data_4FMD
#
_model_server_result.job_id            '_Gn2V0QvUT2D4BWq7uEo7Q' 
_model_server_result.datetime_utc      '2024-11-05 01:15:52' 
_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          4fmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":202}' 
#
_entry.id    4FMD 
#
_exptl.entry_id    4FMD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            4FMD 
_cell.length_a            106.568 
_cell.length_b            153.221 
_cell.length_c            230.805 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4FMD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,R,S 1 1 
C,D,J,K,L,M,T,U 2 1 
E,F,N,O,P,Q,V,W 3 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
? 5 H N N 
? 5 L N N 
? 5 P 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
metalc ? metalc1 R O HOH . A HOH 401 1_555 G AL AF3 . B AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc2 B OG SER 20 B SER 25 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc3 B OG1 THR 38 B THR 43 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc4 G AL AF3 . B AF3 201 1_555 H O2B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc5 H O3B GDP . B GDP 202 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc6 I MG MG . B MG 203 1_555 S O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc7 I MG MG . B MG 203 1_555 S O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc8 T O HOH . C HOH 501 1_555 K AL AF3 . D AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.798 ? 
metalc ? metalc9 D OG SER 20 D SER 25 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc10 D OG1 THR 38 D THR 43 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? 
metalc ? metalc11 K AL AF3 . D AF3 201 1_555 L O3B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc12 L O3B GDP . D GDP 202 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.135 ? 
metalc ? metalc13 L O1B GDP . D GDP 202 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? 
metalc ? metalc14 M MG MG . D MG 203 1_555 U O HOH . D HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? 
metalc ? metalc15 M MG MG . D MG 203 1_555 U O HOH . D HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc16 V O HOH . E HOH 501 1_555 O AL AF3 . F AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? 
metalc ? metalc17 F OG SER 13 F SER 25 1_555 Q MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? 
metalc ? metalc18 F OG1 THR 31 F THR 43 1_555 Q MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? 
metalc ? metalc19 O AL AF3 . F AF3 201 1_555 P O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc20 P O3B GDP . F GDP 202 1_555 Q MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? 
metalc ? metalc21 Q MG MG . F MG 203 1_555 W O HOH . F HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? 
#
_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 86 n n 
PB O2B GDP sing 87 n n 
PB O3B GDP sing 88 n n 
PB O3A GDP sing 89 n n 
O2B HOB2 GDP sing 90 n n 
O3B HOB3 GDP sing 91 n n 
O3A PA GDP sing 92 n n 
PA O1A GDP doub 93 n n 
PA O2A GDP sing 94 n n 
PA O5' GDP sing 95 n n 
O2A HOA2 GDP sing 96 n n 
O5' C5' GDP sing 97 n n 
C5' C4' GDP sing 98 n n 
C5' H5' GDP sing 99 n n 
C5' "H5''" GDP sing 100 n n 
C4' O4' GDP sing 101 n n 
C4' C3' GDP sing 102 n n 
C4' H4' GDP sing 103 n n 
O4' C1' GDP sing 104 n n 
C3' O3' GDP sing 105 n n 
C3' C2' GDP sing 106 n n 
C3' H3' GDP sing 107 n n 
O3' HO3' GDP sing 108 n n 
C2' O2' GDP sing 109 n n 
C2' C1' GDP sing 110 n n 
C2' H2' GDP sing 111 n n 
O2' HO2' GDP sing 112 n n 
C1' N9 GDP sing 113 n n 
C1' H1' GDP sing 114 n n 
N9 C8 GDP sing 115 n y 
N9 C4 GDP sing 116 n y 
C8 N7 GDP doub 117 n y 
C8 H8 GDP sing 118 n n 
N7 C5 GDP sing 119 n y 
C5 C6 GDP sing 120 n n 
C5 C4 GDP doub 121 n y 
C6 O6 GDP doub 122 n n 
C6 N1 GDP sing 123 n n 
N1 C2 GDP sing 124 n n 
N1 HN1 GDP sing 125 n n 
C2 N2 GDP sing 126 n n 
C2 N3 GDP doub 127 n n 
N2 HN21 GDP sing 128 n n 
N2 HN22 GDP sing 129 n n 
N3 C4 GDP sing 130 n n 
#
_atom_sites.entry_id                     4FMD 
_atom_sites.fract_transf_matrix[1][1]    0.009384 
_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]    0.006527 
_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]    0.004333 
_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
G 4 AF3 B 1 201 506 AF3 AF3 . 
H 5 GDP B 1 202 501 GDP GDP . 
I 6 MG B 1 203 502 MG MG . 
J 7 PGE C 1 401 1 PGE PEG . 
K 4 AF3 D 1 201 506 AF3 AF3 . 
L 5 GDP D 1 202 501 GDP GDP . 
