1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kitazawa, S. Kameda, T. Kumo, A. Utsumi, M. Baxter, N. Kato, K. Williamson, M.P. Kitahara, R. 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 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 C5 H11 N O2 S 149.211 y METHIONINE 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Biochemistry BICHAW 0033 0006-2960 53 447 449 10.1021/bi401617n 24401037 Close Identity between Alternatively Folded State N2 of Ubiquitin and the Conformation of the Protein Bound to the Ubiquitin-Activating Enzyme 2014 10.2210/pdb2ru6/pdb pdb_00002ru6 8562.805 Ubiquitin Q41N 1 man polymer no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQNRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQNRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 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 n n n n n n n n n n n human sample UBC 9606 Homo sapiens 562 Escherichia coli pCGN vector database_2 pdbx_database_status pdbx_nmr_software pdbx_nmr_spectrometer struct_ref_seq_dif repository Initial release Structure summary Data collection Database references Other 1 0 2014-02-12 1 1 2014-03-05 1 2 2023-06-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_ref_seq_dif.details alternatively folded state is 70% populated BMRB Y PDBJ 2013-12-04 REL REL REL REL 2450 0 454 231 1765 0 0 36 36 structures with the lowest energy 200 20 1 2D 1H-15N HSQC 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aromatic 2D HNCO 3D 1H-13C/15N simultaneous evolutio NOESY HSQC 20 mM [U-100% 2H] 2 mM [U-100% 13C; U-100% 15N] 0.2 mM 20 7.2 250 0 298 K torsion angle dynamics, Energy minimization 1 lowest energy 20 mM [U-100% 2H] Tris(hydroxymethyl)aminomethane-1, 2 mM [U-100% 13C; U-100% 15N] ubiquitin-2, 0.2 mM DSS-3, 88% H2O/12% D2O 88% H2O/12% D2O Guntert, Mumenthaler and Wuthrich chemical shift assignment CYANA 3.93 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman refinement Amber 11 Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Johnson, One Moon Scientific peak picking NMRView refinement CYANA_3.93 800 Bruker AVANCE Bruker Avance MET 1 n 1 MET 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A PHE 4 n 4 PHE 4 A VAL 5 n 5 VAL 5 A LYS 6 n 6 LYS 6 A THR 7 n 7 THR 7 A LEU 8 n 8 LEU 8 A THR 9 n 9 THR 9 A GLY 10 n 10 GLY 10 A LYS 11 n 11 LYS 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A THR 14 n 14 THR 14 A LEU 15 n 15 LEU 15 A GLU 16 n 16 GLU 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A PRO 19 n 19 PRO 19 A SER 20 n 20 SER 20 A ASP 21 n 21 ASP 21 A THR 22 n 22 THR 22 A ILE 23 n 23 ILE 23 A GLU 24 n 24 GLU 24 A ASN 25 n 25 ASN 25 A VAL 26 n 26 VAL 26 A LYS 27 n 27 LYS 27 A ALA 28 n 28 ALA 28 A LYS 29 n 29 LYS 29 A ILE 30 n 30 ILE 30 A GLN 31 n 31 GLN 31 A ASP 32 n 32 ASP 32 A LYS 33 n 33 LYS 33 A GLU 34 n 34 GLU 34 A GLY 35 n 35 GLY 35 A ILE 