data_4TQ3
#
_model_server_result.job_id            m9LPe5Mivj1CKGwJ8b6hsg 
_model_server_result.datetime_utc      '2025-03-05 19:19:10' 
_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          4tq3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    4TQ3 
#
_exptl.entry_id    4TQ3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              314.209 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'GERANYL DIPHOSPHATE' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.13 
_cell.angle_gamma         90 
_cell.entry_id            4TQ3 
_cell.length_a            54.605 
_cell.length_b            218.922 
_cell.length_c            65.292 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4TQ3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,Q 1 1 
B,H,I,J,R 2 1 
C,K,L,M,S 3 1 
D,N,O,P,T 4 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
? 2 E N N 
? 2 H N N 
? 2 K N N 
? 2 N 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 A OD1 ASN 68 A ASN 68 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc2 A OD2 ASP 72 A ASP 72 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc3 A OD2 ASP 198 A ASP 198 1_555 G MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc4 A OD1 ASP 202 A ASP 202 1_555 G MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc5 E O1A GPP . A GPP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc6 E O2B GPP . A GPP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc7 G MG MG . A MG 403 1_555 Q O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc8 G MG MG . A MG 403 1_555 Q O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc9 G MG MG . A MG 403 1_555 Q O HOH . A HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc10 B OD1 ASN 68 B ASN 68 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc11 B OD2 ASP 72 B ASP 72 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? 
metalc ? metalc12 B OD2 ASP 198 B ASP 198 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? 
metalc ? metalc13 B OD1 ASP 202 B ASP 202 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? 
metalc ? metalc14 H O1A GPP . B GPP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc15 H O2B GPP . B GPP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc16 C OD1 ASN 68 C ASN 68 1_555 M MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc17 C OD2 ASP 72 C ASP 72 1_555 M MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? 
metalc ? metalc18 C OD2 ASP 198 C ASP 198 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc19 C OD1 ASP 202 C ASP 202 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? 
metalc ? metalc20 K O1A GPP . C GPP 401 1_555 M MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc21 K O2B GPP . C GPP 401 1_555 M MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc22 L MG MG . C MG 402 1_555 S O HOH . C HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc23 D OD1 ASN 68 D ASN 68 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc24 D OD2 ASP 72 D ASP 72 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc25 D OD2 ASP 198 D ASP 198 1_555 P MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc26 D OD1 ASP 202 D ASP 202 1_555 P MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc27 N O1A GPP . D GPP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? 
metalc ? metalc28 N O2B GPP . D GPP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
#
_chem_comp.formula           'C10 H20 O7 P2' 
_chem_comp.formula_weight    314.209 
_chem_comp.id                GPP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'GERANYL DIPHOSPHATE' 
_chem_comp.type              non-polymer 
_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
C1 O1 GPP sing 129 n n 
C1 C2 GPP sing 130 n n 
C1 H11 GPP sing 131 n n 
C1 H12 GPP sing 132 n n 
O1 PA GPP sing 133 n n 
C2 C3 GPP doub 134 e n 
C2 H2 GPP sing 135 n n 
C3 C4 GPP sing 136 n n 
C3 C5 GPP sing 137 n n 
C4 H41 GPP sing 138 n n 
C4 H42 GPP sing 139 n n 
C4 H43 GPP sing 140 n n 
C5 C6 GPP sing 141 n n 
C5 H51 GPP sing 142 n n 
C5 H52 GPP sing 143 n n 
C6 C7 GPP sing 144 n n 
C6 H61 GPP sing 145 n n 
C6 H62 GPP sing 146 n n 
C7 C8 GPP doub 147 n n 
C7 H7 GPP sing 148 n n 
C8 C9 GPP sing 149 n n 
C8 C10 GPP sing 150 n n 
C9 H91 GPP sing 151 n n 
C9 H92 GPP sing 152 n n 
C9 H93 GPP sing 153 n n 
C10 H101 GPP sing 154 n n 
C10 H102 GPP sing 155 n n 
C10 H103 GPP sing 156 n n 
PA O1A GPP doub 157 n n 
PA O2A GPP sing 158 n n 
PA O3A GPP sing 159 n n 
O2A HOA2 GPP sing 160 n n 
O3A PB GPP sing 161 n n 
PB O1B GPP doub 162 n n 
PB O2B GPP sing 163 n n 
PB O3B GPP sing 164 n n 
O2B HOB2 GPP sing 165 n n 
O3B HOB3 GPP sing 166 n n 
#
_atom_sites.entry_id                     4TQ3 
_atom_sites.fract_transf_matrix[1][1]    0.018313 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000042 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004568 
_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]    0.015316 
_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
E 2 GPP A 1 401 1 GPP GPP . 
F 3 MG A 1 402 1 MG MG . 
