1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Chiva, C. Barthe, P. Codina, A. Giralt, E. 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 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 C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID 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 C5 H11 N O2 117.146 y VALINE L-peptide linking US J.Am.Chem.Soc. JACSAT 0004 0002-7863 125 1508 1517 10.1021/ja0207908 12568610 Synthesis and NMR structure of P41ICF, a potent inhibitor of human cathepsin L 2003 10.2210/pdb1l3h/pdb pdb_00001l3h 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 7261.075 MHC CLASS II-ASSOCIATED P41 INVARIANT CHAIN FRAGMENT (P41icf) THYROGLOBULIN-LIKE DOMAIN 1 syn polymer HLA class II histocompatibility antigen, gamma chain no no LTKCQEEVSHIPAVHPGSFRPKCDENGNYLPLQCYGSIGYCWCVFPNGTEVPNTRSRGHHNCSES LTKCQEEVSHIPAVHPGSFRPKCDENGNYLPLQCYGSIGYCWCVFPNGTEVPNTRSRGHHNCSES 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 n n n n n n n n n n n n n n n n n n n n n n database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-03-04 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name 1ICF contains the same protein complexed with Cathepsin L. RCSB Y RCSB 2002-02-27 REL REL This sequence occurs naturally in humans. sample This structure was determined using standard 2D homonuclear techniques. structures with the lowest energy,target function 600 30 DQF-COSY 2D TOCSY 2D NOESY 5.7 ambient 288 K the structures are based on a total of 981 restraints, 925 are NOE-derived distance constraints, 56 dihedral angle restraints torsion angle dynamics and simulated annealing with restrained molecular dynamics 1 fewest violations 1mM P41icf; 20mM phosphate buffer, 0.01mM NaN3 85% H20, 15% D2O Delaglio processing NMRPipe Johnson data analysis NMRView Guntert structure solution DYANA 1.5 Case refinement Amber 5.0 800 Bruker DRX 600 Bruker DRX LEU 1 n 1 LEU 1 A THR 2 n 2 THR 2 A LYS 3 n 3 LYS 3 A CYS 4 n 4 CYS 4 A GLN 5 n 5 GLN 5 A GLU 6 n 6 GLU 6 A GLU 7 n 7 GLU 7 A VAL 8 n 8 VAL 8 A SER 9 n 9 SER 9 A HIS 10 n 10 HIS 10 A ILE 11 n 11 ILE 11 A PRO 12 n 12 PRO 12 A ALA 13 n 13 ALA 13 A VAL 14 n 14 VAL 14 A HIS 15 n 15 HIS 15 A PRO 16 n 16 PRO 16 A GLY 17 n 17 GLY 17 A SER 18 n 18 SER 18 A PHE 19 n 19 PHE 19 A ARG 20 n 20 ARG 20 A PRO 21 n 21 PRO 21 A LYS 22 n 22 LYS 22 A CYS 23 n 23 CYS 23 A ASP 24 n 24 ASP 24 A GLU 25 n 25 GLU 25 A ASN 26 n 26 ASN 26 A GLY 27 n 27 GLY 27 A ASN 28 n 28 ASN 28 A TYR 29 n 29 TYR 29 A LEU 30 n 30 LEU 30 A PRO 31 n 31 PRO 31 A LEU 32 n 32 LEU 32 A GLN 33 n 33 GLN 33 A CYS 34 n 34 CYS 34 A TYR 35 n 35 TYR 35 A