data_4WTI
#
_model_server_result.job_id            uH0sT08RHjqnvKtLabl_2A 
_model_server_result.datetime_utc      '2024-11-22 11:51:56' 
_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          4wti 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":605}' 
#
_entry.id    4WTI 
#
_exptl.entry_id    4WTI 
_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    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         120 
_cell.entry_id            4WTI 
_cell.length_a            140.15 
_cell.length_b            140.15 
_cell.length_c            92.76 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WTI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K 
_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                      6 
_struct_asym.id                             H 
_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
disulf ? disulf1 C SG CYS 318 A CYS 316 1_555 C SG CYS 368 A CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc1 B O3' C 2 P C 2 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc2 C OD1 ASP 222 A ASP 220 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
metalc ? metalc3 C OD1 ASP 222 A ASP 220 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc4 C O THR 223 A THR 221 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc5 C OE2 GLU 239 A GLU 237 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc6 C ND1 HIS 256 A HIS 254 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc7 C OD1 ASP 320 A ASP 318 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc8 C OD2 ASP 320 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc9 C OD1 ASP 321 A ASP 319 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc10 D MN MN . A MN 601 1_555 H O1A GDP . A GDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc11 D MN MN . A MN 601 1_555 K O HOH . A HOH 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? 
metalc ? metalc12 E MN MN . A MN 602 1_555 H O1B GDP . A GDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc13 E MN MN . A MN 602 1_555 H O1A GDP . A GDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc14 E MN MN . A MN 602 1_555 K O HOH . A HOH 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? 
hydrog WATSON-CRICK hydrog1 A N1 G 3 T G 3 1_555 B N3 C 2 P C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N2 G 3 T G 3 1_555 B O2 C 2 P C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O6 G 3 T G 3 1_555 B N4 C 2 P C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 G 4 T G 4 1_555 B N3 C 1 P C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 G 4 T G 4 1_555 B O2 C 1 P C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 G 4 T G 4 1_555 B N4 C 1 P C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 242 n n 
PB O2B GDP sing 243 n n 
PB O3B GDP sing 244 n n 
PB O3A GDP sing 245 n n 
O2B HOB2 GDP sing 246 n n 
O3B HOB3 GDP sing 247 n n 
O3A PA GDP sing 248 n n 
PA O1A GDP doub 249 n n 
PA O2A GDP sing 250 n n 
PA O5' GDP sing 251 n n 
O2A HOA2 GDP sing 252 n n 
O5' C5' GDP sing 253 n n 
C5' C4' GDP sing 254 n n 
C5' H5' GDP sing 255 n n 
C5' "H5''" GDP sing 256 n n 
C4' O4' GDP sing 257 n n 
C4' C3' GDP sing 258 n n 
C4' H4' GDP sing 259 n n 
O4' C1' GDP sing 260 n n 
C3' O3' GDP sing 261 n n 
C3' C2' GDP sing 262 n n 
C3' H3' GDP sing 263 n n 
O3' HO3' GDP sing 264 n n 
C2' O2' GDP sing 265 n n 
C2' C1' GDP sing 266 n n 
C2' H2' GDP sing 267 n n 
O2' HO2' GDP sing 268 n n 
C1' N9 GDP sing 269 n n 
C1' H1' GDP sing 270 n n 
N9 C8 GDP sing 271 n y 
N9 C4 GDP sing 272 n y 
C8 N7 GDP doub 273 n y 
C8 H8 GDP sing 274 n n 
N7 C5 GDP sing 275 n y 
C5 C6 GDP sing 276 n n 
C5 C4 GDP doub 277 n y 
C6 O6 GDP doub 278 n n 
C6 N1 GDP sing 279 n n 
N1 C2 GDP sing 280 n n 
N1 HN1 GDP sing 281 n n 
C2 N2 GDP sing 282 n n 
C2 N3 GDP doub 283 n n 
N2 HN21 GDP sing 284 n n 
N2 HN22 GDP sing 285 n n 
N3 C4 GDP sing 286 n n 
#
_atom_sites.entry_id                     4WTI 
_atom_sites.fract_transf_matrix[1][1]    0.007135 
_atom_sites.fract_transf_matrix[1][2]    0.00412 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008239 
_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]    0.010781 
_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
D 4 MN A 1 601 1 MN MN . 
E 4 MN A 1 602 2 MN MN . 
F 4 MN A 1 603 3 MN MN . 
G 5 CL A 1 604 4 CL CL . 
H 6 GDP A 1 605 1 GDP GDP . 
