PDB Short entry for 2DCO HEADER 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 PROTEIN 2, COMPND 6 PARTNER OF RAC1, PROTEIN POR1PHINGOSINE 1-PHOSPHATE RECEPTOR EDG-6, COMPND 7 S1P RECEPTOR EDG-6, ENDOTHELIAL DIFFERENTIATION G-PROTEIN COUPLED COMPND 8 RECEPTOR 6, SPHINGOSINE 1-PHOSPHATE RECEPTOR 4, S1P4; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 OTHER_DETAILS: THIS PROTEIN IS A FUSION PROTEIN. RESIDUES 13-26 AND COMPND 12 29-30 ARE FROM THE FIRST EXTRACELLULAR LOOP OF S1P4 RECEPTOR. THE COMPND 13 REST, RESIDUES 3-12, 27-28, AND 31-34 ARE FROM ARFATIN (PDB ENTRY COMPND 14 1I49) SEGMENTS 139-148, 164-164, 168-171 OF 1I49 THAT WE DESIGNED TO COMPND 15 BE IN THE 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, MEMBRANE KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.C.T.PHAM,R.W.KRIWACKI,A.L.PARRILL REVDAT 4 10-NOV-21 2DCO 1 REMARK SEQADV 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 A GPCR JRNL TITL 2 LOOP MIMETIC JRNL REF BIOPOLYMERS V. 86 298 2007 JRNL REFN ISSN 0006-3525 JRNL PMID 17443712 JRNL DOI 10.1002/BIP.20745 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 3.1, ARIA 1.2, AMBER 8.0 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), LINGE (ARIA), CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 748 NOE-DERIVED REMARK 3 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 13-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000025257. 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 PHOSPHATE REMARK 210 BUFFER PH 6; 20% TFE-D3, 0.025% REMARK 210 NAN3; 3MM CCE1A U-15N,13C; 10MM REMARK 210 PHOSPHATE BUFFER PH 6; 20% TFE- REMARK 210 D3, 0.025% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -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 : 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 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OD1 ASP A 9 HG SER A 27 1.50 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 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 REMARK 500 THIS ENTRY HAS 103 RAMACHANDRAN OUTLIERS. 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 MUTATION SEQADV 2DCO CYS A 28 UNP P53365 ALA 261 ENGINEERED MUTATION 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