data_2BM1
#
_model_server_result.job_id            KCCgMpHsWAzUpFq5CVMsnA 
_model_server_result.datetime_utc      '2025-02-18 06:37:02' 
_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          2bm1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1689}' 
#
_entry.id    2BM1 
#
_exptl.entry_id    2BM1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            2BM1 
_cell.length_a            76.3 
_cell.length_b            89.7 
_cell.length_c            114.9 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2BM1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 A OG1 THR 26 A THR 26 1_555 C MG MG . A MG 1690 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc2 B O2B GDP . A GDP 1689 1_555 C MG MG . A MG 1690 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc3 C MG MG . A MG 1690 1_555 D O HOH . A HOH 2034 3_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc4 C MG MG . A MG 1690 1_555 D O HOH . A HOH 2060 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
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
PB O1B GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     2BM1 
_atom_sites.fract_transf_matrix[1][1]    0.013106 
_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]    0.011148 
_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]    0.008703 
_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 GDP A 1 1689 1689 GDP GDP . 
C 3 MG A 1 1690 1690 MG MG . 
D 4 HOH A 1 2001 2001 HOH HOH . 
D 4 HOH A 2 2002 2002 HOH HOH . 
D 4 HOH A 3 2003 2003 HOH HOH . 
D 4 HOH A 4 2004 2004 HOH HOH . 
D 4 HOH A 5 2005 2005 HOH HOH . 
D 4 HOH A 6 2006 2006 HOH HOH . 
D 4 HOH A 7 2007 2007 HOH HOH . 
D 4 HOH A 8 2008 2008 HOH HOH . 
D 4 HOH A 9 2009 2009 HOH HOH . 
D 4 HOH A 10 2010 2010 HOH HOH . 
D 4 HOH A 11 2011 2011 HOH HOH . 
D 4 HOH A 12 2012 2012 HOH HOH . 
D 4 HOH A 13 2013 2013 HOH HOH . 
D 4 HOH A 14 2014 2014 HOH HOH . 
D 4 HOH A 15 2015 2015 HOH HOH . 
D 4 HOH A 16 2016 2016 HOH HOH . 
D 4 HOH A 17 2017 2017 HOH HOH . 
D 4 HOH A 18 2018 2018 HOH HOH . 
D 4 HOH A 19 2019 2019 HOH HOH . 
D 4 HOH A 20 2020 2020 HOH HOH . 
D 4 HOH A 21 2021 2021 HOH HOH . 
D 4 HOH A 22 2022 2022 HOH HOH . 
D 4 HOH A 23 2023 2023 HOH HOH . 
D 4 HOH A 24 2024 2024 HOH HOH . 
D 4 HOH A 25 2025 2025 HOH HOH . 
D 4 HOH A 26 2026 2026 HOH HOH . 
D 4 HOH A 27 2027 2027 HOH HOH . 
D 4 HOH A 28 2028 2028 HOH HOH . 
D 4 HOH A 29 2029 2029 HOH HOH . 
D 4 HOH A 30 2030 2030 HOH HOH . 
D 4 HOH A 31 2031 2031 HOH HOH . 
D 4 HOH A 32 2032 2032 HOH HOH . 
D 4 HOH A 33 2033 2033 HOH HOH . 
D 4 HOH A 34 2034 2034 HOH HOH . 
D 4 HOH A 35 2035 2035 HOH HOH . 
D 4 HOH A 36 2036 2036 HOH HOH . 
D 4 HOH A 37 2037 2037 HOH HOH . 
D 4 HOH A 38 2038 2038 HOH HOH . 
D 4 HOH A 39 2039 2039 HOH HOH . 
D 4 HOH A 40 2040 2040 HOH HOH . 
D 4 HOH A 41 2041 2041 HOH HOH . 
D 4 HOH A 42 2042 2042 HOH HOH . 
D 4 HOH A 43 2043 2043 HOH HOH . 
D 4 HOH A 44 2044 2044 HOH HOH . 
D 4 HOH A 45 2045 2045 HOH HOH . 
D 4 HOH A 46 2046 2046 HOH HOH . 
D 4 HOH A 47 2047 2047 HOH HOH . 
D 4 HOH A 48 2048 2048 HOH HOH . 
D 4 HOH A 49 2049 2049 HOH HOH . 
D 4 HOH A 50 2050 2050 HOH HOH . 
D 4 HOH A 51 2051 2051 HOH HOH . 
D 4 HOH A 52 2052 2052 HOH HOH . 
D 4 HOH A 53 2053 2053 HOH HOH . 
