1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 RESIDUES PRO 36 AND PRO 42 ARE CIS PROLINES. Clore, G.M. Driscoll, P.C. Gronenborn, A.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking US Biochemistry BICHAW 0033 0006-2960 28 2188 2198 10.1021/bi00431a033 2566326 Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. 1989 US Biochemistry BICHAW 0033 0006-2960 28 2178 A Proton Nuclear Magnetic Resonance Study of the Antihypertensive and Antiviral Protein Bds-I from the Sea Anemone Anemonia Sulcata. Sequential and Stereospecific Resonance Assignment and Secondary Structure 1989 NE FEBS Lett. FEBLAL 0165 0014-5793 243 223 The Influence of Stereospecific Assignments on the Determination of Three-Dimensional Structures of Proteins by Nuclear Magnetic Resonance Spectroscopy. Application to the Sea Anemone Protein Bds-I 1989 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 4719.434 BDS-I 1 man polymer no no AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n snake-locks sea anemone Anemonia sample 6108 Anemonia sulcata pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_conf repository Initial release Version format compliance Version format compliance Derived calculations Other 1 0 1989-01-09 1 1 2008-03-24 1 2 2011-07-13 1 3 2017-11-29 _pdbx_database_status.process_site Y BNL 1988-11-14 REL 1 REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317-324 (1988)) USING THE PROGRAM XPLOR (A.T. BRUENGER, YALE UNIVERSITY, CT 06511). STRUCTURAL STATISTICS RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)* RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS) ALL 513 0.079 INTERRESIDUE SHORT RANGE 150 0.086 INTERRESIDUE LONG RANGE 105 0.100 INTRARESIDUE 234 0.065 HBOND *(2)* 24 0.043 POTENTIAL ENERGY TERMS TYPE ENERGY (KCAL/MOL) F(NOE) *(3)* 160 F(TOR) *(4)* 24 F(REPEL) *(5)* 72 LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS -117 KCAL/MOL. DEVIATIONS FROM IDEALIZED GEOMETRY *(6)* TYPE TOTAL NUMBER RMS DEVIATION BONDS 646 0.013 (ANGSTROMS) ANGLES 1157 2.517 (DEGREES) IMPROPERS 242 0.797 (DEGREES) NOTES. *(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS ARE CALCULATED WITH RESPECT TO THE UPPER AND LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN 0.5 ANGSTROMS. *(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO RESTRAINTS - R(NH-O) .LT. 2.3 ANGSTROMS AND R(N-O) .LT. 3.3 ANGSTROMS. THE LOWER LIMITS ARE GIVEN BY THE SUM OF THE VAN DER WAALS RADII OF THE RELEVANT ATOMS. *(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL F(NOE) ARE CALCULATED WITH A FORCE CONSTANT OF 50 KCAL/MOL/ANGSTROM**2. *(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO RESTRICT THE RANGES OF 23 PHI AND 21 CHI1 TORSION ANGLES, AND THE OMEGA PEPTIDE BOND TORSION ANGLES OF THE FIVE PROLINE RESIDUES (PRO 36 AND 42 BEING RESTRAINED TO THE CIS CONFORMATION AND THE OTHERS TO TRANS). *(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF 4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY FUNCTION. *(6)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION OF PROLINES) IN THE TRANS CONFORMATION. IN THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS, THE RESTRAINTS FOR THE DISULFIDE BRIDGES