0.028598 0.016511 0.000000 0.000000 0.033023 0.000000 0.000000 0.000000 0.015566 0.00000 0.00000 0.00000 Fisher, R.D. Wang, B. Alam, S.L. Higginson, D.S. Rich, R. Myszka, D. Sundquist, W.I. Hill, C.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 34.967 34.967 64.243 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE 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 H2 O 18.015 WATER non-polymer 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 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N O N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N N N 58 S C N 59 N C N 60 N O N 61 N C N 62 N C N 63 N C N 64 N O N 65 N N N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N N N 78 S C N 79 N C N 80 N O N 81 N C N 82 N C N 83 N C N 84 N O N 85 N O N 86 N O N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N O N 97 N H N 98 N H N 99 N N N 100 S C N 101 N C N 102 N O N 103 S C N 104 N C N 105 N C N 106 N C N 107 N O N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N N N 122 S C N 123 N C N 124 N O N 125 N C N 126 N C N 127 N C N 128 N C N 129 N O N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N N N 144 S C N 145 N C N 146 N O N 147 N C N 148 N C N 149 N C N 150 N C N 151 N N N 152 N O N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N N N 169 S C N 170 N C N 171 N O N 172 N C N 173 N C N 174 N C N 175 N O N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N N N 186 S C N 187 N C N 188 N O N 189 N C N 190 N O N 191 N O N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N ZN N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N doub N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N doub N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N doub N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N doub N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N doub N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N doub N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing US J.Biol.Chem. JBCHA3 0071 0021-9258 278 28976 28984 10.1074/jbc.M302596200 12750381 Structure and ubiquitin binding of the ubiquitin-interacting motif. 2003 10.2210/pdb1o06/pdb pdb_00001o06 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 100 1 IMAGE PLATE 2002-01-10 RIGAKU RAXIS IV Yale mirrors SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 2245.353 Vacuolar protein sorting-associated protein VPS27 Residues 301-320 1 syn polymer 65.409 ZINC ION 3 syn non-polymer 18.015 water 26 nat water no no EEDPDLKAAIQESLREAEEA EEDPDLKAAIQESLREAEEA A polypeptide(L) n n n n n n n n n n n n n n n n n n n n 1 1.98 37.24 VAPOR DIFFUSION, SITTING DROP 6.5 0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K 293.0 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle pdbx_struct_special_symmetry struct_conn struct_site repository Initial release Version format compliance Derived calculations Version format compliance Data collection Database references Derived calculations 1 0 2003-07-22 1 1 2008-04-29 1 2 2011-07-13 1 3 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2003-02-20 REL REL ZN ZINC ION HOH water This sequence occurs naturally in Saccharomyces cerevisiae Vps27p and was synthesized by standard peptide synthesis methods sample ZN 101 2 ZN ZN 101 A ZN 102 2 ZN ZN 102 A ZN 103 2 ZN ZN 103 A HOH 201 3 HOH HOH 201 A HOH 202 3 HOH HOH 202 A HOH 203 3 HOH HOH 203 A HOH 204 3 HOH HOH 204 A HOH 205 3 HOH HOH 205 A HOH 206 3 HOH HOH 206 A HOH 207 3 HOH HOH 207 A HOH 208 3 HOH HOH 208 A HOH 209 3 HOH HOH 209 