GLY 36 n 36 GLY 36 A SER 37 n 37 SER 37 A ILE 38 n 38 ILE 38 A GLY 39 n 39 GLY 39 A TYR 40 n 40 TYR 40 A CYS 41 n 41 CYS 41 A TRP 42 n 42 TRP 42 A CYS 43 n 43 CYS 43 A VAL 44 n 44 VAL 44 A PHE 45 n 45 PHE 45 A PRO 46 n 46 PRO 46 A ASN 47 n 47 ASN 47 A GLY 48 n 48 GLY 48 A THR 49 n 49 THR 49 A GLU 50 n 50 GLU 50 A VAL 51 n 51 VAL 51 A PRO 52 n 52 PRO 52 A ASN 53 n 53 ASN 53 A THR 54 n 54 THR 54 A ARG 55 n 55 ARG 55 A SER 56 n 56 SER 56 A ARG 57 n 57 ARG 57 A GLY 58 n 58 GLY 58 A HIS 59 n 59 HIS 59 A HIS 60 n 60 HIS 60 A ASN 61 n 61 ASN 61 A CYS 62 n 62 CYS 62 A SER 63 n 63 SER 63 A GLU 64 n 64 GLU 64 A SER 65 n 65 SER 65 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 A N GLN 33 A N GLN 33 A O TRP 42 A O TRP 42 1 A A HG1 O THR GLY 2 27 1.49 1 A A O HG GLN SER 5 9 1.54 1 A A O HG SER SER 18 37 1.56 1 A A OD1 HG1 ASN THR 47 49 1.57 2 A A HG1 O THR GLY 2 27 1.52 2 A A O HG GLN SER 5 9 1.53 2 A A O HG THR SER 54 56 1.54 2 A A O HG CYS SER 62 63 1.58 3 A A HG1 O THR GLY 2 27 1.47 3 A A O HG GLN SER 5 9 1.55 3 A A O HG THR SER 54 56 1.56 3 A A OD1 HG1 ASN THR 47 49 1.56 3 A A O HH GLY TYR 17 35 1.57 4 A A O HG GLN SER 5 9 1.52 4 A A O HG SER SER 18 37 1.56 4 A A HG1 O THR ASN 2 26 1.57 4 A A O HH GLY TYR 17 35 1.58 4 A A O HG1 VAL THR 51 54 1.60 4 A A O HG GLU SER 64 65 1.60 5 A A O HG GLN SER 5 9 1.54 5 A A OD1 HG1 ASN THR 47 49 1.54 5 A A O HH GLY TYR 17 35 1.57 5 A A O HG1 VAL THR 51 54 1.57 5 A A O HG HIS SER 15 18 1.58 5 A A O HG CYS SER 62 63 1.58 5 A A O HG GLU SER 64 65 1.59 6 A A O HG GLU SER 6 9 1.50 6 A A HG1 O THR GLY 2 27 1.53 6 A A O HG THR SER 54 56 1.56 7 A A HG1 O THR GLY 2 27 1.50 7 A A O HG GLN SER 5 9 1.54 7 A A O HG THR SER 54 56 1.55 7 A A O HG CYS SER 62 65 1.55 7 A A O HH GLY TYR 17 35 1.57 8 A A HG1 O THR GLY 2 27 1.51 8 A A O HG HIS SER 15 37 1.51 8 A A O HG GLN SER 5 9 1.52 8 A A O HH GLY TYR 17 35 1.56 9 A A HG1 O THR GLY 2 27 1.50 9 A A O HG THR SER 54 56 1.54 9 A A O HG HIS SER 15 37 1.55 9 A A OD1 HG1 ASN THR 47 49 1.56 9 A A O HG GLU SER 6 9 1.56 9 A A O HH GLY TYR 17 35 1.56 10 A A HG1 O THR GLY 2 27 1.50 10 A A O HG GLN SER 5 9 1.53 10 A A O HH GLY TYR 17 35 1.56 10 A A OD1 HG1 ASN THR 47 49 1.57 10 A A O HG HIS SER 15 37 1.57 10 A A O HG1 VAL THR 51 54 1.58 11 A A HG1 O THR GLY 2 27 1.50 11 A A O HG GLN SER 5 9 1.54 11 A A O HG THR SER 54 56 1.54 11 A A O HH GLY TYR 17 35 1.57 12 A A O HG VAL SER 44 65 1.50 12 A A HG1 O THR GLY 2 27 1.51 12 A A O HG GLN SER 5 9 1.53 12 A A OD1 HG1 ASN THR 47 49 1.55 12 A A O HH GLY TYR 17 35 1.56 12 A A O HG ASN SER 61 63 1.58 12 A A O HG1 VAL THR 51 54 1.59 13 A A HG1 O THR GLY 2 27 1.49 13 