data_4FMC
#
_model_server_result.job_id            nmlTYWhuAT_bEz3ttsSs2g 
_model_server_result.datetime_utc      '2024-11-05 00:17:08' 
_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          4fmc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":202}' 
#
_entry.id    4FMC 
#
_exptl.entry_id    4FMC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          6 
_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            4FMC 
_cell.length_a            107.566 
_cell.length_b            152.707 
_cell.length_c            226.706 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4FMC 
_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,J,Q,R 1 1 
C,D,K,L,M,S,T 2 1 
E,F,N,O,P 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
? 6 I N N 
? 6 L N N 
? 6 O 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 Q O HOH . A HOH 501 1_555 H AL AF3 . B AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc2 B OG SER 20 B SER 25 1_555 J MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
metalc ? metalc3 B OG1 THR 38 B THR 43 1_555 J MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc4 H AL AF3 . B AF3 201 1_555 I O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? 
metalc ? metalc5 I O3B GDP . B GDP 202 1_555 J MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc6 J MG MG . B MG 203 1_555 R O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.747 ? 
metalc ? metalc7 J MG MG . B MG 203 1_555 R O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? 
metalc ? metalc8 S O HOH . C HOH 401 1_555 K AL AF3 . D AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc9 D OG SER 20 D SER 25 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc10 D OG1 THR 38 D THR 43 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc11 K AL AF3 . D AF3 201 1_555 L O3B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc12 K AL AF3 . D AF3 201 1_555 L O1B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.395 ? 
metalc ? metalc13 L O3B GDP . D GDP 202 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.674 ? 
metalc ? metalc14 L O1B GDP . D GDP 202 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc15 F OG SER 12 F SER 25 1_555 P MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc16 F OG1 THR 30 F THR 43 1_555 P MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc17 F OD2 ASP 53 F ASP 66 1_555 P MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? 
metalc ? metalc18 N AL AF3 . F AF3 201 1_555 O O2B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc19 N AL AF3 . F AF3 201 1_555 O O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.11 ? 
metalc ? metalc20 O O3B GDP . F GDP 202 1_555 P MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
#
_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                     4FMC 
_atom_sites.fract_transf_matrix[1][1]    0.009297 
_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]    0.006548 
_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]    0.004411 
_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 PGE A 1 401 1 PGE PEG . 
H 5 AF3 B 1 201 506 AF3 AF3 . 
I 6 GDP B 1 202 501 GDP GDP . 
J 7 MG B 1 203 502 MG MG . 
K 5 AF3 D 1 201 505 AF3 AF3 . 
L 6 GDP D 1 202 501 GDP GDP . 
M 7 MG D 1 203 502 MG MG . 
N 5 AF3 F 1 201 503 AF3 AF3 . 
O 6 GDP F 1 202 501 GDP GDP . 
P 7 MG F 1 203 502 MG MG . 
Q 8 HOH A 1 501 505 HOH HOH . 
R 8 HOH B 1 301 503 HOH HOH . 
R 8 HOH B 2 302 504 HOH HOH . 
S 8 HOH C 1 401 504 HOH HOH . 
T 8 HOH D 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 . . . L 6 -4.086 25.748 27.092 1 72.3 ? PB GDP 202 D 1 
HETATM 2 O O1B GDP . . . L 6 -5.276 26.274 26.142 1 70.09 ? O1B GDP 202 D 1 
HETATM 3 O O2B GDP . . . L 6 -4.615 24.72 28.202 1 69.99 ? O2B GDP 202 D 1 
HETATM 4 O O3B GDP . . . L 6 -3.448 26.842 27.848 1 73.28 ? O3B GDP 202 D 1 
HETATM 5 O O3A GDP . . . L 6 -2.99 24.882 26.274 1 77.66 ? O3A GDP 202 D 1 
HETATM 6 P PA GDP . . . L 6 -2.896 25.256 24.709 1 81.26 ? PA GDP 202 D 1 
HETATM 7 O O1A GDP . . . L 6 -4.008 24.624 23.936 1 80.08 ? O1A GDP 202 D 1 
HETATM 8 O O2A GDP . . . L 6 -2.964 26.868 24.621 1 79.12 ? O2A GDP 202 D 1 
HETATM 9 O O5' GDP . . . L 6 -1.49 24.676 24.182 1 85.37 ? O5' GDP 202 D 1 
HETATM 10 C C5' GDP . . . L 6 -0.714 25.731 23.612 1 88.33 ? C5' GDP 202 D 1 
HETATM 11 C C4' GDP . . . L 6 0.467 25.123 22.873 1 94.9 ? C4' GDP 202 D 1 
HETATM 12 O O4' GDP . . . L 6 0.882 23.882 23.476 1 96.55 ? O4' GDP 202 D 1 
HETATM 13 C C3' GDP . . . L 6 0.091 24.772 21.434 1 99.11 ? C3' GDP 202 D 1 
HETATM 14 O O3' GDP . . . L 6 0.309 25.843 20.499 1 102.17 ? O3' GDP 202 D 1 
HETATM 15 C C2' GDP . . . L 6 0.946 23.563 21.121 1 103.01 ? C2' GDP 202 D 1 
HETATM 16 O O2' GDP . . . L 6 2.18 24.004 20.562 1 106.85 ? O2' GDP 202 D 1 
HETATM 17 C C1' GDP . . . L 6 1.169 22.888 22.47 1 101.2 ? C1' GDP 202 D 1 
HETATM 18 N N9 GDP . . . L 6 0.278 21.677 22.54 1 101.49 ? N9 GDP 202 D 1 
HETATM 19 C C8 GDP . . . L 6 -0.973 21.588 23.032 1 97.5 ? C8 GDP 202 D 1 
HETATM 20 N N7 GDP . . . L 6 -1.429 20.311 22.893 1 98.59 ? N7 GDP 202 D 1 
HETATM 21 C C5 GDP . . . L 6 -0.463 19.6 22.301 1 102.98 ? C5 GDP 202 D 1 
HETATM 22 C C6 GDP . . . L 6 -0.321 18.188 21.867 1 108.35 ? C6 GDP 202 D 1 
HETATM 23 O O6 GDP . . . L 6 -1.326 17.277 22.051 1 107.6 ? O6 GDP 202 D 1 
HETATM 24 N N1 GDP . . . L 6 0.849 17.821 21.28 1 113.52 ? N1 GDP 202 D 1 
HETATM 25 C C2 GDP . . . L 6 1.848 18.717 21.092 1 114.19 ? C2 GDP 202 D 1 
HETATM 26 N N2 GDP . . . L 6 3.014 18.357 20.509 1 120.52 ? N2 GDP 202 D 1 
HETATM 27 N N3 GDP . . . L 6 1.715 19.996 21.482 1 110.67 ? N3 GDP 202 D 1 
HETATM 28 C C4 GDP . . . L 6 0.595 20.46 22.078 1 105.17 ? C4 GDP 202 D 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#