A HOH 210 3 HOH HOH 210 A HOH 211 3 HOH HOH 211 A HOH 212 3 HOH HOH 212 A HOH 213 3 HOH HOH 213 A HOH 214 3 HOH HOH 214 A HOH 215 3 HOH HOH 215 A HOH 216 3 HOH HOH 216 A HOH 217 3 HOH HOH 217 A HOH 218 3 HOH HOH 218 A HOH 219 3 HOH HOH 219 A HOH 220 3 HOH HOH 220 A HOH 221 3 HOH HOH 221 A HOH 222 3 HOH HOH 222 A HOH 223 3 HOH HOH 223 A HOH 224 3 HOH HOH 224 A HOH 225 3 HOH HOH 225 A HOH 226 3 HOH HOH 226 A GLU 1 n 1 GLU 1 A GLU 2 n 2 GLU 2 A ASP 3 n 3 ASP 3 A PRO 4 n 4 PRO 4 A ASP 5 n 5 ASP 5 A LEU 6 n 6 LEU 6 A LYS 7 n 7 LYS 7 A ALA 8 n 8 ALA 8 A ALA 9 n 9 ALA 9 A ILE 10 n 10 ILE 10 A GLN 11 n 11 GLN 11 A GLU 12 n 12 GLU 12 A SER 13 n 13 SER 13 A LEU 14 n 14 LEU 14 A ARG 15 n 15 ARG 15 A GLU 16 n 16 GLU 16 A ALA 17 n 17 ALA 17 A GLU 18 n 18 GLU 18 A GLU 19 n 19 GLU 19 A ALA 20 n 20 ALA 20 A author_and_software_defined_assembly PQS 1 monomeric software_defined_assembly PISA 2 dimeric software_defined_assembly PISA 2 dimeric 1300 -75 3310 530 -66 4080 A GLU 1 A N GLU 1 1_555 A ZN 103 B D ZN ZN 1_555 A GLU 18 A OE1 GLU 18 11_665 84.6 A GLU 1 A N GLU 1 1_555 A ZN 103 B D ZN ZN 1_555 A ALA 20 A OXT ALA 20 8_675 84.7 A GLU 18 A OE1 GLU 18 11_665 A ZN 103 B D ZN ZN 1_555 A ALA 20 A OXT ALA 20 8_675 110.7 A GLU 1 A N GLU 1 1_555 A ZN 103 B D ZN ZN 1_555 A ALA 20 A O ALA 20 8_675 143.8 A GLU 18 A OE1 GLU 18 11_665 A ZN 103 B D ZN ZN 1_555 A ALA 20 A O ALA 20 8_675 122.2 A ALA 20 A OXT ALA 20 8_675 A ZN 103 B D ZN ZN 1_555 A ALA 20 A O ALA 20 8_675 64.2 A GLU 1 A N GLU 1 1_555 A ZN 103 A D ZN ZN 1_555 A GLU 18 A OE1 GLU 18 11_665 115.2 A GLU 1 A N GLU 1 1_555 A ZN 103 A D ZN ZN 1_555 A ALA 20 A OXT ALA 20 8_675 96.5 A GLU 18 A OE1 GLU 18 11_665 A ZN 103 A D ZN ZN 1_555 A ALA 20 A OXT ALA 20 8_675 106.2 A ASP 3 A OD2 ASP 3 12_575 A ZN 101 B ZN ZN 1_555 A ASP 5 A OD2 ASP 5 1_555 129.2 A ASP 3 A OD2 ASP 3 12_575 A ZN 101 B ZN ZN 1_555 A ASP 5 A OD1 ASP 5 1_555 91.0 A ASP 5 A OD2 ASP 5 1_555 A ZN 101 B ZN ZN 1_555 A ASP 5 A OD1 ASP 5 1_555 51.1 A ASP 3 A OD2 ASP 3 12_575 A ZN 101 B ZN ZN 1_555 A GLU 16 A OE1 GLU 16 9_665 96.4 A ASP 5 A OD2 ASP 5 1_555 A ZN 101 B ZN ZN 1_555 A GLU 16 A OE1 GLU 16 9_665 109.2 A ASP 5 A OD1 ASP 5 1_555 A ZN 101 B ZN ZN 1_555 A GLU 16 A OE1 GLU 16 9_665 157.3 A ASP 3 A OD2 ASP 3 12_575 A ZN 101 B ZN ZN 1_555 A GLU 19 A OE1 GLU 19 9_665 96.8 A ASP 5 A OD2 ASP 5 1_555 A ZN 101 B ZN ZN 1_555 A GLU 19 A OE1 GLU 19 9_665 116.0 A ASP 5 A OD1 ASP 5 1_555 A ZN 101 B ZN ZN 1_555 A GLU 19 A OE1 GLU 19 9_665 94.5 A GLU 16 A OE1 GLU 16 9_665 A ZN 101 B ZN ZN 1_555 A GLU 19 A OE1 GLU 19 9_665 105.8 A ASP 5 A OD2 ASP 5 1_555 A ZN 102 C ZN ZN 1_555 A ASP 5 A OD2 ASP 5 12_575 82.3 A ASP 5 A OD2 ASP 5 1_555 A ZN 102 C ZN ZN 1_555 A GLU 16 A OE2 GLU 16 9_665 91.4 A ASP 5 A OD2 ASP 5 12_575 A ZN 102 C ZN ZN 1_555 A GLU 16 A OE2 GLU 16 9_665 113.9 A ASP 5 A OD2 ASP 5 1_555 A ZN 102 C ZN ZN 1_555 A GLU 16 A OE2 GLU 16 4_675 116.5 A ASP 5 A OD2 ASP 5 12_575 A ZN 102 C ZN ZN 1_555 A GLU 16 A OE2 GLU 16 4_675 81.1 A GLU 16 A OE2 GLU 16 9_665 A ZN 102 C ZN ZN 1_555 A GLU 16 A OE2 GLU 16 4_675 150.5 A ASP 5 A OD2 ASP 5 1_555 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 4_675 85.6 A ASP 5 A OD2 ASP 5 12_575 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 4_675 148.2 A GLU 16 A OE2 GLU 16 9_665 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 4_675 95.7 A GLU 16 A OE2 GLU 16 4_675 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 4_675 78.3 A ASP 5 A OD2 ASP 5 1_555 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 9_665 146.8 