data_4M8N
#
_model_server_result.job_id            4GxqkzhlsrnAzmceCp-d4w 
_model_server_result.datetime_utc      '2024-11-05 00:36:06' 
_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          4m8n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":201}' 
#
_entry.id    4M8N 
#
_exptl.entry_id    4M8N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         91.09 
_cell.angle_beta          95.15 
_cell.angle_gamma         90.32 
_cell.entry_id            4M8N 
_cell.length_a            76.276 
_cell.length_b            84.734 
_cell.length_c            138.752 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4M8N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,H,I,J,K,R,S,T,U,X,Y 1 1 
B,C,F,G,L,M,N,O,P,Q,V,W 2 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
? 4 J N N 
? 4 M N N 
? 4 P N N 
? 4 S 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 E OG SER 20 E SER 17 1_555 I MG MG . E MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc2 E OG1 THR 38 E THR 35 1_555 I MG MG . E MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc3 I MG MG . E MG 200 1_555 J O2B GDP . E GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc4 F OG SER 20 F SER 17 1_555 L MG MG . F MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc5 F OG1 THR 38 F THR 35 1_555 L MG MG . F MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc6 L MG MG . F MG 200 1_555 M O2B GDP . F GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
metalc ? metalc7 L MG MG . F MG 200 1_555 M O1B GDP . F GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? 
metalc ? metalc8 G OG SER 20 G SER 17 1_555 O MG MG . G MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? 
metalc ? metalc9 G OG1 THR 38 G THR 35 1_555 O MG MG . G MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc10 O MG MG . G MG 200 1_555 P O2B GDP . G GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? 
metalc ? metalc11 H OG SER 20 H SER 17 1_555 R MG MG . H MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc12 H OG1 THR 38 H THR 35 1_555 R MG MG . H MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc13 H OD2 ASP 60 H ASP 57 1_555 R MG MG . H MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? 
metalc ? metalc14 R MG MG . H MG 200 1_555 S O2B GDP . H GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
#
_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                     4M8N 
_atom_sites.fract_transf_matrix[1][1]    0.01311 
_atom_sites.fract_transf_matrix[1][2]    0.000073 
_atom_sites.fract_transf_matrix[1][3]    0.001183 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011802 
_atom_sites.fract_transf_matrix[2][3]    0.000231 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.007238 
_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
I 3 MG E 1 200 200 MG MG . 
J 4 GDP E 1 201 201 GDP GDP . 
K 5 AF3 E 1 202 202 AF3 AF3 . 
L 3 MG F 1 200 200 MG MG . 
M 4 GDP F 1 201 201 GDP GDP . 
N 5 AF3 F 1 202 202 AF3 AF3 . 
O 3 MG G 1 200 200 MG MG . 
P 4 GDP G 1 201 201 GDP GDP . 
Q 5 AF3 G 1 202 202 AF3 AF3 . 
R 3 MG H 1 200 200 MG MG . 
S 4 GDP H 1 201 201 GDP GDP . 
T 5 AF3 H 1 202 202 AF3 AF3 . 
U 6 HOH A 1 1201 1 HOH HOH . 
U 6 HOH A 2 1202 5 HOH HOH . 
U 6 HOH A 3 1203 7 HOH HOH . 
U 6 HOH A 4 1204 10 HOH HOH . 
V 6 HOH B 1 1201 2 HOH HOH . 
W 6 HOH C 1 1201 3 HOH HOH . 
W 6 HOH C 2 1202 6 HOH HOH . 
W 6 HOH C 3 1203 8 HOH HOH . 
X 6 HOH D 1 1201 4 HOH HOH . 
Y 6 HOH H 1 301 9 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 . . . J 4 -20.578 181.567 -218.258 1 101.76 ? PB GDP 201 E 1 
HETATM 2 O O1B GDP . . . J 4 -19.826 182.311 -219.331 1 94.16 ? O1B GDP 201 E 1 
HETATM 3 O O2B GDP . . . J 4 -19.614 180.733 -217.451 1 92.47 ? O2B GDP 201 E 1 
HETATM 4 O O3B GDP . . . J 4 -21.289 182.549 -217.352 1 91.26 ? O3B GDP 201 E 1 
HETATM 5 O O3A GDP . . . J 4 -21.645 180.608 -218.987 1 183.04 ? O3A GDP 201 E 1 
HETATM 6 P PA GDP . . . J 4 -21.735 179.023 -218.709 1 105.24 ? PA GDP 201 E 1 
HETATM 7 O O1A GDP . . . J 4 -20.418 178.36 -219.04 1 104.81 ? O1A GDP 201 E 1 
HETATM 8 O O2A GDP . . . J 4 -22.133 178.725 -217.281 1 103.25 ? O2A GDP 201 E 1 
HETATM 9 O O5' GDP . . . J 4 -22.876 178.573 -219.748 1 102.94 ? O5' GDP 201 E 1 
HETATM 10 C C5' GDP . . . J 4 -24.234 178.475 -219.322 1 115.95 ? C5' GDP 201 E 1 
HETATM 11 C C4' GDP . . . J 4 -24.991 177.576 -220.29 1 121.01 ? C4' GDP 201 E 1 
HETATM 12 O O4' GDP . . . J 4 -24.627 177.899 -221.633 1 125.87 ? O4' GDP 201 E 1 
HETATM 13 C C3' GDP . . . J 4 -24.654 176.108 -220.081 1 123.34 ? C3' GDP 201 E 1 
HETATM 14 O O3' GDP . . . J 4 -25.764 175.416 -219.504 1 125.11 ? O3' GDP 201 E 1 
HETATM 15 C C2' GDP . . . J 4 -24.382 175.548 -221.462 1 131.5 ? C2' GDP 201 E 1 
HETATM 16 O O2' GDP . . . J 4 -25.306 174.498 -221.758 1 139.18 ? O2' GDP 201 E 1 
HETATM 17 C C1' GDP . . . J 4 -24.598 176.707 -222.422 1 132.04 ? C1' GDP 201 E 1 
HETATM 18 N N9 GDP . . . J 4 -23.484 176.756 -223.4 1 131.63 ? N9 GDP 201 E 1 
HETATM 19 C C8 GDP . . . J 4 -22.244 177.202 -223.134 1 127.53 ? C8 GDP 201 E 1 
HETATM 20 N N7 GDP . . . J 4 -21.455 177.122 -224.232 1 128.53 ? N7 GDP 201 E 1 
HETATM 21 C C5 GDP . . . J 4 -22.201 176.617 -225.229 1 132.31 ? C5 GDP 201 E 1 
HETATM 22 C C6 GDP . . . J 4 -21.978 176.277 -226.651 1 136.6 ? C6 GDP 201 E 1 
HETATM 23 O O6 GDP . . . J 4 -20.859 176.459 -227.178 1 135.86 ? O6 GDP 201 E 1 
HETATM 24 N N1 GDP . . . J 4 -23.005 175.774 -227.346 1 141.28 ? N1 GDP 201 E 1 
HETATM 25 C C2 GDP . . . J 4 -24.216 175.572 -226.793 1 140.69 ? C2 GDP 201 E 1 
HETATM 26 N N2 GDP . . . J 4 -25.198 175.06 -227.575 1 145.85 ? N2 GDP 201 E 1 
HETATM 27 N N3 GDP . . . J 4 -24.494 175.86 -225.493 1 136.02 ? N3 GDP 201 E 1 
HETATM 28 C C4 GDP . . . J 4 -23.541 176.376 -224.68 1 133.1 ? C4 GDP 201 E 1 
#
_model_server_stats.io_time_ms              55 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           344 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#