M 6 MG D 1 203 502 MG MG . 
N 8 PEG E 1 401 2 PEG PEG . 
O 4 AF3 F 1 201 505 AF3 AF3 . 
P 5 GDP F 1 202 501 GDP GDP . 
Q 6 MG F 1 203 502 MG MG . 
R 9 HOH A 1 401 505 HOH HOH . 
S 9 HOH B 1 301 503 HOH HOH . 
S 9 HOH B 2 302 504 HOH HOH . 
T 9 HOH C 1 501 501 HOH HOH . 
U 9 HOH D 1 301 503 HOH HOH . 
U 9 HOH D 2 302 504 HOH HOH . 
V 9 HOH E 1 501 501 HOH HOH . 
W 9 HOH F 1 301 503 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 . . . P 5 -12.251 -47.657 -18.419 1 118.03 ? PB GDP 202 F 1 
HETATM 2 O O1B GDP . . . P 5 -11.733 -46.279 -18.664 1 117.3 ? O1B GDP 202 F 1 
HETATM 3 O O2B GDP . . . P 5 -10.995 -48.659 -18.411 1 119.3 ? O2B GDP 202 F 1 
HETATM 4 O O3B GDP . . . P 5 -13.024 -47.815 -17.017 1 118.39 ? O3B GDP 202 F 1 
HETATM 5 O O3A GDP . . . P 5 -13.245 -48.102 -19.618 1 120.92 ? O3A GDP 202 F 1 
HETATM 6 P PA GDP . . . P 5 -14.682 -47.35 -19.719 1 120.65 ? PA GDP 202 F 1 
HETATM 7 O O1A GDP . . . P 5 -15.769 -48.27 -19.311 1 122.58 ? O1A GDP 202 F 1 
HETATM 8 O O2A GDP . . . P 5 -14.756 -46.053 -18.773 1 118.37 ? O2A GDP 202 F 1 
HETATM 9 O O5' GDP . . . P 5 -14.863 -46.929 -21.269 1 121.73 ? O5' GDP 202 F 1 
HETATM 10 C C5' GDP . . . P 5 -16.116 -46.265 -21.42 1 123.28 ? C5' GDP 202 F 1 
HETATM 11 C C4' GDP . . . P 5 -16.471 -46.058 -22.892 1 125.66 ? C4' GDP 202 F 1 
HETATM 12 O O4' GDP . . . P 5 -15.853 -47.028 -23.745 1 127.26 ? O4' GDP 202 F 1 
HETATM 13 C C3' GDP . . . P 5 -17.97 -46.184 -23.116 1 128.25 ? C3' GDP 202 F 1 
HETATM 14 O O3' GDP . . . P 5 -18.588 -44.891 -23.127 1 128.64 ? O3' GDP 202 F 1 
HETATM 15 C C2' GDP . . . P 5 -18.12 -46.873 -24.454 1 130.54 ? C2' GDP 202 F 1 
HETATM 16 O O2' GDP . . . P 5 -18.346 -45.891 -25.472 1 130.61 ? O2' GDP 202 F 1 
HETATM 17 C C1' GDP . . . P 5 -16.786 -47.557 -24.698 1 130.2 ? C1' GDP 202 F 1 
HETATM 18 N N9 GDP . . . P 5 -16.898 -49.04 -24.549 1 132.63 ? N9 GDP 202 F 1 
HETATM 19 C C8 GDP . . . P 5 -16.575 -49.74 -23.448 1 132.1 ? C8 GDP 202 F 1 
HETATM 20 N N7 GDP . . . P 5 -16.79 -51.058 -23.667 1 134.8 ? N7 GDP 202 F 1 
HETATM 21 C C5 GDP . . . P 5 -17.257 -51.188 -24.925 1 136.87 ? C5 GDP 202 F 1 
HETATM 22 C C6 GDP . . . P 5 -17.678 -52.351 -25.759 1 140.02 ? C6 GDP 202 F 1 
HETATM 23 O O6 GDP . . . P 5 -17.636 -53.619 -25.27 1 141.46 ? O6 GDP 202 F 1 
HETATM 24 N N1 GDP . . . P 5 -18.105 -52.12 -27.018 1 141.8 ? N1 GDP 202 F 1 
HETATM 25 C C2 GDP . . . P 5 -18.147 -50.859 -27.513 1 140.88 ? C2 GDP 202 F 1 
HETATM 26 N N2 GDP . . . P 5 -18.584 -50.665 -28.782 1 143.34 ? N2 GDP 202 F 1 
HETATM 27 N N3 GDP . . . P 5 -17.766 -49.786 -26.766 1 137.8 ? N3 GDP 202 F 1 
HETATM 28 C C4 GDP . . . P 5 -17.32 -49.918 -25.483 1 135.75 ? C4 GDP 202 F 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#