A A O HG HIS SER 15 18 1.53 13 A A O HG GLN SER 5 9 1.53 13 A A O HG ASN SER 61 63 1.60 14 A A HG1 O THR GLY 2 27 1.52 14 A A O HG CYS SER 62 65 1.52 14 A A O HG GLU SER 6 9 1.57 14 A A O HG1 VAL THR 51 54 1.59 15 A A HG1 O THR GLY 2 27 1.50 15 A A O HG GLU SER 64 65 1.53 15 A A O HG GLN SER 5 9 1.54 15 A A O HG THR SER 54 56 1.55 15 A A O HH GLY TYR 17 35 1.57 15 A A O HG HIS SER 15 18 1.59 16 A A HG1 O THR GLY 2 27 1.52 16 A A O HG GLN SER 5 9 1.53 16 A A OD1 HG1 ASN THR 47 49 1.54 16 A A O HG SER SER 18 37 1.55 16 A A O HG GLU SER 64 65 1.58 17 A A HG1 O THR GLY 2 27 1.50 17 A A O HG GLN SER 5 9 1.53 17 A A OD1 HG1 ASN THR 47 49 1.55 17 A A O HG VAL SER 44 65 1.56 17 A A O HH GLY TYR 17 35 1.57 17 A A O HG THR SER 54 56 1.57 18 A A HG1 O THR GLY 2 27 1.52 18 A A O HG SER SER 18 37 1.55 18 A A OD1 HG1 ASN THR 47 49 1.55 18 A A O HG GLU SER 6 9 1.56 18 A A O HH GLY TYR 17 35 1.57 18 A A O HG GLU SER 64 65 1.58 19 A A HG1 O THR GLY 2 27 1.50 19 A A O HG GLN SER 5 9 1.52 19 A A OD1 HG1 ASN THR 47 49 1.53 19 A A O HH GLY TYR 17 35 1.57 19 A A O HG CYS SER 62 63 1.60 20 A A O HG GLN SER 5 9 1.52 20 A A HG1 O THR GLY 2 27 1.55 20 A A O HG1 VAL THR 51 54 1.57 20 A A OD1 HG1 ASN THR 47 49 1.57 21 A A HG1 O THR GLY 2 27 1.50 21 A A O HG GLN SER 5 9 1.53 21 A A O HG GLU SER 64 65 1.56 21 A A OD1 HG1 ASN THR 47 49 1.56 21 A A O HG SER SER 18 37 1.58 21 A A O HH GLY TYR 17 35 1.59 21 A A O HG CYS SER 62 63 1.60 22 A A O HG GLN SER 5 9 1.53 22 A A O HG THR SER 54 56 1.54 22 A A HG1 O THR GLY 2 27 1.55 22 A A O HH GLY TYR 17 35 1.56 22 A A OD1 HG1 ASN THR 47 49 1.56 23 A A HG1 O THR GLY 2 27 1.47 23 A A O HG HIS SER 15 18 1.52 23 A A O HG VAL SER 44 65 1.52 23 A A O HG GLN SER 5 9 1.54 24 A A HG1 O THR GLY 2 27 1.48 24 A A O HG VAL SER 44 65 1.53 24 A A O HH PRO TYR 16 35 1.55 24 A A OD1 HG1 ASN THR 47 49 1.57 24 A A O HG THR SER 54 56 1.57 24 A A O HG GLY SER 17 18 1.60 25 A A O HG THR SER 54 56 1.53 25 A A O HG GLN SER 5 9 1.53 25 A A OD1 HG1 ASN THR 47 49 1.58 25 A A HG1 O THR GLY 2 27 1.59 26 A A HG1 O THR GLY 2 27 1.49 26 A A O HG GLN SER 5 9 1.52 26 A A O HG THR SER 54 56 1.55 26 A A O HH GLY TYR 17 35 1.57 27 A A HG1 O THR GLY 2 27 1.49 27 A A O HG VAL SER 44 65 1.54 27 A A OD1 HG1 ASN THR 47 49 1.55 27 A A O HH HIS TYR 15 35 1.59 28 A A HG1 O THR GLY 2 27 1.48 28 A A O HG VAL SER 44 65 1.53 28 A A O HG GLN SER 5 9 1.55 28 A A OD1 HG1 ASN THR 47 49 1.56 29 A A HG1 O THR GLY 2 27 1.51 29 A A O HG GLN SER 5 9 1.53 29 A A OD1 HG1 ASN THR 47 49 1.55 29 A A O HG GLU SER 64 65 1.56 29 A A O HG SER SER 18 37 1.58 30 A A HG1 O THR GLY 2 27 1.46 30 A A O HG GLN SER 5 9 