data_6YXI
#
_model_server_result.job_id            op4h9-pBfXQlGjkKG35-iQ 
_model_server_result.datetime_utc      '2024-11-05 14:04:33' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          6yxi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1512}' 
#
_entry.id    6YXI 
#
_exptl.entry_id    6YXI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            6YXI 
_cell.length_a            59.52 
_cell.length_b            72.16 
_cell.length_c            77.93 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YXI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 6 L N N 
? 6 M N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.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_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_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_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
disulf ? disulf1 A SG CYS 24 A CYS 101 1_555 A SG CYS 106 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf2 A SG CYS 53 A CYS 130 1_555 A SG CYS 59 A CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 A SG CYS 229 A CYS 306 1_555 A SG CYS 241 A CYS 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf4 A SG CYS 309 A CYS 386 1_555 A SG CYS 372 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf5 A SG CYS 336 A CYS 413 1_555 A SG CYS 355 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf6 A SG CYS 363 A CYS 440 1_555 A SG CYS 368 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
covale ? covale1 A ND2 ASN 19 A ASN 96 1_555 C C1 NAG . A NAG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
#
_chem_comp.formula           'C2 H6 O2' 
_chem_comp.formula_weight    62.068 
_chem_comp.id                EDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-ETHANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ETHYLENE GLYCOL' 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C1 O1 EDO sing 92 n n 
C1 C2 EDO sing 93 n n 
C1 H11 EDO sing 94 n n 
C1 H12 EDO sing 95 n n 
O1 HO1 EDO sing 96 n n 
C2 O2 EDO sing 97 n n 
C2 H21 EDO sing 98 n n 
C2 H22 EDO sing 99 n n 
O2 HO2 EDO sing 100 n n 
#
_atom_sites.entry_id                     6YXI 
_atom_sites.fract_transf_matrix[1][1]    0.016801 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013858 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.012832 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 PZ8 A 1 1501 1501 PZ8 XXX . 
C 3 NAG A 1 1502 1502 NAG NAG . 
D 4 DMS A 1 1503 13 DMS DMS . 
E 5 SO4 A 1 1504 13 SO4 SO4 . 
F 5 SO4 A 1 1505 14 SO4 SO4 . 
G 5 SO4 A 1 1506 15 SO4 SO4 . 
H 5 SO4 A 1 1507 16 SO4 SO4 . 
I 5 SO4 A 1 1508 18 SO4 SO4 . 
J 5 SO4 A 1 1509 19 SO4 SO4 . 
K 5 SO4 A 1 1510 20 SO4 SO4 . 
L 6 EDO A 1 1511 2 EDO EDO . 
M 6 EDO A 1 1512 3 EDO EDO . 
N 7 HOH A 1 1601 284 HOH HOH . 
N 7 HOH A 2 1602 250 HOH HOH . 
N 7 HOH A 3 1603 33 HOH HOH . 
N 7 HOH A 4 1604 145 HOH HOH . 
N 7 HOH A 5 1605 292 HOH HOH . 
N 7 HOH A 6 1606 164 HOH HOH . 
N 7 HOH A 7 1607 222 HOH HOH . 
N 7 HOH A 8 1608 82 HOH HOH . 
N 7 HOH A 9 1609 251 HOH HOH . 
N 7 HOH A 10 1610 146 HOH HOH . 
N 7 HOH A 11 1611 107 HOH HOH . 
N 7 HOH A 12 1612 186 HOH HOH . 
N 7 HOH A 13 1613 22 HOH HOH . 
N 7 HOH A 14 1614 190 HOH HOH . 
N 7 HOH A 15 1615 61 HOH HOH . 
N 7 HOH A 16 1616 39 HOH HOH . 
N 7 HOH A 17 1617 57 HOH HOH . 
N 7 HOH A 18 1618 12 HOH HOH . 
N 7 HOH A 19 1619 64 HOH HOH . 
N 7 HOH A 20 1620 230 HOH HOH . 
