72 -1 O TYR A 70 N LEU A 63 SHEET 3 AA3 4 GLN A 76 ASN A 81 -1 O VAL A 80 N LEU A 69 SHEET 4 AA3 4 LYS A 94 THR A 97 -1 O LYS A 94 N THR A 79 SHEET 1 AA4 4 ILE A 122 PRO A 127 0 SHEET 2 AA4 4 MET A 132 GLY A 137 -1 O PHE A 134 N VAL A 126 SHEET 3 AA4 4 MET A 144 ARG A 149 -1 O MET A 144 N GLY A 137 SHEET 4 AA4 4 ILE A 160 SER A 161 -1 O ILE A 160 N CYS A 145 SHEET 1 AA5 4 VAL A 175 ALA A 179 0 SHEET 2 AA5 4 LYS A 182 VAL A 188 -1 O LYS A 182 N ALA A 179 SHEET 3 AA5 4 ALA A 196 SER A 201 -1 O VAL A 197 N THR A 187 SHEET 4 AA5 4 LEU A 208 ARG A 209 -1 O LEU A 208 N ARG A 200 SHEET 1 AA6 5 HIS A 222 TYR A 229 0 SHEET 2 AA6 5 TYR A 232 ILE A 240 -1 O PHE A 236 N HIS A 225 SHEET 3 AA6 5 VAL A 251 CYS A 259 -1 O TYR A 252 N GLU A 239 SHEET 4 AA6 5 LEU A 278 LEU A 282 -1 O LEU A 282 N SER A 253 SHEET 5 AA6 5 LEU A 398 VAL A 403 1 O VAL A 403 N ARG A 281 SHEET 1 AA7 2 SER A 285 VAL A 286 0 SHEET 2 AA7 2 PHE A 292 TYR A 293 -1 O PHE A 292 N VAL A 286 SHEET 1 AA8 3 VAL A 296 ILE A 300 0 SHEET 2 AA8 3 ILE A 309 THR A 317 -1 O VAL A 315 N GLN A 298 SHEET 3 AA8 3 ILE A 304 ILE A 306 -1 N ILE A 304 O THR A 311 SHEET 1 AA9 4 VAL A 296 ILE A 300 0 SHEET 2 AA9 4 ILE A 309 THR A 317 -1 O VAL A 315 N GLN A 298 SHEET 3 AA9 4 SER A 326 GLY A 332 -1 O PHE A 331 N VAL A 312 SHEET 4 AA9 4 PHE A 412 LYS A 414 -1 O LYS A 414 N SER A 326 SHEET 1 AB1 2 LYS A 345 GLU A 346 0 SHEET 2 AB1 2 THR A 355 ALA A 356 -1 O THR A 355 N GLU A 346 SHEET 1 AB2 2 CYS A 533 LEU A 536 0 SHEET 2 AB2 2 VAL A 540 ARG A 543 -1 O GLU A 542 N GLY A 534 SHEET 1 AB3 5 ASN B 31 VAL B 33 0 SHEET 2 AB3 5 VAL B 464 GLU B 470 1 O GLU B 470 N VAL B 33 SHEET 3 AB3 5 VAL B 447 LEU B 452 -1 N VAL B 448 O ILE B 469 SHEET 4 AB3 5 TYR B 436 VAL B 441 -1 N ILE B 439 O VAL B 451 SHEET 5 AB3 5 ILE B 424 ALA B 430 -1 N ALA B 430 O TYR B 436 SHEET 1 AB4 4 VAL B 43 PHE B 44 0 SHEET 2 AB4 4 VAL B 507 ARG B 509 -1 O VAL B 507 N PHE B 44 SHEET 3 AB4 4 ALA B 498 ALA B 502 -1 N VAL B 501 O VAL B 508 SHEET 4 AB4 4 LEU B 492 ASP B 493 -1 N ASP B 493 O ALA B 498 SHEET 1 AB5 4 LEU B 61 ILE B 65 0 SHEET 2 AB5 4 THR B 68 ALA B 72 -1 O TYR B 70 N LEU B 63 SHEET 3 AB5 4 GLN B 76 ASN B 81 -1 O TYR B 78 N ILE B 71 SHEET 4 AB5 4 LYS B 95 THR B 97 -1 O LEU B 96 N VAL B 77 SHEET 1 AB6 4 ILE B 122 PRO B 127 0 SHEET 2 AB6 4 MET B 132 GLY B 137 -1 O PHE B 134 N VAL B 126 SHEET 3 AB6 4 