PDB Short entry for 3C59 HEADER SIGNALING PROTEIN/SIGNALING PROTEIN 31-JAN-08 3C59 TITLE CRYSTAL STRUCTURE OF THE LIGAND-BOUND GLUCAGON-LIKE PEPTIDE-1 RECEPTOR TITLE 2 EXTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCAGON-LIKE PEPTIDE 1 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL EXTRACELLULAR DOMAIN, UNP RESIDUES 24-145; COMPND 5 SYNONYM: GLP-1 RECEPTOR, GLP-1-R, GLP-1R; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: EXENDIN-4; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 56-86; COMPND 11 SYNONYM: EXENATIDE; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GLUCAGON-LIKE PEPTIDE-1 RECEPTOR(GLP1R); SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS PEPTIDE HAS BEEN CHEMICALLY SYNTHESIZED; THIS SOURCE 14 SEQUENCE OCCURS NATURALLY IN HELODERMA SUSPECTUM. KEYWDS LIGAND-BOUND G PROTEIN-COUPLED RECEPTOR, G-PROTEIN COUPLED RECEPTOR, KEYWDS 2 GLYCOPROTEIN, MEMBRANE, TRANSDUCER, TRANSMEMBRANE, AMIDATION, KEYWDS 3 CLEAVAGE ON PAIR OF BASIC RESIDUES, SECRETED, SIGNALING PROTEIN- KEYWDS 4 SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.RUNGE REVDAT 5 23-MAY-18 3C59 1 REMARK REVDAT 4 13-JUL-11 3C59 1 VERSN REVDAT 3 24-FEB-09 3C59 1 VERSN REVDAT 2 06-MAY-08 3C59 1 JRNL REVDAT 1 19-FEB-08 3C59 0 JRNL AUTH S.RUNGE,H.THOGERSEN,K.MADSEN,J.LAU,R.RUDOLPH JRNL TITL CRYSTAL STRUCTURE OF THE LIGAND-BOUND GLUCAGON-LIKE JRNL TITL 2 PEPTIDE-1 RECEPTOR EXTRACELLULAR DOMAIN JRNL REF J.BIOL.CHEM. V. 283 11340 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18287102 JRNL DOI 10.1074/JBC.M708740200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0040 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 12615 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 658 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 914 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1059 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 105 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) : 54.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.491 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1130 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1539 ; 1.994 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 128 ;19.764 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;34.747 ;23.929 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 171 ;17.264 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;15.888 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 157 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 865 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 479 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 748 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 98 ; 0.164 ; 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): 24 ; 0.206 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.253 ; 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): 669 ; 1.398 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1050 ; 2.078 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 553 ; 2.960 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 489 ; 4.576 ; 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 : 2 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 29 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2190 49.0430 7.3580 REMARK 3 T TENSOR REMARK 3 T11: -0.2040 T22: -0.2406 REMARK 3 T33: -0.2602 T12: 0.0312 REMARK 3 T13: -0.0438 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 1.6888 L22: 3.8775 REMARK 3 L33: 5.0338 L12: 0.5820 REMARK 3 L13: 1.0861 L23: -1.3784 REMARK 3 S TENSOR REMARK 3 S11: -0.3038 S12: -0.0492 S13: 0.1225 REMARK 3 S21: -0.0338 S22: 0.1273 S23: 0.1824 REMARK 3 S31: -0.6874 S32: -0.0872 S33: 0.1764 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 : B 9 B 35 REMARK 3 ORIGIN FOR THE GROUP (A): -13.0260 34.4990 7.1020 REMARK 3 T TENSOR REMARK 3 T11: -0.3904 T22: -0.1280 REMARK 3 T33: -0.1648 T12: -0.1292 REMARK 3 T13: -0.0270 T23: 0.1154 REMARK 3 L TENSOR REMARK 3 L11: 3.5734 L22: 32.9234 REMARK 3 L33: 6.8451 L12: 5.6583 REMARK 3 L13: 3.5320 L23: 3.9685 REMARK 3 S TENSOR REMARK 3 S11: -0.0318 S12: -0.1565 S13: 0.1944 REMARK 3 S21: 0.0295 S22: 0.4030 S23: 1.1760 REMARK 3 S31: 0.2179 S32: -0.9370 S33: -0.3711 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 3C59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-06 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 : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9782, 0.9790, 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13273 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.5, 0.1M MGCL2, 0.4M REMARK 