10 20 30 40 50 60 70 80 2DCO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER MEMBRANE PROTEIN 11-JAN-06 2DCO
TITLE S1P4 FIRST EXTRACELLULAR LOOP PEPTIDOMIMETIC
COMPND MOL_ID: 1; COMPND 2 MOLECULE: S1P4 FIRST EXTRACELLULAR LOOP PEPTIDOMIMETIC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR LOOP 1; COMPND 5 SYNONYM: ARFAPTIN-2, ADP-RIBOSYLATION FACTOR-INTERACTING COMPND 6 PROTEIN 2, PARTNER OF RAC1, PROTEIN POR1PHINGOSINE 1- COMPND 7 PHOSPHATE RECEPTOR EDG-6, S1P RECEPTOR EDG-6, ENDOTHELIAL COMPND 8 DIFFERENTIATION G-PROTEIN COUPLED RECEPTOR 6, SPHINGOSINE COMPND 9 1-PHOSPHATE RECEPTOR 4, S1P4; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 OTHER_DETAILS: THIS PROTEIN IS A FUSION PROTEIN. RESIDUES COMPND 13 13-26 AND 29-30 ARE FROM THE FIRST EXTRACELLULAR LOOP OF COMPND 14 S1P4 RECEPTOR. THE REST, RESIDUES 3-12, 27-28, AND 31-34 COMPND 15 ARE FROM ARFATIN (PDB ENTRY 1I49) SEGMENTS 139-148, 164- COMPND 16 164, 168-171 OF 1I49 THAT WE DESIGNED TO BE IN THE COMPND 17 SEQUENCE.
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: S1P4; 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: PET-32A, CCE1A
KEYWDS COILED COIL, DISULFIDE, HELIX-TURN-HELIX, 3-10 HELIX, KEYWDS 2 MEMBRANE PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR T.C.T.PHAM,R.W.KRIWACKI,A.L.PARRILL
REVDAT 3 24-FEB-09 2DCO 1 VERSN REVDAT 2 19-JUN-07 2DCO 1 JRNL REVDAT 1 23-JAN-07 2DCO 0
JRNL AUTH T.C.T.PHAM,R.W.KRIWACKI,A.L.PARRILL JRNL TITL PEPTIDE DESIGN AND STRUCTURAL CHARACTERIZATION OF JRNL TITL 2 A GPCR LOOP MIMETIC JRNL REF BIOPOLYMERS V. 86 298 2007 JRNL REFN ISSN 0006-3525 JRNL PMID 17443712 JRNL DOI 10.1002/BIP.20745
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, AMBER 8.0 REMARK 3 AUTHORS : LINGE (ARIA), CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 748 NOE-DERIVED DISTANCE CONSTRAINTS
REMARK 4 REMARK 4 2DCO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-06. REMARK 100 THE RCSB ID CODE IS RCSB025257.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.06 MOL/KG REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM CCE1A U-15N; 10MM REMARK 210 PHOSPHATE BUFFER PH 6; 20% TFE REMARK 210 -D3, 0.025% NAN3; 3MM CCE1A U- REMARK 210 15N,13C; 10MM PHOSPHATE BUFFER REMARK 210 PH 6; 20% TFE-D3, 0.025% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 3.1, FELIX 98, CNS 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, MATRIX REMARK 210 RELAXATION, TORSION ANGLE REMARK 210 DYNAMICS, ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY.
