HEADER RECEPTOR 06-JUL-07 2V5O TITLE STRUCTURE OF HUMAN IGF2R DOMAINS 11-14 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAINS 11-14, RESIDUES 1508-2128; COMPND 5 SYNONYM: INSULIN-LIKE GROWTH FACTOR II RECEPTOR, CI MAN-6-P RECEPTOR, COMPND 6 CI-MPR, M6PR, INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR, IGF-II RECEPTOR, COMPND 7 M6P/IGF2 RECEPTOR, M6P/IGF2R, 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR, COMPND 8 MPR 300, MPR300, CD222 ANTIGEN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ATCC: 95661; SOURCE 6 ORGAN: PLACENTA; SOURCE 7 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: LECR 3.2.8.1; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: CHO; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PEE14 KEYWDS CATION INDEPENDENT MANNOSE 6-PHOSPHATE, MEMBRANE, RECEPTOR, LYSOSOME, KEYWDS 2 TRANSPORT, BETA BARREL, PHOSPHORYLATION, FIBRONECTIN TYPE II, KEYWDS 3 INSULIN-LIKE GROWTH FACTOR, GLYCOPROTEIN, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR J.BROWN,C.DELAINE,O.J.ZACCHEO,C.SIEBOLD,R.J.GILBERT,G.VAN BOXEL, AUTHOR 2 A.DENLEY,J.C.WALLACE,A.B.HASSAN,B.E.FORBES,E.Y.JONES REVDAT 8 23-OCT-24 2V5O 1 REMARK REVDAT 7 13-DEC-23 2V5O 1 HETSYN REVDAT 6 29-JUL-20 2V5O 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 28-FEB-18 2V5O 1 SOURCE REVDAT 4 13-JUL-11 2V5O 1 VERSN REVDAT 3 24-FEB-09 2V5O 1 VERSN REVDAT 2 22-APR-08 2V5O 1 JRNL REMARK MASTER REVDAT 1 11-DEC-07 2V5O 0 JRNL AUTH J.BROWN,C.DELAINE,O.J.ZACCHEO,C.SIEBOLD,R.J.GILBERT, JRNL AUTH 2 G.VAN BOXEL,A.DENLEY,J.C.WALLACE,A.B.HASSAN,B.E.FORBES, JRNL AUTH 3 E.Y.JONES JRNL TITL STRUCTURE AND FUNCTIONAL ANALYSIS OF THE IGF-II/IGF2R JRNL TITL 2 INTERACTION JRNL REF EMBO J. V. 27 265 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 18046459 JRNL DOI 10.1038/SJ.EMBOJ.7601938 REMARK 2 REMARK 2 RESOLUTION. 2.91 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) : 2.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 18893 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) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.304 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1024 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1342 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.01000 REMARK 3 B22 (A**2) : -3.31000 REMARK 3 B33 (A**2) : 4.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.39000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.749 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.449 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.465 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 56.509 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.892 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.837 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4814 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6549 ; 1.164 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 601 ; 6.782 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;35.395 ;23.418 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 