1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Phan Chan Du, A. Limal, D. Semetey, V. Dali, H. Jolivet, M. Desgranges, C. Cung, M.T. Briand, J.P. Petit, M.C. Muller, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE 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 C3 H8 N2 O2 104.108 n DIAMINOPROPANOIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE 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 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 323 503 521 10.1016/S0022-2836(02)00701-5 12381305 Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein. 2002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1373.556 Transmembrane protein gp41 1 syn polymer TM, Glycoprotein 41, gp41 no yes (ACE)IWG(DPP)SGKLIDTTA XIWGASGKLIDTTA A polypeptide(L) n n n n n n n n n n n n n n database_PDB_caveat pdbx_struct_assembly pdbx_struct_assembly_prop pdbx_struct_oper_list pdbx_validate_polymer_linkage atom_site cell chem_comp database_PDB_caveat diffrn diffrn_radiation diffrn_radiation_wavelength entity entity_name_com entity_poly entity_poly_seq pdbx_entity_src_syn pdbx_nmr_details pdbx_nmr_exptl_sample_conditions pdbx_nmr_refine pdbx_nmr_sample_details pdbx_nmr_software pdbx_poly_seq_scheme pdbx_struct_mod_residue pdbx_unobs_or_zero_occ_atoms pdbx_validate_chiral pdbx_validate_close_contact pdbx_validate_torsion struct struct_conn struct_ref struct_ref_seq struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Advisory Data collection Derived calculations Advisory Atomic model Data collection Database references Derived calculations Experimental preparation Non-polymer description Other Polymer sequence Refinement description Source and taxonomy Structure summary 1 0 2003-07-01 1 1 2008-04-27 1 2 2011-07-13 1 3 2018-10-03 2 0 2018-10-10 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _entity.formula_weight _entity.pdbx_description _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly_seq.mon_id _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_nmr_details.text _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_refine.method _pdbx_nmr_refine.software_ordinal _pdbx_nmr_sample_details.contents _pdbx_nmr_software.authors _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.label_comp_id _struct.pdbx_descriptor _struct.title _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_db_accession _struct_ref_seq.seq_align_beg 1IM7 contains the parent peptide 1J8N contains the beta3-ser analogue peptide (HSER) 1J8Z contains the beta3-Cys analogue peptide (HCYS) 1J9V contains the lactam analogue peptide DabD 1JAR contains the lactam analogue peptidev DDab 1JC8 contains the lactam analogue peptide DDap 1JAA contains the lactam analogue peptide DapE 1JCP contains the lactam analogue peptide EDap RCSB Y RCSB 2001-06-13 REL REL The parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41 11676 Human immunodeficiency virus 1 sample 1 14 Classical 2D homonuclear NMR technques were used. Different NOESY with different mixing time (from 80ms to 800ms) were recorded in order to determine the best conditions without spin diffusion. structures with the lowest energy 50 20 2D NOESY DQF-COSY TOCSY ambient 298 K 50 initial structures were generated using DYANA software, followed by 500 steps restrained minimization.Then using DISCOVER 3, 35 ps MD and 750 steps conjugate gradient EM. torsion dynamics, molecular dynamics, energy minimization 1 lowest energy 4mM peptide in 500 ul solvent 100% DMSO-D6 Bruker GMBH collection XWINNMR 2.6 Bruker GMBH processing