1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Gordon, L.M. Mobley, P.W. Lee, W. Eskandari, S. Kaznessis, Y.N. Sherman, M.A. Waring, A.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE 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 C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking H2 N 16.023 AMINO GROUP non-polymer C9 H11 N O2 165.189 y PHENYLALANINE 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 C5 H11 N O2 117.146 y VALINE L-peptide linking US Protein Sci. PRCIEI 0795 0961-8368 13 1012 1030 10.1110/ps.03407704 15044732 Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy. 2004 NE BIOCHIM.BIOPHYS.ACTA BBACAQ 0113 0006-3002 1559 96 120 10.1016/S0005-2736(01)00443-6 CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 GP41 IN MEMBRANE ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY 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 1 SINGLE WAVELENGTH M 1 1.0 C-terminus has been amidated 2123.481 Envelope polyprotein GP160 residues 519-541 1 syn polymer N-terminal fusion peptide of HIV-1 GP41 no yes AVGIGALFLGFLGAAGSTMGARS(NH2) AVGIGALFLGFLGAAGSTMGARSX 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 repository Initial release Version format compliance Version format compliance 1 0 2003-05-20 1 1 2008-04-29 1 2 2011-07-13 CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 GP41 IN MEMBRANE ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY REMARK: THIS STRUCTURE WAS DETERMINED BY MEANS OF 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR). DATA SET CONSISTS OF 19 CONFORMERS DERIVED FROM MOLECULAR DYNAMICS IN A MODELED SDS MICELLE SURROUNDED BY WATER WITH PEPTIDE BACKBONE CONSTRAINTS FROM FTIR. EXPERIMENTAL DETAILS EXPERIMENT TYPE : INFRARED SPECTROSCOPY TEMPERATURE (KELVIN) : 298 PH : 7.4 IONIC STRENGTH : 0.271 PRESSURE : AMBIENT SAMPLE CONTENTS : THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 519,521,523,524,525,526,527, 528,529,530,531,532,533,534,538,539. EXPERIMENTS CONDUCTED : 13C-ISOTOPE ENHANCED FTIR SPECTROMETER FIELD STRENGTH : NULL SPECTROMETER MODEL : RESEARCH SERIES SPECTROMETER MANUFACTURER : MATTSON FTIR STRUCTURE DETERMINATION. SOFTWARE USED : WINFIRST FTIR CURVE FITTING SOFTWARE METHOD USED : MOLECULAR DYNAMICS CONFORMERS, NUMBER CALCULATED : 20 CONFORMERS, NUMBER SUBMITTED : 19 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY STRUCTURE INFORMATION. PEPTIDE CONCENTRATION WAS 47 MICROMOLAR. PEPTIDE/SDS RATIO WAS 1/200. FTIR SPECTRA WERE AVERAGED OVER 256 SCANS AT A GAIN OF 4 AND A RESOLUTION OF 2 CM-1 RCSB Y RCSB 2003-04-25 REL The sequence of this peptide occurs naturally in human immunodeficiency virus glycoprotein 41. sample The coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information. Peptide concentration was 47 micromolar. Peptide/SDS ratio was 1/200. FTIR spectra were averaged over 256 scans at a gain of 4 and a resolution of 2 cm-1 structures with acceptable covalent geometry 20 19 13C-isotope enhanced FTIR 0.271 7.4 ambient 298 The system of more than 16,000 atoms (peptide, SDS micelle, water, sodium counterions) was simulated for 2.5 nanoseconds at a constant pressure P=1 atm and constant temperature T=303.15 K. molecular dynamics 1 closest to the average THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 519,521,523,524,525,526,527,528,529,530,531,532,533,534,538,539. 