775 ;18.579 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;12.974 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 727 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3652 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1983 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3207 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 136 ; 0.155 ; 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): 39 ; 0.179 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.105 ; 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): 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1516 A 1650 REMARK 3 ORIGIN FOR THE GROUP (A): 41.1560 -9.2144 18.2047 REMARK 3 T TENSOR REMARK 3 T11: 0.3220 T22: 0.3733 REMARK 3 T33: -0.1071 T12: -0.4368 REMARK 3 T13: 0.0730 T23: -0.2726 REMARK 3 L TENSOR REMARK 3 L11: 10.4427 L22: 7.1821 REMARK 3 L33: 5.6249 L12: 1.8469 REMARK 3 L13: -1.6545 L23: -1.5538 REMARK 3 S TENSOR REMARK 3 S11: -0.8429 S12: 1.3340 S13: -0.3973 REMARK 3 S21: -0.9818 S22: 0.4703 S23: 0.6056 REMARK 3 S31: 1.0598 S32: -1.3612 S33: 0.3726 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1651 A 1797 REMARK 3 ORIGIN FOR THE GROUP (A): 56.3806 12.2860 9.7040 REMARK 3 T TENSOR REMARK 3 T11: 0.0312 T22: 0.2302 REMARK 3 T33: -0.4400 T12: 0.0666 REMARK 3 T13: 0.1038 T23: 0.0610 REMARK 3 L TENSOR REMARK 3 L11: 10.2008 L22: 4.5864 REMARK 3 L33: 5.9668 L12: 2.6796 REMARK 3 L13: 2.6862 L23: 0.5622 REMARK 3 S TENSOR REMARK 3 S11: -0.0047 S12: 1.6485 S13: 0.2684 REMARK 3 S21: -0.8725 S22: 0.1373 S23: 0.3343 REMARK 3 S31: 0.0219 S32: -0.4619 S33: -0.1326 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1798 A 1988 REMARK 3 ORIGIN FOR THE GROUP (A): 66.0787 18.4291 36.4062 REMARK 3 T TENSOR REMARK 3 T11: -0.3286 T22: -0.4254 REMARK 3 T33: -0.5139 T12: 0.0246 REMARK 3 T13: -0.0225 T23: 0.0563 REMARK 3 L TENSOR REMARK 3 L11: 9.3825 L22: 5.0552 REMARK 3 L33: 0.9335 L12: 3.7949 REMARK 3 L13: -0.7867 L23: 0.6482 REMARK 3 S TENSOR REMARK 3 S11: -0.0977 S12: 0.5286 S13: 0.0347 REMARK 3 S21: 0.1044 S22: 0.0487 S23: -0.1392 REMARK 3 S31: 0.0078 S32: 0.0493 S33: 0.0490 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1989 A 2128 REMARK 3 ORIGIN FOR THE GROUP (A): 86.7480 56.5171 39.4484 REMARK 3 T TENSOR REMARK 3 T11: -0.3137 T22: -0.5077 REMARK 3 T33: 0.0741 T12: -0.0268 REMARK 3 T13: -0.2001 T23: 0.0485 REMARK 3 L TENSOR REMARK 3 L11: 9.7019 L22: 7.3276 REMARK 3 L33: 7.4265 L12: 0.2122 REMARK 3 L13: -0.0097 L23: -0.6046 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: 0.5706 S13: 0.2250 REMARK 3 S21: -0.6228 S22: 0.0865 S23: 0.9809 REMARK 3 S31: -0.0124 S32: 0.1558 S33: -0.0613 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2V5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1290033119. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : DIAMOND (111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19919 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: PDB ENTRY 2V5N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH6.4, 2.5% (W/V) PEG 3000 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 69.27700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.62350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.27700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.62350 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 1508 REMARK 465 LYS A 1509 REMARK 465 SER A 1510 REMARK 465 ASN A 1511 REMARK 465 GLU A 1512 REMARK 465 HIS A 1513 REMARK 465 ASP A 1514 REMARK 465 ASP A 1515 REMARK 465 GLU A 1680 REMARK 465 ASP A 1681 REMARK 465 ASP A 1682 REMARK 465 ALA A 1683 REMARK 465 SER A 1684 REMARK 465 ASP A 1685 REMARK 465 LYS A 1754 REMARK 465 HIS A 1755 REMARK 465 PHE A 1756 REMARK 465 HIS A 2129 REMARK 465 HIS A 2130 REMARK 465 HIS A 2131 REMARK 465 HIS A 2132 REMARK 465 HIS A 2133 REMARK 465 HIS A 2134 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 THR A1686 OG1 CG2 REMARK 470 ASN A1687 CG OD1 ND2 REMARK 470 ASP A1753 CG OD1 OD2 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 O GLY A 1773 NE1 TRP A 1789 2.13 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 SER A1543 -153.49 48.14 REMARK 500 ARG A1571 75.42 5.78 REMARK 500 SER A1573 106.54 -59.02 REMARK 500 ARG A1580 90.50 -64.41 REMARK 500 ASP A1585 81.22 41.15 REMARK 500 GLN A1586 -3.82 64.47 REMARK 500 ARG A1615 114.39 -160.24 REMARK 500 ALA A1618 -120.39 -72.58 REMARK 500 GLN A1648 -160.77 -117.01 REMARK 500 GLU A1678 -104.63 -68.53 REMARK 500 ASP A1689 -73.45 -142.81 REMARK 500 ASP A1718 96.85 76.64 REMARK 500 VAL A1727 100.54 -49.42 REMARK 500 ALA A1728 -97.65 -77.83 REMARK 500 ILE A1736 -132.67 -96.65 REMARK 500 ALA A1737 87.95 -63.10 REMARK 500 LEU A1742 107.51 -165.48 REMARK 500 ALA A1752 -10.86 -152.56 REMARK 500 LEU A1778 -81.28 -112.15 REMARK 500 SER A1781 105.67 -18.31 REMARK 500 CYS A1804 34.82 -98.92 REMARK 500 LEU A1812 -20.05 65.22 REMARK 500 SER A1821 -19.55 -47.39 REMARK 500 SER A1831 -9.18 80.08 REMARK 500 PRO A1845 25.77 -70.82 REMARK 500 ASP A1852 -26.89 70.21 REMARK 500 MET A1872 134.92 -38.81 REMARK 500 GLU A1881 11.48 58.86 REMARK 500 ASN A1889 42.21 70.01 REMARK 500 SER A1921 19.40 57.78 REMARK 500 ASP A1934 -39.38 -37.08 REMARK 500 ASP A1960 46.28 -103.15 REMARK 500 VAL A1986 46.55 -108.22 REMARK 500 CYS A1987 -53.26 -127.02 REMARK 500 PRO A1988 75.49 -100.40 REMARK 500 CYS A2029 9.41 53.34 REMARK 500 GLU A2041 -176.66 -52.25 REMARK 500 ARG A2042 -5.60 50.86 REMARK 500 THR A2050 104.80 -51.31 REMARK 500 THR A2051 -14.81 79.28 REMARK 500 ASP A2070 -9.74 66.33 REMARK 500 ASN A2085 11.38 43.99 REMARK 500 LYS A2106 -74.58 -104.68 REMARK 500 ALA A2124 37.65 -82.25 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 SER A 1781 GLU A 1782 -148.59 REMARK 500 CYS A 1987 PRO A 1988 -130.49 REMARK 500 PRO A 1988 PRO A 1989 147.