36 n 36 ILE 36 A PRO 37 n 37 PRO 37 A PRO 38 n 38 PRO 38 A ASP 39 n 39 ASP 39 A GLN 40 n 40 GLN 40 A ASN 41 n 41 ASN 41 A ARG 42 n 42 ARG 42 A LEU 43 n 43 LEU 43 A ILE 44 n 44 ILE 44 A PHE 45 n 45 PHE 45 A ALA 46 n 46 ALA 46 A GLY 47 n 47 GLY 47 A LYS 48 n 48 LYS 48 A GLN 49 n 49 GLN 49 A LEU 50 n 50 LEU 50 A GLU 51 n 51 GLU 51 A ASP 52 n 52 ASP 52 A GLY 53 n 53 GLY 53 A ARG 54 n 54 ARG 54 A THR 55 n 55 THR 55 A LEU 56 n 56 LEU 56 A SER 57 n 57 SER 57 A ASP 58 n 58 ASP 58 A TYR 59 n 59 TYR 59 A ASN 60 n 60 ASN 60 A ILE 61 n 61 ILE 61 A GLN 62 n 62 GLN 62 A LYS 63 n 63 LYS 63 A GLU 64 n 64 GLU 64 A SER 65 n 65 SER 65 A THR 66 n 66 THR 66 A LEU 67 n 67 LEU 67 A HIS 68 n 68 HIS 68 A LEU 69 n 69 LEU 69 A VAL 70 n 70 VAL 70 A LEU 71 n 71 LEU 71 A ARG 72 n 72 ARG 72 A LEU 73 n 73 LEU 73 A ARG 74 n 74 ARG 74 A GLY 75 n 75 GLY 75 A GLY 76 n 76 GLY 76 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 O ILE 13 A O ILE 13 A N VAL 5 A N VAL 5 A N PHE 4 A N PHE 4 A O LEU 67 A O LEU 67 A O VAL 70 A O VAL 70 A N ARG 42 A N ARG 42 A N PHE 45 A N PHE 45 A O LYS 48 A O LYS 48 8 A A HG1 OE2 THR GLU 22 24 1.55 15 A A HG1 OE2 THR GLU 22 24 1.55 2 A A LEU VAL 69 70 136.04 2 A A VAL LEU 70 71 143.70 3 A A LEU VAL 69 70 140.11 3 A A VAL LEU 70 71 142.94 4 A A LEU VAL 69 70 147.17 4 A A VAL LEU 70 71 147.36 4 A A LEU ARG 71 72 145.21 5 A A LEU VAL 69 70 141.79 5 A A VAL LEU 70 71 146.22 5 A A LEU ARG 71 72 142.12 5 A A ARG LEU 72 73 -149.50 6 A A LEU VAL 69 70 144.35 6 A A VAL LEU 70 71 140.93 7 A A LEU VAL 69 70 145.86 7 A A VAL LEU 70 71 142.13 8 A A LEU VAL 69 70 143.18 8 A A VAL LEU 70 71 142.32 9 A A LEU VAL 69 70 143.98 9 A A VAL LEU 70 71 148.37 10 A A LEU VAL 69 70 146.38 10 A A VAL LEU 70 71 141.09 10 A A LEU ARG 71 72 146.92 12 A A LEU VAL 69 70 148.99 13 A A LEU VAL 69 70 146.01 13 A A VAL LEU 70 71 146.91 13 A A LEU ARG 71 72 148.66 14 A A LEU VAL 69 70 149.41 14 A A VAL LEU 70 71 146.60 15 A A LEU VAL 69 70 142.52 15 A A VAL LEU 70 71 142.82 16 A A LEU VAL 69 70 149.17 16 A A VAL LEU 70 71 148.62 17 A A LEU VAL 69 70 142.93 17 A A VAL LEU 70 71 140.85 18 A A LEU VAL 69 70 144.95 18 A A VAL LEU 70 71 147.62 18 A A LEU ARG 71 72 138.07 18 A A GLY GLY 75 76 149.96 19 A A LEU VAL 69 70 149.76 19 A A VAL LEU 70 71 147.61 20 A A VAL LEU 70 71 146.66 20 A A LEU ARG 71 72 140.26 1 A TYR 59 0.070 SIDE CHAIN 3 A ARG 72 0.121 SIDE CHAIN 4 A TYR 59 0.076 SIDE CHAIN 5 A ARG 54 0.086 SIDE CHAIN 10 A TYR 59 0.082 SIDE CHAIN 11 A TYR 59 0.091 SIDE CHAIN 12 A TYR 59 0.065 SIDE CHAIN 13 A TYR 59 0.079 SIDE CHAIN 16 A TYR 59 0.081 SIDE CHAIN 17 A ARG 42 0.086 SIDE CHAIN 18 A ARG 72 0.097 SIDE CHAIN 19 A ARG 42 0.089 SIDE CHAIN 19 A TYR 59 0.066 SIDE CHAIN 20 A TYR 59 0.070 SIDE CHAIN 1 3.12 0.50 120.30 123.42 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 1 3.29 0.50 120.30 123.59 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 