10 20 30 40 50 60 70 80 2I85 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN 01-SEP-06 2I85
TITLE NMR SOLUTION STRUCTURE OF HUMAN EPHRINB2 ECTODOMAIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN-B2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN, RESIDUES 1-142; COMPND 5 SYNONYM: EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5, COMPND 6 LERK-5, HTK LIGAND, HTK-L; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: HELA CELLS; 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
KEYWDS EPHRINB2 ECTODOMAIN, NMR SOLUTION STRUCTURE, SIGNALING KEYWDS 2 PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR X.RAN,J.FAN,J.SONG
REVDAT 2 24-FEB-09 2I85 1 VERSN REVDAT 1 04-SEP-07 2I85 0
JRNL AUTH X.RAN,J.FAN,J.SONG JRNL TITL NMR SOLUTION STRUCTURE OF HUMAN EPHRINB2 ECTODOMAIN JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE DA ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2I85 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-06. REMARK 100 THE RCSB ID CODE IS RCSB039257.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 293 REMARK 210 PH : NULL; NULL REMARK 210 IONIC STRENGTH : 6.8; 6.8 REMARK 210 PRESSURE : 1ATM; 1ATM REMARK 210 SAMPLE CONTENTS : 0.5MM EPHRINB2 ECTODOMAIN U- REMARK 210 15N,13C; 20MM PHOSPHATE REMARK 210 BUFFER(PH 6.8); 90% H2O, 10% REMARK 210 D2O; 0.5MM EPHRINB2 ECTODOMAIN REMARK 210 U-15N,13C; 20MM PHOSPHATE REMARK 210 BUFFER(PH 6.8); 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-EDITED HSQC-TOCSY, 15N- REMARK 210 EDITED HSQC-NOESY, HNCACB, REMARK 210 CBCA(CO)NH, HNCO, 13C-NOESY, REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRPIPE, NMRVIEW REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNTION LESS THAN 2 REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL
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: 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 SER A 3 73.49 -155.26 REMARK 500 1 TYR A 10 70.05 -116.71 REMARK 500 1 TRP A 11 -59.04 77.29 REMARK 500 1 ASN A 12 64.40 -166.68 REMARK 500 1 LEU A 19 68.65 36.30 REMARK 500 1 LYS A 40 158.53 62.12 REMARK 500 1 ASP A 42 -87.59 -159.94 REMARK 500 1 GLN A 48 76.82 51.41 REMARK 500 1 THR A 72 -45.04 -176.73 REMARK 500 1 ASN A 76 -65.85 83.48 REMARK 500 1 CYS A 77 93.45 166.83 REMARK 500 1 PRO A 80 49.15 -76.83 REMARK 500 1 ASP A 81 -19.03 -161.37 REMARK 500 1 GLN A 82 -143.83 57.79 REMARK 500 1 THR A 131 -62.71 -139.39 REMARK 500 1 ALA A 133 92.51 53.56 REMARK 500 1 MET A 134 72.59 -112.31 REMARK 500 2 SER A 3 -39.73 -150.58 REMARK 500 2 ILE A 4 -55.36 -142.62 REMARK 500 2 VAL A 5 93.51 57.97 REMARK 500 2 TYR A 10 56.96 -115.58 REMARK 500 2 TRP A 11 -58.02 65.38 REMARK 500 2 SER A 13 -34.08 72.85 REMARK 500 2 SER A 14 -166.24 54.77 REMARK 500 2 PHE A 18 55.78 37.53 REMARK 500 2 LEU A 19 