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E6F RELATED DB: PDB REMARK 900 HUMAN MIR-RECEPTOR, REPEAT 11 REMARK 900 RELATED ID: 1GP0 RELATED DB: PDB REMARK 900 STRUCTURE OF A FUNCTIONAL IGF2R FRAGMENT DETERMINED FROM ANOMALOUS REMARK 900 SCATTERING OF SULPHUR REMARK 900 RELATED ID: 1GP3 RELATED DB: PDB REMARK 900 STRUCTURE OF A FUNCTIONAL IGF2R FRAGMENT DETERMINED FROM ANOMALOUS REMARK 900 SCATTERING OF SULPHUR REMARK 900 RELATED ID: 1GQB RELATED DB: PDB REMARK 900 HUMAN MIR-RECEPTOR, REPEAT 11 REMARK 900 RELATED ID: 1JPL RELATED DB: PDB REMARK 900 GGA3 VHS DOMAIN COMPLEXED WITH C-TERMINAL PEPTIDE FROMCATION- REMARK 900 INDEPENDENT MANNOSE 6- PHOSPHATE RECEPTOR REMARK 900 RELATED ID: 1JWG RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH CATION-INDEPENDENTM6PR C- REMARK 900 TERMINAL PEPTIDE REMARK 900 RELATED ID: 1LF8 RELATED DB: PDB REMARK 900 COMPLEX OF GGA3-VHS DOMAIN AND CI-MPR C -TERMINALPHOSPHOPEPTIDE REMARK 900 RELATED ID: 2CNJ RELATED DB: PDB REMARK 900 NMR STUDIES ON THE INTERACTION OF INSULIN- GROWTH FACTOR II (IGF-II) REMARK 900 WITH IGF2R DOMAIN 11 REMARK 900 RELATED ID: 2V5N RELATED DB: PDB REMARK 900 RELATED ID: 2V5P RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONFLICT INDICATED IN THE SEQADV RECORDS BELOW HAS BEEN REMARK 999 DESCRIBED IN UNIPROT ENTRY P11717 UNDER REFERENCE WITH REMARK 999 PUBMEDID: 2957598. DBREF 2V5O A 1508 2128 UNP P11717 MPRI_HUMAN 1508 2128 DBREF 2V5O A 2129 2134 PDB 2V5O 2V5O 2129 2134 SEQADV 2V5O ALA A 1703 UNP P11717 GLY 1703 CONFLICT SEQRES 1 A 627 MET LYS SER ASN GLU HIS ASP ASP CYS GLN VAL THR ASN SEQRES 2 A 627 PRO SER THR GLY HIS LEU PHE ASP LEU SER SER LEU SER SEQRES 3 A 627 GLY ARG ALA GLY PHE THR ALA ALA TYR SER GLU LYS GLY SEQRES 4 A 627 LEU VAL TYR MET SER ILE CYS GLY GLU ASN GLU ASN CYS SEQRES 5 A 627 PRO PRO GLY VAL GLY ALA CYS PHE GLY GLN THR ARG ILE SEQRES 6 A 627 SER VAL GLY LYS ALA ASN LYS ARG LEU ARG TYR VAL ASP SEQRES 7 A 627 GLN VAL LEU GLN LEU VAL TYR LYS ASP GLY SER PRO CYS SEQRES 8 A 627 PRO SER LYS SER GLY LEU SER TYR LYS SER VAL ILE SER SEQRES 9 A 627 PHE VAL CYS ARG PRO GLU ALA GLY PRO THR ASN ARG PRO SEQRES 10 A 627 MET LEU ILE SER LEU ASP LYS GLN THR CYS THR LEU PHE SEQRES 11 A 627 PHE SER TRP HIS THR PRO LEU ALA CYS GLU GLN ALA THR SEQRES 12 A 627 GLU CYS SER VAL ARG ASN GLY SER SER ILE VAL ASP LEU SEQRES 13 A 627 SER PRO LEU ILE HIS ARG THR GLY GLY TYR GLU ALA TYR SEQRES 14 A 627 ASP GLU SER GLU ASP ASP ALA SER ASP THR ASN PRO ASP SEQRES 15 A 627 PHE TYR ILE ASN ILE CYS GLN PRO LEU ASN PRO MET HIS SEQRES 16 A 627 ALA VAL PRO CYS PRO ALA GLY ALA ALA VAL CYS LYS VAL SEQRES 17 A 627 PRO ILE ASP GLY PRO PRO ILE ASP ILE GLY ARG VAL ALA SEQRES 18 A 627 GLY PRO PRO ILE LEU ASN PRO ILE ALA ASN GLU ILE TYR SEQRES 19 A 627 LEU ASN PHE GLU SER SER THR PRO CYS LEU ALA ASP LYS SEQRES 20 A 627 HIS PHE ASN TYR THR SER LEU ILE ALA PHE HIS CYS LYS SEQRES 21 A 627 ARG GLY VAL SER MET GLY THR PRO LYS LEU LEU ARG THR SEQRES 22 A 627 SER GLU CYS ASP PHE VAL PHE GLU TRP GLU THR PRO VAL SEQRES 23 A 627 VAL CYS PRO ASP GLU VAL ARG MET ASP GLY CYS THR LEU SEQRES 24 A 627 THR ASP GLU GLN LEU LEU TYR SER PHE ASN LEU SER SER SEQRES 25 A 627 LEU SER THR SER THR PHE LYS VAL THR ARG ASP SER ARG SEQRES 26 A 627 THR TYR SER VAL GLY VAL CYS THR PHE ALA VAL GLY PRO SEQRES 27 A 627 GLU GLN GLY GLY CYS LYS