G 3 MG A 1 403 2 MG MG . 
H 2 GPP B 1 401 1 GPP GPP . 
I 3 MG B 1 402 3 MG MG . 
J 3 MG B 1 403 4 MG MG . 
K 2 GPP C 1 401 1 GPP GPP . 
L 3 MG C 1 402 5 MG MG . 
M 3 MG C 1 403 6 MG MG . 
N 2 GPP D 1 401 1 GPP GPP . 
O 3 MG D 1 402 7 MG MG . 
P 3 MG D 1 403 8 MG MG . 
Q 4 HOH A 1 501 1 HOH HOH . 
Q 4 HOH A 2 502 2 HOH HOH . 
Q 4 HOH A 3 503 4 HOH HOH . 
Q 4 HOH A 4 504 5 HOH HOH . 
Q 4 HOH A 5 505 6 HOH HOH . 
Q 4 HOH A 6 506 7 HOH HOH . 
Q 4 HOH A 7 507 13 HOH HOH . 
Q 4 HOH A 8 508 24 HOH HOH . 
Q 4 HOH A 9 509 25 HOH HOH . 
Q 4 HOH A 10 510 26 HOH HOH . 
R 4 HOH B 1 501 20 HOH HOH . 
R 4 HOH B 2 502 22 HOH HOH . 
R 4 HOH B 3 503 23 HOH HOH . 
S 4 HOH C 1 501 8 HOH HOH . 
S 4 HOH C 2 502 9 HOH HOH . 
S 4 HOH C 3 503 10 HOH HOH . 
S 4 HOH C 4 504 11 HOH HOH . 
S 4 HOH C 5 505 12 HOH HOH . 
T 4 HOH D 1 501 21 HOH HOH . 
T 4 HOH D 2 502 14 HOH HOH . 
T 4 HOH D 3 503 15 HOH HOH . 
T 4 HOH D 4 504 16 HOH HOH . 
T 4 HOH D 5 505 17 HOH HOH . 
T 4 HOH D 6 506 18 HOH HOH . 
T 4 HOH D 7 507 19 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 GPP . . . H 2 35.504 -37.984 -4.263 1 46 ? C1 GPP 401 B 1 
HETATM 2 O O1 GPP . . . H 2 35.99 -37.029 -5.216 1 50.32 ? O1 GPP 401 B 1 
HETATM 3 C C2 GPP . . . H 2 34.015 -37.73 -4.086 1 45.02 ? C2 GPP 401 B 1 
HETATM 4 C C3 GPP . . . H 2 33.098 -38.713 -4.104 1 45.1 ? C3 GPP 401 B 1 
HETATM 5 C C4 GPP . . . H 2 33.501 -40.143 -4.316 1 42.13 ? C4 GPP 401 B 1 
HETATM 6 C C5 GPP . . . H 2 31.631 -38.389 -3.937 1 39.68 ? C5 GPP 401 B 1 
HETATM 7 C C6 GPP . . . H 2 31.164 -38.044 -5.345 1 39.72 ? C6 GPP 401 B 1 
HETATM 8 C C7 GPP . . . H 2 29.762 -38.529 -5.574 1 42.45 ? C7 GPP 401 B 1 
HETATM 9 C C8 GPP . . . H 2 28.963 -37.833 -6.389 1 39.63 ? C8 GPP 401 B 1 
HETATM 10 C C9 GPP . . . H 2 29.488 -36.597 -7.072 1 34.48 ? C9 GPP 401 B 1 
HETATM 11 C C10 GPP . . . H 2 27.562 -38.313 -6.618 1 35.62 ? C10 GPP 401 B 1 
HETATM 12 P PA GPP . . . H 2 37.545 -36.69 -5.523 1 50 ? PA GPP 401 B 1 
HETATM 13 O O1A GPP . . . H 2 38.25 -37.903 -6.066 1 48.3 ? O1A GPP 401 B 1 
HETATM 14 O O2A GPP . . . H 2 37.57 -35.407 -6.329 1 60.12 ? O2A GPP 401 B 1 
HETATM 15 O O3A GPP . . . H 2 38.048 -36.279 -4.053 1 49.85 ? O3A GPP 401 B 1 
HETATM 16 P PB GPP . . . H 2 39.176 -37.059 -3.219 1 50.36 ? PB GPP 401 B 1 
HETATM 17 O O1B GPP . . . H 2 38.82 -36.669 -1.8 1 47.21 ? O1B GPP 401 B 1 
HETATM 18 O O2B GPP . . . H 2 38.92 -38.523 -3.523 1 45.48 ? O2B GPP 401 B 1 
HETATM 19 O O3B GPP . . . H 2 40.505 -36.514 -3.728 1 50.2 ? O3B GPP 401 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           19 
#