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 5 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.5 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 1 TYR A 3 103.80 -40.01 REMARK 500 1 ASP A 4 42.26 33.97 REMARK 500 1 ALA A 5 9.12 58.67 REMARK 500 1 ARG A 20 -75.20 -130.15 REMARK 500 1 LEU A 21 -4.96 36.37 REMARK 500 1 ALA A 22 -50.81 -137.46 REMARK 500 1 SER A 27 -68.36 -133.44 REMARK 500 1 GLU A 30 -35.31 -151.35 REMARK 500 2 TYR A 3 106.56 -32.28 REMARK 500 2 ASP A 4 41.98 33.75 REMARK 500 2 ALA A 5 -0.67 56.04 REMARK 500 2 ARG A 20 -72.33 -133.31 REMARK 500 2 LEU A 21 -2.53 33.17 REMARK 500 2 ALA A 22 -48.15 -136.73 REMARK 500 2 GLN A 25 44.34 -74.02 REMARK 500 2 TRP A 26 14.01 -140.55 REMARK 500 2 SER A 27 -66.54 -133.63 REMARK 500 2 GLU A 30 -29.64 -145.47 REMARK 500 3 SER A 2 163.20 66.14 REMARK 500 3 ASP A 4 50.94 36.71 REMARK 500 3 ALA A 5 11.51 56.63 REMARK 500 3 CYS A 10 7.07 -62.29 REMARK 500 3 ARG A 20 -70.77 -132.63 REMARK 500 3 LEU A 21 -3.28 35.34 REMARK 500 3 ALA A 22 -47.28 -134.98 REMARK 500 3 GLN A 25 37.56 -72.20 REMARK 500 3 SER A 27 -76.89 -127.46 REMARK 500 3 GLU A 30 -40.45 -142.60 REMARK 500 3 PHE A 32 15.51 -144.28 REMARK 500 4 SER A 2 20.59 48.52 REMARK 500 4 TYR A 3 112.70 -35.48 REMARK 500 4 ASP A 4 41.28 34.00 REMARK 500 4 ALA A 5 13.66 57.85 REMARK 500 4 CYS A 10 6.57 -61.04 REMARK 500 4 ARG A 20 -75.83 -131.52 REMARK 500 4 LEU A 21 -2.08 35.69 REMARK 500 4 ALA A 22 -43.94 -139.80 REMARK 500 4 SER A 27 -70.40 -131.83 REMARK 500 4 GLU A 30 -31.25 -151.54 REMARK 500 4 PHE A 32 12.61 -144.14 REMARK 500 5 TYR A 3 104.45 -41.44 REMARK 500 5 ASP A 4 43.56 36.70 REMARK 500 5 ALA A 5 -21.67 59.97 REMARK 500 5 CYS A 10 6.11 -62.61 REMARK 500 5 ARG A 20 -66.68 -130.42 REMARK 500 5 LEU A 21 -5.10 34.48 REMARK 500 5 ALA A 22 -53.10 -135.75 REMARK 500 5 GLN A 25 44.36 -78.48 REMARK 500 5 SER A 27 -59.96 -129.01 REMARK 500 5 GLU A 30 -36.03 -151.20 REMARK 500 5 PHE A 32 11.33 -143.48 REMARK 500 6 TYR A 3 101.77 -37.86 REMARK 500 6 ASP A 4 44.47 31.47 REMARK 500 6 ALA A 5 6.93 59.33 REMARK 500 6 ARG A 20 -78.69 -128.48 REMARK 500 6 LEU A 21 -5.58 38.00 REMARK 500 6 ALA A 22 -49.99 -134.82 REMARK 500 6 GLN A 25 42.52 -72.73 REMARK 500 6 TRP A 26 20.12 -148.06 REMARK 500 6 SER A 27 -77.96 -129.96 REMARK 500 6 GLU A 30 -37.07 -150.00 REMARK 500 7 TYR A 3 108.91 -39.13 REMARK 500 7 ASP A 4 43.76 35.92 REMARK 500 7 ALA A 5 -27.68 57.24 REMARK 500 7 ARG A 20 -69.87 -130.87 REMARK 500 7 LEU A 21 -7.95 34.52 REMARK 500 7 ALA A 22 -51.63 -137.14 REMARK 500 7 GLN A 25 40.04 -79.40 REMARK 500 7 TRP A 26 28.47 -145.38 REMARK 500 7 SER A 27 -75.21 -136.31 REMARK 500 7 GLU A 30 -34.38 -152.04 REMARK 500 8 TYR A 3 106.36 -37.62 REMARK 500 8 ASP A 4 43.25 33.82 REMARK 500 8 ALA A 5 3.99 56.93 REMARK 500 8 ARG A 20 -76.88 -128.63 REMARK 500 8 LEU A 21 -4.73 37.00 REMARK 500 8 ALA A 22 -47.64 -140.44 REMARK 500 8 GLN A 25 46.57 -73.29 REMARK 500 8 TRP A 26 30.76 -147.58 REMARK 500 8 SER A 27 -82.61 -135.38 REMARK 500 8 GLU A 30 -41.11 -143.85 REMARK 500 8 PHE A 32 10.22 -143.61 REMARK 500 9 SER A 2 19.98 46.26 REMARK 500 9 TYR A 3 104.71 -32.84 REMARK 500 9 ASP A 4 45.34 33.74 REMARK 500 9 ALA A 5 10.78 57.42 REMARK 500 9 CYS A 10 -1.60 -58.08 REMARK 500 9 ARG A 20 -80.21 -127.82 REMARK 500 9 LEU A 21 -4.39 38.28 REMARK 500 9 ALA A 22 -47.87 -136.87 REMARK 500 9 GLN A 25 27.87 -71.38 REMARK 500 9 SER A 27 -71.45 -128.31 REMARK 500 9 GLU A 30 -35.01 -150.72 REMARK 500 10 TYR A 3 101.41 -37.51 REMARK 500 10 ASP A 4 40.84 35.91 REMARK 500 10 ALA A 5 8.60 59.08 REMARK 500 10 ARG A 20 -75.45 -131.66 REMARK 500 10 LEU A 21 -6.78 38.78 REMARK 500 10 ALA A 22 -45.12 -136.00 REMARK 500 10 GLN A 25 30.66 -70.74 REMARK 500 10 SER A 27 -74.78 -133.62 REMARK 500 10 GLU A 30 -43.84 -139.97 REMARK 500 10 PHE A 32 16.56 -141.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 1 SER A 2 2 141.83 REMARK 500 GLY A 1 SER A 2 4 149.49 REMARK 500 GLY A 1 SER A 2 5 143.59 REMARK 500 GLY A 1 SER A 2 7 144.71 REMARK 500 GLY A 1 SER A 2 8 148.16 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 4 TYR A 6 0.08 SIDE_CHAIN REMARK 500 8 TYR A 6 0.10 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 2DCO A 3 12 UNP P53365 ARFP2_HUMAN 235 244 DBREF 2DCO A 13 26 UNP O95977 EDG6_HUMAN 105 118 DBREF 2DCO A 27 28 UNP P53365 ARFP2_HUMAN 260 261 DBREF 2DCO A 29 30 UNP O95977 EDG6_HUMAN 121 122 DBREF 2DCO A 31 34 UNP P53365 ARFP2_HUMAN 264 267
SEQADV 2DCO GLY A 1 UNP P53365 CLONING ARTIFACT SEQADV 2DCO SER A 2 UNP P53365 CLONING ARTIFACT SEQADV 2DCO CYS A 10 UNP P53365 LEU 241 ENGINEERED SEQADV 2DCO CYS A 28 UNP P53365 ALA 261 ENGINEERED
SEQRES 1 A 34 GLY SER TYR ASP ALA TYR ARG THR ASP CYS GLU GLU LEU SEQRES 2 A 34 SER GLY ALA ARG THR PHE ARG LEU ALA PRO ALA GLN TRP SEQRES 3 A 34 SER CYS ARG GLU THR PHE GLN ALA
HELIX 1 1 SER A 2 ALA A 5 5 4 HELIX 2 2 TYR A 6 GLY A 15 1 10 HELIX 3 3 ALA A 16 ARG A 20 5 5 HELIX 4 4 SER A 27 PHE A 32 1 6
SSBOND 1 CYS A 10 CYS A 28 1555 1555 2.03
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000