ASP GLY GLY VAL CYS LEU LEU SEQRES 28 A 627 SER GLY THR LYS GLY ALA SER PHE GLY ARG LEU GLN SER SEQRES 29 A 627 MET LYS LEU ASP TYR ARG HIS GLN ASP GLU ALA VAL VAL SEQRES 30 A 627 LEU SER TYR VAL ASN GLY ASP ARG CYS PRO PRO GLU THR SEQRES 31 A 627 ASP ASP GLY VAL PRO CYS VAL PHE PRO PHE ILE PHE ASN SEQRES 32 A 627 GLY LYS SER TYR GLU GLU CYS ILE ILE GLU SER ARG ALA SEQRES 33 A 627 LYS LEU TRP CYS SER THR THR ALA ASP TYR ASP ARG ASP SEQRES 34 A 627 HIS GLU TRP GLY PHE CYS ARG HIS SER ASN SER TYR ARG SEQRES 35 A 627 THR SER SER ILE ILE PHE LYS CYS ASP GLU ASP GLU ASP SEQRES 36 A 627 ILE GLY ARG PRO GLN VAL PHE SER GLU VAL ARG GLY CYS SEQRES 37 A 627 ASP VAL THR PHE GLU TRP LYS THR LYS VAL VAL CYS PRO SEQRES 38 A 627 PRO LYS LYS LEU GLU CYS LYS PHE VAL GLN LYS HIS LYS SEQRES 39 A 627 THR TYR ASP LEU ARG LEU LEU SER SER LEU THR GLY SER SEQRES 40 A 627 TRP SER LEU VAL HIS ASN GLY VAL SER TYR TYR ILE ASN SEQRES 41 A 627 LEU CYS GLN LYS ILE TYR LYS GLY PRO LEU GLY CYS SER SEQRES 42 A 627 GLU ARG ALA SER ILE CYS ARG ARG THR THR THR GLY ASP SEQRES 43 A 627 VAL GLN VAL LEU GLY LEU VAL HIS THR GLN LYS LEU GLY SEQRES 44 A 627 VAL ILE GLY ASP LYS VAL VAL VAL THR TYR SER LYS GLY SEQRES 45 A 627 TYR PRO CYS GLY GLY ASN LYS THR ALA SER SER VAL ILE SEQRES 46 A 627 GLU LEU THR CYS THR LYS THR VAL GLY ARG PRO ALA PHE SEQRES 47 A 627 LYS ARG PHE ASP ILE ASP SER CYS THR TYR TYR PHE SER SEQRES 48 A 627 TRP ASP SER ARG ALA ALA CYS ALA VAL LYS HIS HIS HIS SEQRES 49 A 627 HIS HIS HIS MODRES 2V5O ASN A 1656 ASN GLYCOSYLATION SITE MODRES 2V5O ASN A 1757 ASN GLYCOSYLATION SITE MODRES 2V5O ASN A 1816 ASN GLYCOSYLATION SITE HET NAG A3129 14 HET NAG A3130 14 HET NAG A3131 14 HET CL A3132 1 HET CL A3133 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION 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 2 NAG 3(C8 H15 N O6) FORMUL 5 CL 2(CL 1-) HELIX 1 1 SER A 1530 SER A 1533 5 4 HELIX 2 2 PRO A 1643 CYS A 1646 5 4 HELIX 3 3 SER A 1664 LEU A 1666 5 3 HELIX 4 4 PRO A 1792 CYS A 1795 5 4 HELIX 5 5 SER A 1819 THR A 1822 5 4 HELIX 6 6 ASP A 1932 HIS A 1937 1 6 HELIX 7 7 VAL A 1985 CYS A 1987 5 3 HELIX 8 8 ARG A 2006 SER A 2009 5 4 HELIX 9 9 HIS A 2061 GLN A 2063 5 3 HELIX 10 10 ARG A 2122 CYS A 2125 5 4 SHEET 1 AA 2 GLN A1517 THR A1519 0 SHEET 2 AA 2 LEU A1526 ASP A1528 -1 O PHE A1527 N VAL A1518 SHEET 1 AB 4 PHE A1538 TYR A1542 0 SHEET 2 AB 4 GLY A1546 MET A1550 -1 O GLY A1546 N TYR A1542 SHEET 3 AB 4 VAL A1563 PHE A1567 -1 O CYS A1566 N TYR A1549 SHEET 4 AB 4 ILE A1572 LYS A1576 -1 N VAL A1574 O ALA A1565 SHEET 1 AC 5 LEU A1581 VAL A1584 0 SHEET 2 AC 5 VAL A1587 TYR A1592 -1 O VAL A1587 N VAL A1584 SHEET 3 AC 5 LYS A1607 CYS A1614 -1 O ILE A1610 N LEU A1590 SHEET 4 AC 5 THR A1635 THR A1642 1 O LEU A1636 N VAL A1609 SHEET 5 AC 5 PRO A1624 ASP A1630 -1 O MET A1625 N SER A1639 SHEET 1 AD 2 SER A1653 ASN A1656 0 SHEET 2 AD 2 SER A1659 ASP A1662 -1 O SER A1659 N ASN A1656 SHEET 1 AE 4 TYR A1673 ALA A1675 0 SHEET 2 AE 4 PHE A1690 ILE A1692 -1 O PHE A1690 N ALA A1675 SHEET 3 AE 4 VAL A1712 LYS A1714 -1 O