ARE INCLUDED IN THE BOND AND ANGLE TERMS. A TOTAL OF 42 STRUCTURES CONSISTENT WITH THE NMR DATA WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THESE 42 STRUCTURES ARE GIVEN IN THE PDB ENTRY *2BDS*. THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS ARE AVAILABLE IN THE PDB NMR RESTRAINT FILE. BRUNGER refinement XPLOR ALA 1 n 1 ALA 1 A ALA 2 n 2 ALA 2 A PRO 3 n 3 PRO 3 A CYS 4 n 4 CYS 4 A PHE 5 n 5 PHE 5 A CYS 6 n 6 CYS 6 A SER 7 n 7 SER 7 A GLY 8 n 8 GLY 8 A LYS 9 n 9 LYS 9 A PRO 10 n 10 PRO 10 A GLY 11 n 11 GLY 11 A ARG 12 n 12 ARG 12 A GLY 13 n 13 GLY 13 A ASP 14 n 14 ASP 14 A LEU 15 n 15 LEU 15 A TRP 16 n 16 TRP 16 A ILE 17 n 17 ILE 17 A LEU 18 n 18 LEU 18 A ARG 19 n 19 ARG 19 A GLY 20 n 20 GLY 20 A THR 21 n 21 THR 21 A CYS 22 n 22 CYS 22 A PRO 23 n 23 PRO 23 A GLY 24 n 24 GLY 24 A GLY 25 n 25 GLY 25 A TYR 26 n 26 TYR 26 A GLY 27 n 27 GLY 27 A TYR 28 n 28 TYR 28 A THR 29 n 29 THR 29 A SER 30 n 30 SER 30 A ASN 31 n 31 ASN 31 A CYS 32 n 32 CYS 32 A TYR 33 n 33 TYR 33 A LYS 34 n 34 LYS 34 A TRP 35 n 35 TRP 35 A PRO 36 n 36 PRO 36 A ASN 37 n 37 ASN 37 A ILE 38 n 38 ILE 38 A CYS 39 n 39 CYS 39 A CYS 40 n 40 CYS 40 A TYR 41 n 41 TYR 41 A PRO 42 n 42 PRO 42 A HIS 43 n 43 HIS 43 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A A ALA ALA 1 2 -149.71 1 A ARG 12 0.305 SIDE CHAIN 1 A ARG 19 0.200 SIDE CHAIN 1 5.00 0.80 106.30 111.30 A A A CD1 CG CD2 TRP TRP TRP 16 16 16 N 1 -7.25 1.00 110.10 102.85 A A A CG CD1 NE1 TRP TRP TRP 16 16 16 N 1 5.40 0.90 109.00 114.40 A A A CD1 NE1 CE2 TRP TRP TRP 16 16 16 N 1 10.13 1.10 130.40 140.53 A A A NE1 CE2 CZ2 TRP TRP TRP 16 16 16 N 1 -7.42 1.00 107.30 99.88 A A A NE1 CE2 CD2 TRP TRP TRP 16 16 16 N 1 -6.01 0.90 133.90 127.89 A A A CG CD2 CE3 TRP TRP TRP 16 16 16 N 1 -6.35 1.00 110.10 103.75 A A A CG CD1 NE1 TRP TRP TRP 35 35 35 N 1 9.40 1.10 130.40 139.80 A A A NE1 CE2 CZ2 TRP TRP TRP 35 35 35 N 1 -7.13 1.00 107.30 100.17 A A A NE1 CE2 CD2 TRP TRP TRP 35 35 35 N 1 A A CG CD2 TRP TRP 16 16 -0.129 0.017 1.432 1.303 N 1 A A CG CD2 TRP TRP 35 35 -0.114 0.017 1.432 1.318 N 1 A A CG ND1 HIS HIS 43 43 -0.125 0.015 1.369 1.244 N 1 A PRO 3 -78.66 20.70 1 A PRO 10 -67.48 -161.55 1 A ILE 17 -94.78 -153.52 1 A LEU 18 -67.72 78.73 1 A THR 29 -160.53 -38.20 1 A PRO 36 -78.66 39.10 model building X-PLOR refinement X-PLOR phasing X-PLOR BDS-I (NMR, MINIMIZED MEAN STRUCTURE) DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE ANTIHYPERTENSIVE AND ANTIVIRAL PROTEIN BDS-I FROM THE SEA ANEMONE ANEMONIA SULCATA. A STUDY USING NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING 1 Y N disulf 2.017 A CYS 4 A SG CYS 4 1_555 A CYS 39 A SG CYS 39 1_555 disulf 2.026 A CYS 6 A SG CYS 6 1_555 A CYS 32 A SG CYS 32 1_555 disulf 2.023 A CYS 22 A SG CYS 22 1_555 A CYS 40 A SG CYS 40 1_555 ANTI-HYPERTENSIVE, ANTI-VIRAL PROTEIN ANTI-HYPERTENSIVE, ANTI-VIRAL PROTEIN A TRP 35 A TRP 35 1 A PRO 36 A PRO 36 -7.56 A TYR 41 A TYR 41 1 A PRO 42 A PRO 42 6.48 BDS1_ANESU UNP 1 1 P11494 AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH 1 43 1BDS 1 43 P11494 A 1 1 43 3 anti-parallel anti-parallel A ASP 14 A ASP 14 A ILE 17 A ILE 17 A ASN 37 A ASN 37 A TYR 41 A TYR 41 A SER 30 A SER 30 A LYS 34 A LYS 34 1 P 1