72.66 52.21 REMARK 500 2 ILE A 30 98.39 -60.53 REMARK 500 2 ASP A 42 -100.53 -150.51 REMARK 500 2 THR A 45 45.94 -153.65 REMARK 500 2 VAL A 46 -33.24 -39.66 REMARK 500 2 ASN A 76 60.84 -109.30 REMARK 500 2 CYS A 77 35.21 -69.07 REMARK 500 2 GLN A 91 109.29 -41.82 REMARK 500 2 GLU A 92 -71.60 -80.60 REMARK 500 2 ASN A 105 29.49 47.75 REMARK 500 2 THR A 113 72.65 -106.97 REMARK 500 2 GLN A 124 29.56 -65.22 REMARK 500 2 THR A 131 -45.51 -144.39 REMARK 500 2 ALA A 133 92.38 70.27 REMARK 500 3 SER A 3 113.93 -162.33 REMARK 500 3 VAL A 5 105.76 57.94 REMARK 500 3 TRP A 11 -49.29 71.05 REMARK 500 3 LEU A 19 66.47 35.34 REMARK 500 3 ASP A 42 -56.94 -172.00 REMARK 500 3 THR A 72 -47.30 178.94 REMARK 500 3 LEU A 75 -157.93 -135.37 REMARK 500 3 ASN A 76 -67.99 76.43 REMARK 500 3 CYS A 77 78.20 -168.97 REMARK 500 3 LYS A 79 161.71 61.85 REMARK 500 3 ASP A 81 87.27 -153.18 REMARK 500 3 GLU A 92 -63.21 177.86 REMARK 500 3 LEU A 97 32.34 -81.34 REMARK 500 3 GLN A 124 22.12 -68.35 REMARK 500 3 THR A 131 -53.17 -141.16 REMARK 500 3 ALA A 133 72.02 52.71 REMARK 500 3 MET A 134 76.72 -102.45 REMARK 500 4 SER A 3 -39.28 -148.10 REMARK 500 4 ILE A 4 -43.04 -141.57 REMARK 500 4 VAL A 5 95.11 56.27 REMARK 500 4 TRP A 11 22.34 43.13 REMARK 500 4 ASN A 12 33.79 -93.97 REMARK 500 4 SER A 13 -51.41 65.50 REMARK 500 4 PHE A 18 96.45 -63.73 REMARK 500 4 LEU A 19 -60.15 -159.62 REMARK 500 4 VAL A 41 117.83 63.94 REMARK 500 4 ASP A 42 -57.38 -173.32 REMARK 500 4 THR A 45 -14.69 64.51 REMARK 500 4 GLN A 48 105.32 73.04 REMARK 500 4 CYS A 65 66.61 67.03 REMARK 500 4 THR A 72 -50.40 162.83 REMARK 500 4 PRO A 73 35.81 -80.18 REMARK 500 4 CYS A 77 57.67 -61.10 REMARK 500 4 ALA A 78 -71.34 -165.22 REMARK 500 4 LYS A 79 170.91 53.89 REMARK 500 4 ASP A 81 66.05 -159.22 REMARK 500 4 ASN A 96 24.09 -159.52 REMARK 500 4 SER A 117 155.30 -49.24 REMARK 500 4 ASP A 122 -34.64 -133.10 REMARK 500 4 CYS A 129 -33.86 -39.93 REMARK 500 4 THR A 131 -47.95 -141.91 REMARK 500 4 MET A 134 83.55 -66.63 REMARK 500 5 SER A 3 78.79 48.01 REMARK 500 5 VAL A 5 97.78 62.51 REMARK 500 5 GLU A 7 159.14 173.92 REMARK 500 5 TRP A 11 -69.70 71.92 REMARK 500 5 ASN A 12 -32.65 -176.18 REMARK 500 5 PHE A 18 57.69 39.48 REMARK 500 5 VAL A 41 112.61 70.17 REMARK 500 5 ASP A 42 -77.35 -168.31 REMARK 500 5 THR A 45 -77.78 -114.84 REMARK 500 5 VAL A 46 -36.41 -171.87 REMARK 500 5 GLN A 48 34.86 -159.31 REMARK 500 5 GLU A 50 -176.15 65.78 REMARK 500 5 THR A 72 -47.36 -176.56 REMARK 500 5 ASN A 76 61.45 -69.84 REMARK 500 5 ALA A 78 -24.71 70.68 REMARK 500 5 LYS A 79 -175.01 50.32 REMARK 500 5 ASP A 81 53.09 -159.80 REMARK 500 5 PHE A 90 44.37 -72.35 REMARK 500 5 GLN A 91 97.15 -176.56 REMARK 500 5 GLU A 92 75.37 -156.08 REMARK 500 5 ASN A 96 33.77 -151.26 REMARK 500 5 SER A 117 153.34 -48.13 REMARK 500 5 THR A 