1 4.06 0.50 120.30 124.36 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 2 3.57 0.50 120.30 123.87 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 2 -3.03 0.50 120.30 117.27 A A A NE CZ NH2 ARG ARG ARG 42 42 42 N 2 3.94 0.50 120.30 124.24 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 3 4.76 0.50 120.30 125.06 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 3 3.28 0.50 120.30 123.58 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 4 3.82 0.50 120.30 124.12 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 4 3.57 0.50 120.30 123.87 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 5 3.34 0.50 120.30 123.64 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 5 3.04 0.50 120.30 123.34 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 6 4.07 0.50 120.30 124.37 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 7 4.72 0.50 120.30 125.02 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 8 3.54 0.50 120.30 123.84 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 9 3.65 0.50 120.30 123.95 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 9 3.69 0.50 120.30 123.99 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 9 3.14 0.50 120.30 123.44 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 10 3.61 0.50 120.30 123.91 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 10 4.11 0.50 120.30 124.41 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 10 3.14 0.50 120.30 123.44 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 11 4.04 0.50 120.30 124.34 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 11 3.17 0.50 120.30 123.47 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 11 4.26 0.50 120.30 124.56 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 11 3.84 0.50 120.30 124.14 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 12 3.55 0.50 120.30 123.85 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 12 3.26 0.50 120.30 123.56 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 12 3.55 0.50 120.30 123.85 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 12 3.74 0.50 120.30 124.04 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 13 3.91 0.50 120.30 124.21 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 14 3.51 0.50 120.30 123.81 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 14 5.24 0.50 120.30 125.54 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 15 3.44 0.50 120.30 123.74 A A A NE CZ NH1 ARG ARG ARG 72 72 72 N 17 3.09 0.50 120.30 123.39 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 17 3.56 0.50 120.30 123.86 A A A NE CZ NH2 ARG ARG ARG 72 72 72 N 18 3.43 0.50 120.30 123.73 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 19 3.53 0.50 120.30 123.83 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 20 3.63 0.50 120.30 123.93 A A A NE CZ NH1 ARG ARG ARG 42 42 42 