N 7 HOH A 21 1621 99 HOH HOH . 
N 7 HOH A 22 1622 15 HOH HOH . 
N 7 HOH A 23 1623 193 HOH HOH . 
N 7 HOH A 24 1624 75 HOH HOH . 
N 7 HOH A 25 1625 105 HOH HOH . 
N 7 HOH A 26 1626 137 HOH HOH . 
N 7 HOH A 27 1627 117 HOH HOH . 
N 7 HOH A 28 1628 46 HOH HOH . 
N 7 HOH A 29 1629 240 HOH HOH . 
N 7 HOH A 30 1630 283 HOH HOH . 
N 7 HOH A 31 1631 24 HOH HOH . 
N 7 HOH A 32 1632 49 HOH HOH . 
N 7 HOH A 33 1633 106 HOH HOH . 
N 7 HOH A 34 1634 73 HOH HOH . 
N 7 HOH A 35 1635 4 HOH HOH . 
N 7 HOH A 36 1636 28 HOH HOH . 
N 7 HOH A 37 1637 62 HOH HOH . 
N 7 HOH A 38 1638 53 HOH HOH . 
N 7 HOH A 39 1639 21 HOH HOH . 
N 7 HOH A 40 1640 5 HOH HOH . 
N 7 HOH A 41 1641 48 HOH HOH . 
N 7 HOH A 42 1642 88 HOH HOH . 
N 7 HOH A 43 1643 83 HOH HOH . 
N 7 HOH A 44 1644 59 HOH HOH . 
N 7 HOH A 45 1645 115 HOH HOH . 
N 7 HOH A 46 1646 3 HOH HOH . 
N 7 HOH A 47 1647 91 HOH HOH . 
N 7 HOH A 48 1648 54 HOH HOH . 
N 7 HOH A 49 1649 159 HOH HOH . 
N 7 HOH A 50 1650 34 HOH HOH . 
N 7 HOH A 51 1651 144 HOH HOH . 
N 7 HOH A 52 1652 121 HOH HOH . 
N 7 HOH A 53 1653 125 HOH HOH . 
N 7 HOH A 54 1654 55 HOH HOH . 
N 7 HOH A 55 1655 171 HOH HOH . 
N 7 HOH A 56 1656 72 HOH HOH . 
N 7 HOH A 57 1657 131 HOH HOH . 
N 7 HOH A 58 1658 120 HOH HOH . 
N 7 HOH A 59 1659 41 HOH HOH . 
N 7 HOH A 60 1660 29 HOH HOH . 
N 7 HOH A 61 1661 81 HOH HOH . 
N 7 HOH A 62 1662 32 HOH HOH . 
N 7 HOH A 63 1663 9 HOH HOH . 
N 7 HOH A 64 1664 220 HOH HOH . 
N 7 HOH A 65 1665 36 HOH HOH . 
N 7 HOH A 66 1666 38 HOH HOH . 
N 7 HOH A 67 1667 130 HOH HOH . 
N 7 HOH A 68 1668 17 HOH HOH . 
N 7 HOH A 69 1669 11 HOH HOH . 
N 7 HOH A 70 1670 60 HOH HOH . 
N 7 HOH A 71 1671 8 HOH HOH . 
N 7 HOH A 72 1672 20 HOH HOH . 
N 7 HOH A 73 1673 101 HOH HOH . 
N 7 HOH A 74 1674 68 HOH HOH . 
N 7 HOH A 75 1675 51 HOH HOH . 
N 7 HOH A 76 1676 23 HOH HOH . 
N 7 HOH A 77 1677 276 HOH HOH . 
N 7 HOH A 78 1678 113 HOH HOH . 
N 7 HOH A 79 1679 85 HOH HOH . 
N 7 HOH A 80 1680 150 HOH HOH . 
N 7 HOH A 81 1681 288 HOH HOH . 
N 7 HOH A 82 1682 111 HOH HOH . 