131 20.82 -143.84 REMARK 500 5 ARG A 132 -34.56 -146.79 REMARK 500 6 SER A 3 -77.48 -66.80 REMARK 500 6 ILE A 4 -47.19 -147.64 REMARK 500 6 VAL A 5 82.37 35.26 REMARK 500 6 TYR A 10 63.84 -106.49 REMARK 500 6 TRP A 11 -47.39 64.77 REMARK 500 6 ASN A 12 97.72 -44.47 REMARK 500 6 SER A 14 37.67 -57.51 REMARK 500 6 VAL A 41 109.71 -42.33 REMARK 500 6 ASP A 42 -60.69 168.44 REMARK 500 6 GLN A 48 54.20 -61.71 REMARK 500 6 TYR A 49 -64.29 -98.05 REMARK 500 6 GLU A 50 -70.62 -179.46 REMARK 500 6 VAL A 57 148.44 -171.28 REMARK 500 6 ASN A 71 177.36 -58.66 REMARK 500 6 ALA A 78 101.72 56.35 REMARK 500 6 LYS A 79 -51.37 179.47 REMARK 500 6 PHE A 90 100.53 -49.37 REMARK 500 6 ASN A 96 114.12 -166.23 REMARK 500 6 SER A 117 174.23 -55.32 REMARK 500 6 GLN A 124 32.06 -165.23 REMARK 500 6 THR A 131 -43.86 -138.68 REMARK 500 7 ILE A 4 -39.30 -150.37 REMARK 500 7 VAL A 5 77.38 32.40 REMARK 500 7 SER A 13 -159.48 -134.05 REMARK 500 7 PHE A 18 65.96 35.11 REMARK 500 7 ASP A 42 -95.59 164.56 REMARK 500 7 THR A 45 -71.77 -79.73 REMARK 500 7 VAL A 46 -37.05 -175.00 REMARK 500 7 GLN A 48 70.06 -161.75 REMARK 500 7 TYR A 49 -40.52 -29.14 REMARK 500 7 GLU A 50 59.04 33.12 REMARK 500 7 ASN A 71 171.48 -56.23 REMARK 500 7 THR A 72 -50.36 -175.26 REMARK 500 7 LEU A 75 -130.77 -147.78 REMARK 500 7 ASN A 76 -75.81 73.34 REMARK 500 7 CYS A 77 80.91 -164.70 REMARK 500 7 LYS A 79 77.05 35.32 REMARK 500 7 ASP A 81 15.14 -157.21 REMARK 500 7 LEU A 97 -17.43 64.34 REMARK 500 7 THR A 131 -52.46 -145.95 REMARK 500 8 VAL A 5 86.80 53.39 REMARK 500 8 GLU A 7 56.43 36.55 REMARK 500 8 TRP A 11 -43.59 67.78 REMARK 500 8 PHE A 18 65.37 37.14 REMARK 500 8 ASP A 42 -68.33 -160.39 REMARK 500 8 GLN A 48 -18.76 -160.85 REMARK 500 8 TYR A 49 -153.73 -126.18 REMARK 500 8 CYS A 77 76.54 -54.59 REMARK 500 8 PRO A 80 -84.36 -76.81 REMARK 500 8 ASP A 81 27.98 -165.37 REMARK 500 8 PHE A 90 104.39 -47.67 REMARK 500 8 LEU A 97 114.92 63.92 REMARK 500 8 TRP A 98 2.11 -68.44 REMARK 500 8 SER A 117 150.21 -47.88 REMARK 500 8 ASP A 122 -7.62 -58.19 REMARK 500 8 ASN A 123 170.31 65.14 REMARK 500 8 THR A 131 -46.63 -150.94 REMARK 500 9 ILE A 4 -46.80 -147.25 REMARK 500 9 VAL A 5 94.14 59.96 REMARK 500 9 TYR A 10 54.66 -95.44 REMARK 500 9 TRP A 11 -67.37 63.49 REMARK 500 9 ASN A 12 174.60 179.11 REMARK 500 9 SER A 13 127.11 78.01 REMARK 500 9 SER A 14 25.79 44.78 REMARK 500 9 PHE A 18 94.77 -61.24 REMARK 500 9 LEU A 19 93.83 -35.93 REMARK 500 9 ASP A 42 -81.59 -174.14 REMARK 500 9 VAL A 46 -2.57 59.79 REMARK 500 9 TYR A 49 -73.48 -68.75 REMARK 500 9 GLU A 50 -173.92 -178.26 REMARK 500 9 ARG A 64 -80.81 -85.77 REMARK 500 9 CYS A 65 -35.30 144.88 REMARK 500 9 PRO A 73 88.43 -65.68 REMARK 500 9 ALA A 78 153.80 57.85 REMARK 500 9 LYS A 79 -47.36 139.39 REMARK 500 9 PRO A 80 -107.83 -77.95 REMARK 500 9 ASP