D 4 HOH A 54 2054 2054 HOH HOH . 
D 4 HOH A 55 2055 2055 HOH HOH . 
D 4 HOH A 56 2056 2056 HOH HOH . 
D 4 HOH A 57 2057 2057 HOH HOH . 
D 4 HOH A 58 2058 2058 HOH HOH . 
D 4 HOH A 59 2059 2059 HOH HOH . 
D 4 HOH A 60 2060 2060 HOH HOH . 
D 4 HOH A 61 2061 2061 HOH HOH . 
D 4 HOH A 62 2062 2062 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 P PB GDP . . . B 2 2.119 -61.979 19.66 1 32.84 ? PB GDP 1689 A 1 
HETATM 2 O O1B GDP . . . B 2 0.65 -61.971 19.409 1 30.03 ? O1B GDP 1689 A 1 
HETATM 3 O O2B GDP . . . B 2 2.417 -61.66 21.156 1 25.43 ? O2B GDP 1689 A 1 
HETATM 4 O O3B GDP . . . B 2 2.738 -61.07 18.588 1 30.3 ? O3B GDP 1689 A 1 
HETATM 5 O O3A GDP . . . B 2 2.657 -63.478 19.348 1 34.48 ? O3A GDP 1689 A 1 
HETATM 6 P PA GDP . . . B 2 3.38 -64.425 20.448 1 35.47 ? PA GDP 1689 A 1 
HETATM 7 O O1A GDP . . . B 2 2.523 -64.776 21.581 1 30.88 ? O1A GDP 1689 A 1 
HETATM 8 O O2A GDP . . . B 2 4.745 -63.878 20.926 1 34.4 ? O2A GDP 1689 A 1 
HETATM 9 O O5' GDP . . . B 2 3.615 -65.646 19.454 1 35.63 ? O5' GDP 1689 A 1 
HETATM 10 C C5' GDP . . . B 2 2.525 -66.256 18.802 1 36.35 ? C5' GDP 1689 A 1 
HETATM 11 C C4' GDP . . . B 2 2.928 -67.692 18.505 1 35.18 ? C4' GDP 1689 A 1 
HETATM 12 O O4' GDP . . . B 2 4.027 -67.627 17.62 1 34.82 ? O4' GDP 1689 A 1 
HETATM 13 C C3' GDP . . . B 2 3.398 -68.426 19.725 1 35.6 ? C3' GDP 1689 A 1 
HETATM 14 O O3' GDP . . . B 2 3.132 -69.787 19.544 1 40.63 ? O3' GDP 1689 A 1 
HETATM 15 C C2' GDP . . . B 2 4.874 -68.242 19.63 1 36.42 ? C2' GDP 1689 A 1 
HETATM 16 O O2' GDP . . . B 2 5.574 -69.275 20.247 1 36.31 ? O2' GDP 1689 A 1 
HETATM 17 C C1' GDP . . . B 2 5.092 -68.306 18.141 1 35.03 ? C1' GDP 1689 A 1 
HETATM 18 N N9 GDP . . . B 2 6.382 -67.744 17.745 1 38.84 ? N9 GDP 1689 A 1 
HETATM 19 C C8 GDP . . . B 2 6.997 -66.595 18.183 1 40.03 ? C8 GDP 1689 A 1 
HETATM 20 N N7 GDP . . . B 2 8.214 -66.523 17.577 1 40.68 ? N7 GDP 1689 A 1 
HETATM 21 C C5 GDP . . . B 2 8.375 -67.607 16.77 1 39.48 ? C5 GDP 1689 A 1 
HETATM 22 C C6 GDP . . . B 2 9.418 -68.028 15.951 1 40.58 ? C6 GDP 1689 A 1 
HETATM 23 O O6 GDP . . . B 2 10.556 -67.546 16.082 1 38.86 ? O6 GDP 1689 A 1 
HETATM 24 N N1 GDP . . . B 2 9.256 -69.221 15.262 1 41.25 ? N1 GDP 1689 A 1 
HETATM 25 C C2 GDP . . . B 2 8.104 -69.98 15.386 1 40.06 ? C2 GDP 1689 A 1 
HETATM 26 N N2 GDP . . . B 2 7.799 -70.813 14.415 1 40.44 ? N2 GDP 1689 A 1 
HETATM 27 N N3 GDP . . . B 2 7.095 -69.56 16.201 1 37.38 ? N3 GDP 1689 A 1 
HETATM 28 C C4 GDP . . . B 2 7.235 -68.391 16.875 1 39.14 ? C4 GDP 1689 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#