N 7 HOH A 83 1683 66 HOH HOH . 
N 7 HOH A 84 1684 172 HOH HOH . 
N 7 HOH A 85 1685 124 HOH HOH . 
N 7 HOH A 86 1686 31 HOH HOH . 
N 7 HOH A 87 1687 138 HOH HOH . 
N 7 HOH A 88 1688 74 HOH HOH . 
N 7 HOH A 89 1689 179 HOH HOH . 
N 7 HOH A 90 1690 118 HOH HOH . 
N 7 HOH A 91 1691 116 HOH HOH . 
N 7 HOH A 92 1692 114 HOH HOH . 
N 7 HOH A 93 1693 47 HOH HOH . 
N 7 HOH A 94 1694 13 HOH HOH . 
N 7 HOH A 95 1695 126 HOH HOH . 
N 7 HOH A 96 1696 50 HOH HOH . 
N 7 HOH A 97 1697 10 HOH HOH . 
N 7 HOH A 98 1698 194 HOH HOH . 
N 7 HOH A 99 1699 102 HOH HOH . 
N 7 HOH A 100 1700 42 HOH HOH . 
N 7 HOH A 101 1701 143 HOH HOH . 
N 7 HOH A 102 1702 298 HOH HOH . 
N 7 HOH A 103 1703 27 HOH HOH . 
N 7 HOH A 104 1704 132 HOH HOH . 
N 7 HOH A 105 1705 89 HOH HOH . 
N 7 HOH A 106 1706 100 HOH HOH . 
N 7 HOH A 107 1707 139 HOH HOH . 
N 7 HOH A 108 1708 67 HOH HOH . 
N 7 HOH A 109 1709 30 HOH HOH . 
N 7 HOH A 110 1710 69 HOH HOH . 
N 7 HOH A 111 1711 37 HOH HOH . 
N 7 HOH A 112 1712 35 HOH HOH . 
N 7 HOH A 113 1713 273 HOH HOH . 
N 7 HOH A 114 1714 174 HOH HOH . 
N 7 HOH A 115 1715 14 HOH HOH . 
N 7 HOH A 116 1716 79 HOH HOH . 
N 7 HOH A 117 1717 287 HOH HOH . 
N 7 HOH A 118 1718 95 HOH HOH . 
N 7 HOH A 119 1719 166 HOH HOH . 
N 7 HOH A 120 1720 40 HOH HOH . 
N 7 HOH A 121 1721 6 HOH HOH . 
N 7 HOH A 122 1722 56 HOH HOH . 
N 7 HOH A 123 1723 16 HOH HOH . 
N 7 HOH A 124 1724 63 HOH HOH . 
N 7 HOH A 125 1725 173 HOH HOH . 
N 7 HOH A 126 1726 199 HOH HOH . 
N 7 HOH A 127 1727 290 HOH HOH . 
N 7 HOH A 128 1728 160 HOH HOH . 
N 7 HOH A 129 1729 1 HOH HOH . 
N 7 HOH A 130 1730 19 HOH HOH . 
N 7 HOH A 131 1731 167 HOH HOH . 
N 7 HOH A 132 1732 227 HOH HOH . 
N 7 HOH A 133 1733 80 HOH HOH . 
N 7 HOH A 134 1734 183 HOH HOH . 
N 7 HOH A 135 1735 203 HOH HOH . 
N 7 HOH A 136 1736 77 HOH HOH . 
N 7 HOH A 137 1737 70 HOH HOH . 
N 7 HOH A 138 1738 123 HOH HOH . 
N 7 HOH A 139 1739 45 HOH HOH . 
N 7 HOH A 140 1740 110 HOH HOH . 
N 7 HOH A 141 1741 93 HOH HOH . 
N 7 HOH A 142 1742 129 HOH HOH . 
N 7 HOH A 143 1743 98 HOH HOH . 
N 7 HOH A 144 1744 25 HOH HOH . 