1.52 30 A A O HG THR SER 54 56 1.55 30 A A O HG1 VAL THR 51 54 1.56 30 A A O HG CYS SER 62 65 1.58 14 A TYR 35 0.066 SIDE CHAIN 18 A ARG 20 0.083 SIDE CHAIN 23 A TYR 35 0.109 SIDE CHAIN 27 A TYR 29 0.079 SIDE CHAIN 29 A ARG 55 0.086 SIDE CHAIN 1 3.54 0.50 120.30 123.84 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 2 4.50 0.50 120.30 124.80 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 5 -3.71 0.60 121.00 117.29 A A A CB CG CD2 TYR TYR TYR 35 35 35 N 6 3.40 0.50 120.30 123.70 A A A NE CZ NH1 ARG ARG ARG 55 55 55 N 9 3.57 0.50 120.30 123.87 A A A NE CZ NH1 ARG ARG ARG 20 20 20 N 11 3.63 0.50 120.30 123.93 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 12 3.53 0.50 120.30 123.83 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 14 3.59 0.50 120.30 123.89 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 15 3.58 0.50 120.30 123.88 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 17 -3.62 0.60 121.00 117.38 A A A CB CG CD2 TYR TYR TYR 35 35 35 N 19 3.39 0.50 120.30 123.69 A A A NE CZ NH1 ARG ARG ARG 55 55 55 N 20 3.79 0.50 120.30 124.09 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 22 -4.04 0.60 121.00 116.96 A A A CB CG CD2 TYR TYR TYR 35 35 35 N 22 4.23 0.50 120.30 124.53 A A A NE CZ NH1 ARG ARG ARG 57 57 57 N 24 3.02 0.50 120.30 123.32 A A A NE CZ NH1 ARG ARG ARG 20 20 20 N 25 -3.96 0.60 121.00 117.04 A A A CB CG CD2 TYR TYR TYR 40 40 40 N 1 A VAL 14 -73.92 47.62 1 A PRO 31 -51.25 -8.53 1 A ARG 55 -51.69 103.81 1 A SER 63 -65.81 33.17 1 A GLU 64 -61.64 4.08 2 A PRO 52 -69.15 18.82 2 A ARG 55 -56.77 94.27 2 A ARG 57 -63.56 1.13 2 A SER 63 -167.58 62.99 3 A PRO 52 -70.15 23.20 3 A ARG 55 -45.54 102.84 3 A ASN 61 -76.29 49.55 3 A CYS 62 -56.10 107.87 3 A GLU 64 -69.63 23.69 4 A LYS 3 -21.62 -62.14 4 A HIS 15 -116.40 61.79 4 A ASN 53 65.11 -5.02 4 A ARG 55 -60.95 91.89 4 A ASN 61 -112.11 61.68 4 A CYS 62 -52.24 106.66 4 A SER 63 47.22 25.39 5 A ARG 55 -59.89 106.08 5 A ARG 57 -65.50 1.50 6 A PRO 31 -54.45 -9.09 6 A ASN 53 59.73 6.63 6 A ARG 55 -42.42 109.21 6 A GLU 64 -62.63 68.90 7 A PRO 31 -48.21 -18.76 7 A ASN 53 61.22 -0.47 7 A ARG 55 -43.57 95.22 7 A SER 63 -64.96 18.30 8 A HIS 15 -111.03 70.87 8 A ASN 53 65.18 -0.82 8 A ARG 55 -56.44 98.82 8 A CYS 62 -65.32 -172.64 8 A SER 63 -64.70 51.63 8 A GLU 64 -69.65 32.84 9 A HIS 15 -111.41 63.68 9 A ASN 53 59.44 -2.55 9 A ARG 55 -46.16 99.02 9 A ARG 57 -79.27 23.33 9 A GLU 64 -75.34 26.10 10 A HIS 15 -114.86 53.62 10 A GLU 25 -64.64 0.15 10 A ARG 55 -62.83 94.17 10 A CYS 62 -57.16 105.73 10 A SER 63 54.29 19.31 11 A ARG 55 -43.80 103.02 11 A ARG 57 -69.07 13.72 12 A HIS 15 -114.36 63.19 12 A ASN 53 63.84 -1.51 12 A ARG 55 -54.85 99.17 12 A CYS 62 -52.74 107.54 13 A PRO 52 -68.85 23.20 13 A ARG 55 -57.25 97.94 13 A CYS 62 -53.45 105.83 13 A SER 63 -150.05 13.89 13 A GLU 64 -65.46 7.28 14 A ASN 53 71.42 -3.62 14 A ARG 55 -58.10 97.46 14 A SER 63 49.81 27.09 15 A PRO 52 -69.16 23.62 15 A ARG 55 -53.93 101.83 15 A SER 63 -154.98 20.76 15 A GLU 64 -70.52 21.44 16 A HIS 10 -130.51 -33.16 16 A PRO 16 -43.72 107.45 16 A PRO 31 -51.39 -9.51 16 A ASN 53 62.47 -5.23 16 A ARG 55 -50.23 102.95 16 A GLU 64 -52.07 22.27 17 A ASN 53 61.68 -0.24 17 A ARG 55 -49.76 106.38 17 A GLU 64 57.44 11.11 18 A HIS 15 -118.68 53.20 18 A ARG 55 -52.77 105.17 18 A GLU 64 48.91 19.15 19 A PRO 46 -58.82 -2.21 19 A SER 63 -157.72 19.01 19 A GLU 64 -77.51 25.18 20 A CYS 62 -68.12 -176.20 20 A SER 63 -65.64 74.19 21 A HIS 15 -113.52 63.20 21 A ASN 53 59.99 -2.88 21 A ARG 55 -46.94 106.36 21 A ARG 57 -89.69 36.23 21 A SER 63 -159.62 24.63 21 A GLU 64 -70.97 34.90 22 A TYR 35 -111.22 77.51 22 A ASN 53 59.93 3.60 22 A ARG 55 -46.88 102.83 22 A ARG 57 -59.99 -4.75 22 A CYS 62 -68.92 -178.66 22 A SER 63 -66.95 35.02 22 A GLU 64 -69.51 66.17 23 A SER 18 -49.28 107.99 23 A PHE 19 -152.64 89.10 23 A ASN 53 59.50 15.15 24 A SER 18 69.16 107.08 24 A ASN 53 61.20 -3.03 24 A ARG 55 -40.35 102.91 24 A CYS 62 -60.41 95.39 24 A GLU 64 56.44 19.58 25 A HIS 15 -111.67 71.87 25 A ARG 55 -41.17 93.00 25 A ARG 57 -69.20 9.05 25 A CYS 62 -60.68 95.51 25 A SER 63 -89.05 34.43 26 A ASN 53 59.86 2.24 26 A ARG 55 -45.27 103.86 26 A ASN 61 -74.00 39.88 27 A HIS 15 -118.73 62.04 27 A PRO 46 -57.72 -5.83 27 A PRO 52 -69.31 22.57 27 A ARG 55 -62.51 96.50 27 A ASN 61 -116.43 78.12 27 A SER 63 -67.87 60.41 28 A PRO 52 -71.81 24.01 28 A ARG 55 -57.10 107.88 28 A ARG 57 -67.62 7.72 28 A CYS 62 -46.30 106.95 28 A GLU 64 -141.09 10.93 29 A ASN 53 59.50 2.00 29 A CYS 62 -65.85 98.80 29 A SER 63 -77.13 23.81 30 A HIS 15 -112.98 65.53 30 A ARG 55 -55.64 105.08 30 A CYS 62 -57.14 98.50 30 A SER 63 -76.60 31.62 NMR structure of P41icf, a potent inhibitor of human cathepsin L 1 N N A THR 2 A THR 2 HELX_P A ILE 11 A ILE 11 1 1 10 disulf 2.031 A CYS 4 A SG CYS 4 1_555 A CYS 23 A SG CYS 23 1_555 disulf 2.045 A CYS 34 A SG CYS 34 1_555 A CYS 41 A SG CYS 41 1_555 disulf 2.033 A CYS 43 A SG CYS 43 1_555 A CYS 62 A SG CYS 62 1_555 IMMUNE SYSTEM ALPHA HELIX, BETA SHEET, DISULFIDE BONDS, IMMUNE SYSTEM HG2A_HUMAN UNP 1 210 P04233 LTKCQEEVSHIPAVHPGSFRPKCDENGNYLPLQCYGSIGYCWCVFPNGTEVPNTRSRGHHNCSES 210 274 1L3H 1 65 P04233 A 1 1 65 2 anti-parallel A LEU 32 A LEU 32 A TYR 35 A TYR 35 A TYR 40 A TYR 40 A CYS 43 A CYS 43