MET B 144 ARG B 149 -1 O ARG B 146 N VAL B 135 SHEET 4 AB6 4 ILE B 160 SER B 161 -1 O ILE B 160 N CYS B 145 SHEET 1 AB7 4 VAL B 175 ALA B 179 0 SHEET 2 AB7 4 LYS B 182 VAL B 188 -1 O TYR B 184 N LEU B 177 SHEET 3 AB7 4 ALA B 196 SER B 201 -1 O VAL B 197 N THR B 187 SHEET 4 AB7 4 LEU B 208 ARG B 209 -1 O LEU B 208 N ARG B 200 SHEET 1 AB8 5 HIS B 222 TYR B 229 0 SHEET 2 AB8 5 TYR B 232 ILE B 240 -1 O TYR B 234 N ILE B 227 SHEET 3 AB8 5 VAL B 251 CYS B 259 -1 O TYR B 252 N GLU B 239 SHEET 4 AB8 5 LEU B 278 LEU B 282 -1 O LEU B 282 N SER B 253 SHEET 5 AB8 5 LEU B 398 VAL B 403 1 O MET B 399 N LYS B 279 SHEET 1 AB9 2 CYS B 284 VAL B 286 0 SHEET 2 AB9 2 PHE B 292 PHE B 294 -1 O PHE B 294 N CYS B 284 SHEET 1 AC1 3 VAL B 296 ILE B 300 0 SHEET 2 AC1 3 ILE B 309 THR B 317 -1 O VAL B 315 N GLN B 298 SHEET 3 AC1 3 ILE B 304 ILE B 306 -1 N ILE B 304 O THR B 311 SHEET 1 AC2 4 VAL B 296 ILE B 300 0 SHEET 2 AC2 4 ILE B 309 THR B 317 -1 O VAL B 315 N GLN B 298 SHEET 3 AC2 4 SER B 326 GLY B 332 -1 O CYS B 329 N GLY B 314 SHEET 4 AC2 4 PHE B 412 LYS B 414 -1 O LYS B 414 N SER B 326 SHEET 1 AC3 2 LYS B 345 GLU B 346 0 SHEET 2 AC3 2 THR B 355 ALA B 356 -1 O THR B 355 N GLU B 346 SHEET 1 AC4 2 CYS B 533 GLY B 534 0 SHEET 2 AC4 2 GLU B 542 ARG B 543 -1 O GLU B 542 N GLY B 534 SSBOND 1 CYS A 108 CYS A 118 1555 1555 2.03 SSBOND 2 CYS A 136 CYS A 145 1555 1555 2.03 SSBOND 3 CYS A 259 CYS A 370 1555 1555 2.03 SSBOND 4 CYS A 284 CYS A 329 1555 1555 2.03 SSBOND 5 CYS A 477 CYS A 506 1555 1555 2.03 SSBOND 6 CYS A 515 CYS A 533 1555 1555 2.03 SSBOND 7 CYS A 521 CYS A 568 1555 1555 2.03 SSBOND 8 CYS A 525 CYS A 541 1555 1555 2.02 SSBOND 9 CYS B 108 CYS B 118 1555 1555 2.03 SSBOND 10 CYS B 136 CYS B 145 1555 1555 2.03 SSBOND 11 CYS B 259 CYS B 370 1555 1555 2.03 SSBOND 12 CYS B 284 CYS B 329 1555 1555 2.03 SSBOND 13 CYS B 477 CYS B 506 1555 1555 2.03 SSBOND 14 CYS B 515 CYS B 533 1555 1555 2.03 SSBOND 15 CYS B 521 CYS B 568 1555 1555 2.03 SSBOND 16 CYS B 525 CYS B 541 1555 1555 2.03 LINK ND2 ASN A 283 C1 NAG A 601 1555 1555 1.44 LINK ND2 ASN B 283 C1 NAG B 601 1555 1555 1.44 CISPEP 1 LYS A 364 PRO A 365 0 0.96 CISPEP 2 LYS B 364 PRO B 365 0 0.64 CRYST1 213.147 213.147 191.416 90.00 90.00 90.00 I 41 16 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 0.004692 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005224 0.00000