N 7 HOH A 145 1745 161 HOH HOH . 
N 7 HOH A 146 1746 18 HOH HOH . 
N 7 HOH A 147 1747 43 HOH HOH . 
N 7 HOH A 148 1748 94 HOH HOH . 
N 7 HOH A 149 1749 87 HOH HOH . 
N 7 HOH A 150 1750 162 HOH HOH . 
N 7 HOH A 151 1751 134 HOH HOH . 
N 7 HOH A 152 1752 122 HOH HOH . 
N 7 HOH A 153 1753 147 HOH HOH . 
N 7 HOH A 154 1754 291 HOH HOH . 
N 7 HOH A 155 1755 90 HOH HOH . 
N 7 HOH A 156 1756 158 HOH HOH . 
N 7 HOH A 157 1757 92 HOH HOH . 
N 7 HOH A 158 1758 299 HOH HOH . 
N 7 HOH A 159 1759 169 HOH HOH . 
N 7 HOH A 160 1760 52 HOH HOH . 
N 7 HOH A 161 1761 213 HOH HOH . 
N 7 HOH A 162 1762 189 HOH HOH . 
N 7 HOH A 163 1763 104 HOH HOH . 
N 7 HOH A 164 1764 108 HOH HOH . 
N 7 HOH A 165 1765 163 HOH HOH . 
N 7 HOH A 166 1766 205 HOH HOH . 
N 7 HOH A 167 1767 128 HOH HOH . 
N 7 HOH A 168 1768 109 HOH HOH . 
N 7 HOH A 169 1769 295 HOH HOH . 
N 7 HOH A 170 1770 281 HOH HOH . 
N 7 HOH A 171 1771 277 HOH HOH . 
N 7 HOH A 172 1772 86 HOH HOH . 
N 7 HOH A 173 1773 135 HOH HOH . 
N 7 HOH A 174 1774 84 HOH HOH . 
N 7 HOH A 175 1775 181 HOH HOH . 
N 7 HOH A 176 1776 200 HOH HOH . 
N 7 HOH A 177 1777 210 HOH HOH . 
N 7 HOH A 178 1778 178 HOH HOH . 
N 7 HOH A 179 1779 188 HOH HOH . 
N 7 HOH A 180 1780 127 HOH HOH . 
N 7 HOH A 181 1781 285 HOH HOH . 
N 7 HOH A 182 1782 216 HOH HOH . 
N 7 HOH A 183 1783 197 HOH HOH . 
N 7 HOH A 184 1784 204 HOH HOH . 
N 7 HOH A 185 1785 97 HOH HOH . 
N 7 HOH A 186 1786 103 HOH HOH . 
N 7 HOH A 187 1787 182 HOH HOH . 
N 7 HOH A 188 1788 78 HOH HOH . 
N 7 HOH A 189 1789 275 HOH HOH . 
N 7 HOH A 190 1790 228 HOH HOH . 
N 7 HOH A 191 1791 209 HOH HOH . 
N 7 HOH A 192 1792 165 HOH HOH . 
N 7 HOH A 193 1793 157 HOH HOH . 
N 7 HOH A 194 1794 156 HOH HOH . 
N 7 HOH A 195 1795 185 HOH HOH . 
N 7 HOH A 196 1796 148 HOH HOH . 
N 7 HOH A 197 1797 280 HOH HOH . 
N 7 HOH A 198 1798 248 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C1 EDO . . . M 6 29.927 -24.145 8.385 1 64.58 ? C1 EDO 1512 A 1 
HETATM 2 O O1 EDO . . . M 6 29.243 -23.126 9.12 1 63.27 ? O1 EDO 1512 A 1 
HETATM 3 C C2 EDO . . . M 6 31.118 -23.531 7.661 1 64.79 ? C2 EDO 1512 A 1 
HETATM 4 O O2 EDO . . . M 6 31.909 -24.573 7.08 1 64.56 ? O2 EDO 1512 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           4 
#