CYS A1713 N TYR A1691 SHEET 4 AE 4 ILE A1722 GLY A1725 -1 O ILE A1722 N LYS A1714 SHEET 1 AF 5 ILE A1732 ASN A1734 0 SHEET 2 AF 5 GLU A1739 PHE A1744 -1 O TYR A1741 N ILE A1732 SHEET 3 AF 5 SER A1760 CYS A1766 -1 O SER A1760 N PHE A1744 SHEET 4 AF 5 PHE A1785 THR A1791 1 O PHE A1785 N LEU A1761 SHEET 5 AF 5 PRO A1775 ARG A1779 -1 O LYS A1776 N GLU A1788 SHEET 1 AG 2 CYS A1804 ASP A1808 0 SHEET 2 AG 2 TYR A1813 LEU A1817 -1 O PHE A1815 N LEU A1806 SHEET 1 AH 4 THR A1824 ARG A1829 0 SHEET 2 AH 4 ARG A1832 GLY A1837 -1 O ARG A1832 N ARG A1829 SHEET 3 AH 4 VAL A1855 LEU A1858 -1 O CYS A1856 N SER A1835 SHEET 4 AH 4 GLY A1863 SER A1865 -1 O ALA A1864 N LEU A1857 SHEET 1 AI 5 ARG A1868 ARG A1877 0 SHEET 2 AI 5 ALA A1882 VAL A1888 -1 O ALA A1882 N ARG A1877 SHEET 3 AI 5 THR A1950 CYS A1957 -1 O SER A1951 N TYR A1887 SHEET 4 AI 5 ASP A1976 THR A1983 1 O VAL A1977 N SER A1952 SHEET 5 AI 5 GLN A1967 VAL A1972 -1 O GLN A1967 N GLU A1980 SHEET 1 AJ 3 GLU A1896 ASP A1898 0 SHEET 2 AJ 3 TRP A1939 ARG A1943 -1 O ARG A1943 N GLU A1896 SHEET 3 AJ 3 LEU A1925 THR A1929 -1 O CYS A1927 N GLY A1940 SHEET 1 AK 2 PHE A1907 PHE A1909 0 SHEET 2 AK 2 LYS A1912 TYR A1914 -1 O LYS A1912 N PHE A1909 SHEET 1 AL 2 CYS A1994 GLN A1998 0 SHEET 2 AL 2 LYS A2001 LEU A2005 -1 O TYR A2003 N PHE A1996 SHEET 1 AM 4 TRP A2015 HIS A2019 0 SHEET 2 AM 4 VAL A2022 ILE A2026 -1 O VAL A2022 N HIS A2019 SHEET 3 AM 4 ALA A2043 ARG A2048 -1 N CYS A2046 O TYR A2025 SHEET 4 AM 4 VAL A2054 LEU A2059 -1 O GLY A2058 N SER A2044 SHEET 1 AN 5 LYS A2064 ILE A2068 0 SHEET 2 AN 5 LYS A2071 TYR A2076 -1 O LYS A2071 N ILE A2068 SHEET 3 AN 5 SER A2089 THR A2095 -1 O SER A2090 N TYR A2076 SHEET 4 AN 5 THR A2114 ASP A2120 1 O TYR A2115 N VAL A2091 SHEET 5 AN 5 PRO A2103 ASP A2109 -1 O ALA A2104 N SER A2118 SSBOND 1 CYS A 1516 CYS A 1553 1555 1555 2.04 SSBOND 2 CYS A 1559 CYS A 1566 1555 1555 2.04 SSBOND 3 CYS A 1598 CYS A 1634 1555 1555 2.03 SSBOND 4 CYS A 1614 CYS A 1646 1555 1555 2.04 SSBOND 5 CYS A 1652 CYS A 1695 1555 1555 2.03 SSBOND 6 CYS A 1706 CYS A 1713 1555 1555 2.04 SSBOND 7 CYS A 1750 CYS A 1783 1555 1555 2.03 SSBOND 8 CYS A 1766 CYS A 1795 1555 1555 2.03 SSBOND 9 CYS A 1804 CYS A 1839 1555 1555 2.04 SSBOND 10 CYS A 1850 CYS A 1856 1555 1555 2.04 SSBOND 11 CYS A 1893 CYS A 1975 1555 1555 2.05 SSBOND 12 CYS A 1903 CYS A 1927 1555 1555 2.03 SSBOND 13 CYS A 1917 CYS A 1942 1555 1555 2.03 SSBOND 14 CYS A 1957 CYS A 1987 1555 1555 2.03 SSBOND 15 CYS A 1994 CYS A 2029 1555 1555 2.03 SSBOND 16 CYS A 2039 CYS A 2046 1555 1555 2.04 SSBOND 17 CYS A 2082 CYS A 2113 1555 1555 2.03 SSBOND 18 CYS A 2096 CYS A 2125 1555 1555 2.03 LINK ND2 ASN A1656 C1 NAG A3131 1555 1555 1.45 LINK ND2 ASN A1757 C1 NAG A3130 1555 1555 1.45 LINK ND2 ASN A1816 C1 NAG A3129 1555 1555 1.44 CISPEP 1 PHE A 1905 PRO A 1906 0 -4.82 CRYST1 138.554 69.247 98.012 90.00 103.25 90.00 C 1 2 1 4 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 0.007217 0.000000 0.001699 0.00000 SCALE2 0.000000 0.014441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010482 0.00000