A 81 26.80 -160.06 REMARK 500 9 GLN A 91 -153.34 -165.38 REMARK 500 9 ASP A 122 -31.21 -142.12 REMARK 500 9 THR A 131 -50.46 -142.96 REMARK 500 9 MET A 134 86.58 -68.96 REMARK 500 10 ILE A 4 -129.72 -71.21 REMARK 500 10 VAL A 5 97.34 -169.33 REMARK 500 10 GLU A 7 82.55 -154.92 REMARK 500 10 TRP A 11 44.93 -71.29 REMARK 500 10 SER A 13 80.49 54.17 REMARK 500 10 SER A 14 97.67 73.49 REMARK 500 10 PHE A 18 51.77 27.10 REMARK 500 10 LEU A 19 97.58 -39.42 REMARK 500 10 LYS A 40 31.32 -143.45 REMARK 500 10 VAL A 41 153.06 71.48 REMARK 500 10 ASP A 42 -79.63 -178.59 REMARK 500 10 THR A 45 4.96 55.33 REMARK 500 10 VAL A 46 52.30 -150.83 REMARK 500 10 GLU A 50 -174.88 -68.79 REMARK 500 10 THR A 72 -48.02 -173.67 REMARK 500 10 LEU A 74 -62.76 -160.36 REMARK 500 10 PRO A 80 39.91 -78.20 REMARK 500 10 ASP A 81 -19.36 -163.43 REMARK 500 10 GLN A 82 -155.54 63.30 REMARK 500 10 ASN A 96 53.26 -159.20 REMARK 500 10 LYS A 104 -174.83 -68.02 REMARK 500 10 THR A 113 35.09 -140.46 REMARK 500 10 ASP A 122 0.57 -65.26 REMARK 500 10 ASN A 123 172.59 64.61 REMARK 500 10 THR A 131 40.28 -140.65 REMARK 500 10 ARG A 132 -46.01 -163.27 REMARK 500 10 ALA A 133 79.76 62.38 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 1 TYR A 55 0.08 SIDE_CHAIN REMARK 500 2 TYR A 108 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IKO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SAME PROTEIN FROM MOUSE
DBREF 2I85 A 1 142 UNP P52799 EFNB2_HUMAN 25 166
SEQRES 1 A 142 SER LYS SER ILE VAL LEU GLU PRO ILE TYR TRP ASN SER SEQRES 2 A 142 SER ASN SER LYS PHE LEU PRO GLY GLN GLY LEU VAL LEU SEQRES 3 A 142 TYR PRO GLN ILE GLY ASP LYS LEU ASP ILE ILE CYS PRO SEQRES 4 A 142 LYS VAL ASP SER LYS THR VAL GLY GLN TYR GLU TYR TYR SEQRES 5 A 142 LYS VAL TYR MET VAL ASP LYS ASP GLN ALA ASP ARG CYS SEQRES 6 A 142 THR ILE LYS LYS GLU ASN THR PRO LEU LEU ASN CYS ALA SEQRES 7 A 142 LYS PRO ASP GLN ASP ILE LYS PHE THR ILE LYS PHE GLN SEQRES 8 A 142 GLU PHE SER PRO ASN LEU TRP GLY LEU GLU PHE GLN LYS SEQRES 9 A 142 ASN LYS ASP TYR TYR ILE ILE SER THR SER ASN GLY SER SEQRES 10 A 142 LEU GLU GLY LEU ASP ASN GLN GLU GLY GLY VAL CYS GLN SEQRES 11 A 142 THR ARG ALA MET LYS ILE LEU MET LYS VAL GLY GLN
HELIX 1 1 ASP A 58 CYS A 65 1 8 HELIX 2 2 SER A 117 LEU A 121 5 5
SHEET 1 A 3 LEU A 6 TYR A 10 0 SHEET 2 A 3 LYS A 33 CYS A 38 1 O LYS A 33 N LEU A 6 SHEET 3 A 3 ILE A 84 LYS A 89 -1 O ILE A 88 N LEU A 34 SHEET 1 B 5 GLY A 23 LEU A 26 0 SHEET 2 B 5 LYS A 135 VAL A 140 1 O LEU A 137 N LEU A 26 SHEET 3 B 5 LYS A 106 ILE A 111 -1 N ILE A 110 O ILE A 136 SHEET 4 B 5 TYR A 52 MET A 56 -1 N TYR A 55 O ILE A 111 SHEET 5 B 5 LEU A 75 CYS A 77 -1 O CYS A 77 N TYR A 52
SSBOND 1 CYS A 38 CYS A 77 1555 1555 2.01 SSBOND 2 CYS A 65 CYS A 129 1555 1555 2.02
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