N 20 4.20 0.50 120.30 124.50 A A A NE CZ NH1 ARG ARG ARG 54 54 54 N 20 3.21 0.50 120.30 123.51 A A A NE CZ NH1 ARG ARG ARG 74 74 74 N 1 A GLU 34 -120.52 -55.64 1 A ASP 39 -65.39 14.59 1 A GLN 40 -140.77 -17.84 1 A TYR 59 -65.36 3.15 1 A GLU 64 59.05 9.79 2 A THR 9 -65.95 12.61 2 A GLU 34 -138.02 -56.15 2 A ASP 39 -79.87 35.80 2 A GLN 40 -156.64 -40.42 2 A THR 66 -105.76 62.14 2 A LEU 71 -39.45 161.73 3 A LEU 71 -45.26 161.69 3 A LEU 73 -136.06 -55.31 4 A GLU 34 -145.44 14.50 4 A ASP 39 -66.28 4.37 4 A LEU 71 -54.54 172.05 4 A ARG 72 -69.76 -82.60 4 A LEU 73 -156.64 -46.43 5 A GLU 34 -136.65 -30.56 5 A GLU 64 57.18 15.74 5 A LEU 71 -52.19 178.02 5 A ARG 72 -71.62 -89.85 5 A LEU 73 60.93 158.88 6 A THR 9 -69.63 10.89 6 A GLN 40 -133.66 -37.81 6 A ALA 46 52.13 19.45 6 A GLU 64 58.87 10.21 6 A LEU 71 -49.60 165.71 6 A ARG 72 -77.54 -75.08 6 A ARG 74 -71.76 41.96 7 A GLU 34 -131.52 -36.10 7 A GLN 40 -130.64 -30.52 7 A ALA 46 52.48 19.63 7 A ASP 52 -63.37 -179.73 7 A TYR 59 -69.46 7.33 7 A LEU 71 -46.66 174.91 8 A LEU 71 -47.39 161.51 9 A GLU 34 -145.13 -12.63 9 A LEU 71 -55.10 172.22 9 A LEU 73 64.34 170.67 10 A THR 9 -66.86 4.02 10 A GLU 34 -136.95 -31.61 10 A ALA 46 49.60 28.50 10 A TYR 59 -68.80 9.61 10 A GLU 64 59.97 13.77 10 A LEU 71 -48.07 164.00 11 A THR 9 -82.95 35.73 11 A GLU 34 -141.56 -30.04 11 A ALA 46 54.60 -1.36 11 A GLU 51 -62.93 -175.65 11 A ASP 52 -91.50 -159.21 11 A LEU 73 54.79 -170.86 12 A GLU 34 -137.76 -39.55 12 A ASP 39 -64.40 9.57 12 A GLU 64 58.37 15.48 13 A ALA 46 54.29 -3.31 13 A GLU 64 70.77 -12.11 13 A LEU 71 -52.82 170.35 13 A ARG 74 62.65 -177.07 14 A GLU 16 -115.98 59.11 14 A GLU 34 -144.96 -16.71 15 A GLU 34 -140.47 -26.35 15 A GLN 40 -132.89 -45.17 15 A TYR 59 -67.84 2.62 15 A GLU 64 58.71 19.44 15 A LEU 71 -48.18 167.49 16 A ALA 46 51.95 17.86 16 A ARG 74 52.58 75.99 17 A GLU 34 -132.96 -43.21 17 A GLN 40 -145.14 -44.13 17 A LEU 71 -47.90 164.65 17 A ARG 74 58.90 6.64 18 A ALA 46 51.50 19.04 18 A ARG 72 -35.70 156.96 18 A LEU 73 -138.51 -90.91 19 A GLU 34 -141.36 -52.67 19 A ALA 46 55.43 -6.38 19 A LEU 71 -53.00 174.94 20 A LEU 8 -68.69 5.56 20 A GLU 34 -141.77 10.65 20 A ARG 72 -76.34 -80.52 20 A LEU 73 -155.18 -63.13 lowest energy, model1 The pure alternative state of ubiquitin 1 N N A THR 22 A THR 22 HELX_P A GLU 34 A GLU 34 1 1 13 A PRO 37 A PRO 37 HELX_P A ASP 39 A ASP 39 5 2 3 PROTEIN BINDING ubiquitin, alternatively folded state, high-pressure NMR, Q41N variant, PROTEIN BINDING UBC_HUMAN UNP 1 1 P0CG48 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 1 76 2RU6 1 76 P0CG48 A 1 1 76 1 GLN engineered mutation ASN 41 2RU6 A P0CG48 UNP 41 41 5 anti-parallel parallel anti-parallel anti-parallel A THR 12 A THR 12 A GLU 16 A GLU 16 A GLN 2 A GLN 2 A LYS 6 A LYS 6 A THR 66 A THR 66 A LEU 71 A LEU 71 A ASN 41 A ASN 41 A PHE 45 A PHE 45 A LYS 48 A LYS 48 A GLN 49 A GLN 49