94 mM SDS (sodium dodecyl sulfate) in deuterated PBS (phosphate buffered saline), where PBS is 120 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4 Kauppine et al. data analysis Winfirst FTIR curve fitting software Brooks et al. refinement CHARMM c28b2 Mattson FTIR Research Series ALA 1 n 1 ALA 1 A VAL 2 n 2 VAL 2 A GLY 3 n 3 GLY 3 A ILE 4 n 4 ILE 4 A GLY 5 n 5 GLY 5 A ALA 6 n 6 ALA 6 A LEU 7 n 7 LEU 7 A PHE 8 n 8 PHE 8 A LEU 9 n 9 LEU 9 A GLY 10 n 10 GLY 10 A PHE 11 n 11 PHE 11 A LEU 12 n 12 LEU 12 A GLY 13 n 13 GLY 13 A ALA 14 n 14 ALA 14 A ALA 15 n 15 ALA 15 A GLY 16 n 16 GLY 16 A SER 17 n 17 SER 17 A THR 18 n 18 THR 18 A MET 19 n 19 MET 19 A GLY 20 n 20 GLY 20 A ALA 21 n 21 ALA 21 A ARG 22 n 22 ARG 22 A SER 23 n 23 SER 23 A NH2 24 n 24 NH2 24 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 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 10 A A ALA GLY 15 16 148.84 1 A PHE 11 0.070 SIDE CHAIN 2 A ARG 22 0.179 SIDE CHAIN 5 A PHE 11 0.081 SIDE CHAIN 6 A ARG 22 0.080 SIDE CHAIN 9 A PHE 8 0.086 SIDE CHAIN 9 A ARG 22 0.119 SIDE CHAIN 10 A PHE 11 0.112 SIDE CHAIN 13 A PHE 11 0.093 SIDE CHAIN 14 A PHE 8 0.070 SIDE CHAIN 14 A ARG 22 0.074 SIDE CHAIN 16 A ARG 22 0.115 SIDE CHAIN 19 A ARG 22 0.082 SIDE CHAIN 1 -7.37 0.70 120.80 113.43 A A A CB CG CD1 PHE PHE PHE 8 8 8 N 1 -15.32 1.60 100.20 84.88 A A A CG SD CE MET MET MET 19 19 19 N 1 3.27 0.50 120.30 123.57 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 1 -3.49 0.50 120.30 116.81 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 2 7.04 0.50 120.30 127.34 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 2 -8.04 0.50 120.30 112.26 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 3 -5.70 0.70 120.80 115.10 A A A CB CG CD2 PHE PHE PHE 8 8 8 N 3 -6.47 0.70 120.80 114.33 A A A CB CG CD2 PHE PHE PHE 11 11 11 N 3 5.13 0.70 120.80 125.93 A A A CB CG CD1 PHE PHE PHE 11 11 11 N 3 -4.11 0.50 120.30 116.19 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 4 6.06 0.70 120.80 126.86 A A A CB CG CD1 PHE PHE PHE 11 11 11 N 4 10.39 1.70 111.00 121.39 A A A CB CG CD2 LEU LEU LEU 12 12 12 N 4 3.21 0.50 120.30 123.51 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 5 -5.27 0.70 120.80 115.53 A A A CB CG CD1 PHE PHE PHE 11 11 11 N 5 4.69 0.50 120.30 124.99 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 6 5.03 0.50 120.30 125.33 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 6 -5.79 0.50 120.30 114.51 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 7 -3.05 0.50 120.30 117.25 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 8 -8.35 0.70 120.80 112.45 A A A CB CG CD2 PHE PHE PHE 11 11 11 N 8 4.25 0.70 120.80 125.05 A A A CB CG CD1 PHE PHE PHE 11 11 11 N 9 -7.44 0.70 120.80 113.36 A A A CB CG CD2 PHE PHE PHE 11 11 11 N 9 4.87 0.70 120.80 125.67 A A A CB CG CD1 PHE PHE PHE 11 11 11 N 10 -5.17 0.70 120.80 115.63 A A A CB CG CD2 PHE PHE PHE 11 11 11 N 11 -4.32 0.70 120.80 