280 MGTARTRATE, 9MM N-DECYL-BETA-D-THIOMALTOSIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 29.18333 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 58.36667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.36667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.18333 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: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 ARG A 24 REMARK 465 PRO A 25 REMARK 465 GLN A 26 REMARK 465 GLY A 27 REMARK 465 ALA A 28 REMARK 465 GLY A 132 REMARK 465 GLU A 133 REMARK 465 ARG A 134 REMARK 465 SER A 135 REMARK 465 SER A 136 REMARK 465 PRO A 137 REMARK 465 GLU A 138 REMARK 465 GLU A 139 REMARK 465 GLN A 140 REMARK 465 LEU A 141 REMARK 465 LEU A 142 REMARK 465 PHE A 143 REMARK 465 LEU A 144 REMARK 465 TYR A 145 REMARK 465 PRO B 36 REMARK 465 PRO B 37 REMARK 465 PRO B 38 REMARK 465 SER B 39 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 ARG A 131 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 222 O HOH A 223 3564 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN A 97 N - CA - C ANGL. DEV. = 20.6 DEGREES REMARK 500 ALA A 106 N - CA - C ANGL. DEV. = 17.7 DEGREES REMARK 500 GLU A 107 C - N - CA ANGL. DEV. = 15.3 DEGREES REMARK 500 LEU A 123 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 61 149.09 -171.90 REMARK 500 ARG A 64 153.80 -48.14 REMARK 500 GLU A 68 -19.48 90.54 REMARK 500 GLU A 107 -51.50 129.05 REMARK 500 GLN A 112 -73.26 -115.94 REMARK 500 LYS A 113 -73.60 164.89 REMARK 500 ASN A 115 47.86 -148.52 REMARK 500 SER A 116 -164.47 -115.92 REMARK 500 SER A 117 -173.29 -54.22 REMARK 500 LEU A 118 125.29 89.61 REMARK 500 LYS A 130 -152.05 -66.93 REMARK 500 SER B 33 -81.68 -126.95 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 PRO A 96 GLN A 97 134.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 10M A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C5T RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH THE NATIVE LIGAND EXENDIN-4(9-39) DBREF 3C59 A 24 145 UNP P43220 GLP1R_HUMAN 24 145 DBREF 3C59 B 9 39 UNP P26349 EXE4_HELSU 56 86 SEQADV 3C59 MSE B 21 UNP P26349 LEU 68 MODIFIED RESIDUE SEQRES 1 A 122 ARG PRO GLN GLY ALA THR VAL SER LEU TRP GLU THR VAL SEQRES 2 A 122 GLN LYS TRP ARG GLU TYR ARG ARG GLN CYS GLN ARG SER SEQRES 3 A 122 LEU THR GLU ASP PRO PRO PRO ALA THR ASP LEU PHE CYS SEQRES 4 A 122 ASN ARG THR PHE ASP GLU TYR ALA CYS TRP PRO ASP GLY SEQRES 5 A 122 GLU PRO GLY SER PHE VAL ASN VAL SER CYS PRO TRP TYR SEQRES 6 A 122 LEU PRO TRP ALA SER SER VAL PRO GLN GLY HIS VAL TYR SEQRES 7 A 122 ARG PHE CYS THR ALA GLU GLY LEU TRP LEU GLN LYS ASP SEQRES 8 A 122 ASN SER SER LEU PRO TRP ARG ASP LEU SER GLU CYS GLU SEQRES 9 A 122 GLU SER LYS ARG GLY GLU ARG SER SER PRO GLU GLU GLN SEQRES 10 A 122 LEU LEU PHE LEU TYR SEQRES 1 B 31 ASP LEU SER LYS GLN MSE GLU GLU GLU ALA VAL ARG MSE SEQRES 2 B 31 PHE ILE GLU TRP LEU LYS ASN GLY GLY PRO SER SER GLY SEQRES 3 B 31 ALA PRO PRO PRO SER MODRES 3C59 MSE B 14 MET SELENOMETHIONINE MODRES 3C59 MSE B 21 MET SELENOMETHIONINE HET MSE B 14 8 HET MSE B 21 8 HET 10M A 1 33 HETNAM MSE SELENOMETHIONINE HETNAM 10M DECYL 4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D- HETNAM 2 10M GLUCOPYRANOSIDE HETSYN 10M (2R,3R,4S,5S,6R)-2-((2R,3S,4R,5R,6S)-6-DECYLSULFANYL-4, HETSYN 2 10M 5-DIHYDROXY-2-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3-YLOXY)- HETSYN 3 10M 6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL, N-DECYL- HETSYN 4 10M BETA-D-THIOMALTOSIDE FORMUL 2 MSE 2(C5 H11 N O2 SE) FORMUL 3 10M C22 H42 O10 S FORMUL 4 HOH *105(H2 O) HELIX 1 1 SER A 31 ASP A 53 1 23 HELIX 2 2 TRP A 91 VAL A 95 5 5 HELIX 3 3 LEU A 123 GLU A 127 5 5 HELIX 4 4 ASP B 9 ASN B 28 1 20 SHEET 1 A 2 THR A 65 PHE A 66 0 SHEET 2 A 2 CYS A 71 TRP A 72 -1 O TRP A 72 N THR A 65 SHEET 1 B 2 SER A 79 SER A 84 0 SHEET 2 B 2 HIS A 99 CYS A 104 -1 O CYS A 104 N SER A 79 SSBOND 1 CYS A 46 CYS A 71 1555 1555 2.17 SSBOND 2 CYS A 62 CYS A 104 1555 1555 2.07 SSBOND 3 CYS A 85 CYS A 126 1555 1555 2.03 LINK C GLN B 13 N MSE B 14 1555 1555 1.34 LINK C MSE B 14 N GLU B 15 1555 1555 1.33 LINK C ARG B 20 N MSE B 21 1555 1555 1.35 LINK C MSE B 21 N PHE B 22 1555 1555 1.33 CISPEP 1 ALA A 106 GLU A 107 0 -18.16 CISPEP 2 LYS A 113 ASP A 114 0 -26.53 CISPEP 3 ASN A 115 SER A 116 0 10.62 SITE 1 AC1 7 ARG A 43 PHE A 80 ASN A 82 HIS A 99 SITE 2 AC1 7 TYR A 101 HOH A 155 HOH A 222 CRYST1 75.850 75.850 87.550 90.00 90.00 120.00 P 31 2 1 6 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 0.013184 0.007612 0.000000 0.00000 SCALE2 0.000000 0.015223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011422 0.00000