XWINNMR 2.6 Bartels C., Billeter M., Guentert P. and Wuethrich K. (1995) J.Biomol. NMR, 5, 1-10 data analysis XEASY 1.2 Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol., 273,283-298 refinement DYANA 1.5 MSI, San Diego refinement DISCOVER 3 400 Bruker Avance 600 Bruker Avance ACE 1 n 1 ACE 1 A ILE 2 n 2 ILE 2 A TRP 3 n 3 TRP 3 A GLY 4 n 4 GLY 4 A DNP 5 n 5 DPP 5 A SER 6 n 6 SER 6 A GLY 7 n 7 GLY 7 A LYS 8 n 8 LYS 8 A LEU 9 n 9 LEU 9 A ILE 10 n 10 ILE 10 A ASP 11 n 11 ASP 11 A THR 12 n 12 THR 12 A THR 13 n 13 THR 13 A ALA 14 n 14 ALA 14 A author_defined_assembly 1 monomeric 380 -1 1540 A DPP 5 AMINOSERINE A DPP 5 SER 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 C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 2 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 3 A A C OXT ALA ALA 14 14 0.138 0.019 1.229 1.367 N 4 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 5 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 6 A A C OXT ALA ALA 14 14 0.139 0.019 1.229 1.368 N 7 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 8 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 9 A A C OXT ALA ALA 14 14 0.140 0.019 1.229 1.369 N 10 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 11 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 12 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 13 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 14 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 15 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 16 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 17 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 18 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 19 A A C OXT ALA ALA 14 14 0.140 0.019 1.229 1.369 N 20 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 1 A SER 6 -163.20 115.19 1 A LYS 8 -158.03 -84.61 1 A THR 13 -100.20 79.82 2 A SER 6 -162.16 119.04 2 A LYS 8 -152.98 -85.88 3 A SER 6 -162.34 113.30 3 A LYS 8 -160.73 -82.29 3 A THR 12 -56.00 108.48 4 A LYS 8 -153.47 -94.93 4 A THR 12 -57.84 102.93 5 A SER 6 -162.14 108.37 5 A LYS 8 -154.53 -92.03 5 A THR 12 -69.39 99.48 6 A SER 6 -166.22 113.93 6 A LYS 8 -158.46 -85.48 6 A THR 12 -56.88 108.04 7 A LYS 8 -159.91 -90.32 8 A LYS 8 -159.90 -95.03 9 A LYS 8 -155.06 -90.62 10 A SER 6 -162.62 111.99 10 A LYS 8 -150.87 -92.36 10 A THR 12 -59.46 105.72 11 A DPP 5 -151.48 82.64 11 A SER 6 -167.61 113.24 11 A LYS 8 -148.06 -90.85 12 A LYS 8 -157.75 -85.81 12 A THR 13 -93.43 -65.04 13 A LYS 8 -155.57 -89.19 13 A THR 13 -97.53 -69.42 14 A LYS 8 -156.20 -89.53 14 A THR 13 -130.65 -73.36 15 A LYS 8 -156.30 -99.34 16 A LYS 8 -152.49 -93.57 16 A THR 12 -58.51 104.37 16 A THR 13 -140.87 -72.72 17 A LYS 8 -159.50 -91.36 18 A LYS 8 -161.90 -91.65 19 A LYS 8 -158.81 -94.38 19 A THR 13 -142.33 -73.09 20 A SER 6 -161.00 105.33 20 A LYS 8 -154.29 -92.43 20 A THR 13 -132.04 -77.08 Transmembrane protein gp41 Solution structure of lactam analogue DapD of HIV gp41 600-612 loop 1 N N covale 1.341 A ACE 1 A C ACE 1 1_555 A ILE 2 A N ILE 2 1_555 covale 1.347 A GLY 4 A C GLY 4 1_555 A DPP 5 A N DPP 5 1_555 covale 1.349 A DPP 5 A C DPP 5 1_555 A SER 6 A N SER 6 1_555 covale 1.343 sing A DPP 5 A NG DPP 5 1_555 A ASP 11 A CG ASP 11 1_555 VIRAL PROTEIN cyclic peptide, gp41, HIV, lactam bond, pseudopeptide, Viral protein ENV_HV1BR UNP 1 600 P03377 IWGCSGKLICTTA 600 612 1JD8 2 14 P03377 A 1 2 14 1 acetylation ACE 1 1JD8 A P03377 UNP 1 1 CYS engineered mutation DPP 5 1JD8 A P03377 UNP 603 5 1 CYS engineered mutation ASP 11 1JD8 A P03377 UNP 609 11