116.48 A A A CB CG CD1 PHE PHE PHE 11 11 11 N 11 3.87 0.50 120.30 124.17 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 11 -8.06 0.50 120.30 112.24 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 12 4.58 0.70 120.80 125.38 A A A CB CG CD2 PHE PHE PHE 11 11 11 N 12 4.48 0.50 120.30 124.78 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 12 -8.13 0.50 120.30 112.17 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 13 7.06 0.50 120.30 127.36 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 13 11.17 1.50 110.50 121.67 A A A N CA CB SER SER SER 23 23 23 N 14 -9.55 1.40 110.10 100.55 A A A N CA CB ALA ALA ALA 6 6 6 N 14 -15.99 2.50 113.10 97.11 A A A N CA C GLY GLY GLY 20 20 20 N 14 -3.47 0.50 120.30 116.83 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 15 8.67 1.40 110.10 118.77 A A A N CA CB ALA ALA ALA 15 15 15 N 15 6.71 0.50 120.30 127.01 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 16 -4.77 0.50 120.30 115.53 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 17 3.93 0.50 120.30 124.23 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 17 -3.86 0.50 120.30 116.44 A A A NE CZ NH2 ARG ARG ARG 22 22 22 N 18 3.33 0.50 120.30 123.63 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 19 -7.60 0.70 120.80 113.20 A A A CB CG CD2 PHE PHE PHE 11 11 11 N 19 3.18 0.50 120.30 123.48 A A A NE CZ NH1 ARG ARG ARG 22 22 22 N 1 A A CG CD1 PHE PHE 11 11 0.091 0.015 1.383 1.474 N 3 A A CA CB SER SER 23 23 0.093 0.015 1.525 1.618 N 4 A A CA CB SER SER 17 17 0.095 0.015 1.525 1.620 N 5 A A CA CB SER SER 17 17 0.113 0.015 1.525 1.638 N 12 A A CZ CE2 PHE PHE 8 8 0.122 0.019 1.369 1.491 N 16 A A CG CD2 PHE PHE 11 11 0.100 0.015 1.383 1.483 N 18 A A CG CD2 PHE PHE 8 8 0.095 0.015 1.383 1.478 N 1 A ALA 15 -91.29 -89.98 2 A ALA 14 -73.60 -70.77 2 A SER 17 -145.37 -141.56 2 A MET 19 -91.25 -100.74 3 A ARG 22 -65.84 -90.46 5 A ARG 22 -97.21 -82.71 6 A MET 19 -95.59 -64.87 6 A ARG 22 -78.04 -79.87 7 A LEU 7 -81.09 -71.32 7 A MET 19 -103.44 -95.36 7 A ARG 22 -83.95 -96.63 8 A LEU 12 -57.90 -81.92 8 A ALA 15 -62.66 -88.43 8 A ARG 22 -94.70 -137.81 9 A LEU 7 -73.33 -73.50 9 A ARG 22 -81.08 -106.06 10 A LEU 7 -61.71 -70.00 10 A ARG 22 -93.28 -70.37 11 A LEU 7 -63.86 -82.49 11 A ALA 14 -53.37 -72.21 11 A ARG 22 -100.09 -69.05 12 A ALA 15 -65.27 -71.38 12 A MET 19 -83.30 -74.98 15 A MET 19 -98.21 -84.46 16 A ARG 22 -84.12 -73.65 17 A LEU 7 -70.35 -70.70 18 A VAL 2 -104.46 -167.74 18 A LEU 7 -77.53 -74.68 18 A ARG 22 -79.58 -85.01 19 A ALA 15 -60.57 -83.69 19 A SER 17 -57.47 179.36 19 A ARG 22 -100.92 -103.97 Envelope polyprotein GP160 Conformational Mapping of the N-terminal Peptide of HIV-1 GP41 in lipid detergent and aqueous environments using 13C-enhanced Fourier Transform Infrared Spectroscopy 1 N N A GLY 3 A GLY 3 HELX_P A PHE 8 A PHE 8 1 1 6 covale 1.316 A SER 23 A C SER 23 1_555 A NH2 24 A N NH2 24 1_555 VIRAL PROTEIN human immunodeficiency virus (HIV-1), viral fusion peptide, gp41, Viral protein ENV_HV1BR UNP 1 517 P03377 AVGIGALFLGFLGAAGSTMGARS 517 539 1P5A 1 23 P03377 A 1 1 23 BINDING SITE FOR RESIDUE NH2 A 24 Software 1 A SER 23 A SER 23 1 1_555