A ASP 5 A OD2 ASP 5 12_575 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 9_665 75.1 A GLU 16 A OE2 GLU 16 9_665 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 9_665 76.2 A GLU 16 A OE2 GLU 16 4_675 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 9_665 84.0 A HOH 205 E O HOH 4_675 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 9_665 125.8 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 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 8_675 x-y+1,-y+2,-z crystal symmetry operation 0.0000000000 60.5646205883 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_785 -x+2,-y+3,z crystal symmetry operation 17.4835000000 90.8469308824 0.0000000000 1 A ZN 102 C ZN 12.368 0.45 0.22 0.00 0.45 0.00 -0.67 0.955 0.928 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.22388 0.18535 0.18884 1.45 30.29 443 4496 4053 9.9 99.38 1.026 0.041 RANDOM 1 Isotropic THROUGHOUT 0 0 SAD 0.070 0.076 0.80 0.80 1.40 MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 1.45 30.29 26 186 3 0 157 0.008 0.021 174 0.002 0.020 146 1.365 2.003 236 0.733 3.000 350 3.116 5.000 23 0.051 0.200 25 0.004 0.020 211 0.002 0.020 26 0.346 0.200 49 0.254 0.200 177 0.087 0.200 102 0.293 0.200 20 0.205 0.200 2 0.341 0.200 12 0.142 0.200 13 0.280 0.200 11 0.681 1.500 113 1.340 2.000 180 2.418 3.000 61 4.260 4.500 56 0.259 0.248 1.488 30 262 20 94.2 1.45 30 1O06 4525 4525 -2 0.034 1 33.5 7.1 99.3 0.135 1.45 1.50 10.5 1 94.2 refinement REFMAC 5.1.19 data reduction DENZO data scaling SCALEPACK phasing SOLVE Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) 1 N N 2 N N 2 N N 2 N N 3 N N A ASP 3 A ASP 3 HELX_P A GLU 19 A GLU 19 1 1 17 metalc 2.536 B A GLU 1 A N GLU 1 1_555 A ZN 103 D ZN ZN 1_555 metalc 1.789 A A GLU 1 A N GLU 1 1_555 A ZN 103 D ZN ZN 1_555 metalc 1.906 A ASP 3 A OD2 ASP 3 12_575 A ZN 101 B ZN ZN 1_555 metalc 1.916 A ASP 5 A OD2 ASP 5 1_555 A ZN 101 B ZN ZN 1_555 metalc 2.731 A ASP 5 A OD1 ASP 5 1_555 A ZN 101 B ZN ZN 1_555 metalc 2.311 A ASP 5 A OD2 ASP 5 1_555 A ZN 102 C ZN ZN 1_555 metalc 2.563 A ASP 5 A OD2 ASP 5 12_575 A ZN 102 C ZN ZN 1_555 metalc 1.961 A GLU 16 A OE1 GLU 16 9_665 A ZN 101 B ZN ZN 1_555 metalc 2.107 A GLU 16 A OE2 GLU 16 9_665 A ZN 102 C ZN ZN 1_555 metalc 2.301 A GLU 16 A OE2 GLU 16 4_675 A ZN 102 C ZN ZN 1_555 metalc 2.364 B A GLU 18 A OE1 GLU 18 11_665 A ZN 103 D ZN ZN 1_555 metalc 2.113 A A GLU 18 A OE1 GLU 18 11_665 A ZN 103 D ZN ZN 1_555 metalc 2.006 A GLU 19 A OE1 GLU 19 9_665 A ZN 101 B ZN ZN 1_555 metalc 1.771 B A ALA 20 A OXT ALA 20 8_675 A ZN 103 D ZN ZN 1_555 metalc 2.089 B A ALA 20 A O ALA 20 8_675 A ZN 103 D ZN ZN 1_555 metalc 2.160 A A ALA 20 A OXT ALA 20 8_675 A ZN 103 D ZN ZN 1_555 metalc 2.241 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 4_675 metalc 2.511 A ZN 102 C ZN ZN 1_555 A HOH 205 E O HOH 9_665 TRANSPORT PROTEIN alpha-helix, coiled-coil, tetramer, TRANSPORT PROTEIN VPS27_YEAST UNP 1 301 P40343 EEDPDLKAAIQESLREAEEA 301 320 1O06 1 20 P40343 A 1 1 20 BINDING SITE FOR RESIDUE ZN A 101 A ZN 101 Software 5 BINDING SITE FOR RESIDUE ZN A 102 A ZN 102 Software 7 BINDING SITE FOR RESIDUE ZN A 103 A ZN 103 Software 3 A ASP 3 A ASP 3 5 12_575 A ASP 5 A ASP 5 5 1_555 A GLU 16 A GLU 16 5 9_665 A GLU 19 A GLU 19 5 9_665 A ZN 102 C ZN 5 1_555 A ASP 5 A ASP 5 7 12_575 A ASP 5 A ASP 5 7 1_555 A GLU 16 A GLU 16 7 4_675 A GLU 16 A GLU 16 7 9_665 A ZN 101 B ZN 7 1_555 A HOH 205 E HOH 7 9_665 A HOH 205 E HOH 7 4_675 A GLU 1 A GLU 1 3 1_555 A GLU 18 A GLU 18 3 11_665 A ALA 20 A ALA 20 3 8_675 180 P 62 2 2