I 7 B3P A 1 606 1 B3P B3P . 
J 8 HOH P 1 101 52 HOH HOH . 
K 8 HOH A 1 701 48 HOH HOH . 
K 8 HOH A 2 702 50 HOH HOH . 
K 8 HOH A 3 703 31 HOH HOH . 
K 8 HOH A 4 704 5 HOH HOH . 
K 8 HOH A 5 705 33 HOH HOH . 
K 8 HOH A 6 706 38 HOH HOH . 
K 8 HOH A 7 707 29 HOH HOH . 
K 8 HOH A 8 708 24 HOH HOH . 
K 8 HOH A 9 709 37 HOH HOH . 
K 8 HOH A 10 710 7 HOH HOH . 
K 8 HOH A 11 711 61 HOH HOH . 
K 8 HOH A 12 712 32 HOH HOH . 
K 8 HOH A 13 713 1 HOH HOH . 
K 8 HOH A 14 714 14 HOH HOH . 
K 8 HOH A 15 715 30 HOH HOH . 
K 8 HOH A 16 716 36 HOH HOH . 
K 8 HOH A 17 717 25 HOH HOH . 
K 8 HOH A 18 718 2 HOH HOH . 
K 8 HOH A 19 719 3 HOH HOH . 
K 8 HOH A 20 720 4 HOH HOH . 
K 8 HOH A 21 721 6 HOH HOH . 
K 8 HOH A 22 722 8 HOH HOH . 
K 8 HOH A 23 723 9 HOH HOH . 
K 8 HOH A 24 724 10 HOH HOH . 
K 8 HOH A 25 725 11 HOH HOH . 
K 8 HOH A 26 726 12 HOH HOH . 
K 8 HOH A 27 727 13 HOH HOH . 
K 8 HOH A 28 728 15 HOH HOH . 
K 8 HOH A 29 729 16 HOH HOH . 
K 8 HOH A 30 730 17 HOH HOH . 
K 8 HOH A 31 731 18 HOH HOH . 
K 8 HOH A 32 732 19 HOH HOH . 
K 8 HOH A 33 733 20 HOH HOH . 
K 8 HOH A 34 734 21 HOH HOH . 
K 8 HOH A 35 735 22 HOH HOH . 
K 8 HOH A 36 736 23 HOH HOH . 
K 8 HOH A 37 737 26 HOH HOH . 
K 8 HOH A 38 738 27 HOH HOH . 
K 8 HOH A 39 739 28 HOH HOH . 
K 8 HOH A 40 740 34 HOH HOH . 
K 8 HOH A 41 741 35 HOH HOH . 
K 8 HOH A 42 742 39 HOH HOH . 
K 8 HOH A 43 743 40 HOH HOH . 
K 8 HOH A 44 744 41 HOH HOH . 
K 8 HOH A 45 745 42 HOH HOH . 
K 8 HOH A 46 746 43 HOH HOH . 
K 8 HOH A 47 747 44 HOH HOH . 
K 8 HOH A 48 748 45 HOH HOH . 
K 8 HOH A 49 749 46 HOH HOH . 
K 8 HOH A 50 750 47 HOH HOH . 
K 8 HOH A 51 751 49 HOH HOH . 
K 8 HOH A 52 752 51 HOH HOH . 
K 8 HOH A 53 753 53 HOH HOH . 
K 8 HOH A 54 754 54 HOH HOH . 
K 8 HOH A 55 755 55 HOH HOH . 
K 8 HOH A 56 756 56 HOH HOH . 
K 8 HOH A 57 757 57 HOH HOH . 
K 8 HOH A 58 758 58 HOH HOH . 
K 8 HOH A 59 759 59 HOH HOH . 
K 8 HOH A 60 760 60 HOH HOH . 
K 8 HOH A 61 761 62 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 . . . H 6 42.265 -42.304 2.386 1 58.09 ? PB GDP 605 A 1 
HETATM 2 O O1B GDP . . . H 6 42.383 -43.29 1.242 1 47.51 ? O1B GDP 605 A 1 
HETATM 3 O O2B GDP . . . H 6 42.915 -40.956 2.182 1 58.06 ? O2B GDP 605 A 1 
HETATM 4 O O3B GDP . . . H 6 40.861 -42.143 2.947 1 60.05 ? O3B GDP 605 A 1 
HETATM 5 O O3A GDP . . . H 6 43.123 -42.906 3.626 1 58.54 ? O3A GDP 605 A 1 
HETATM 6 P PA GDP . . . H 6 43.786 -44.375 3.791 1 56.94 ? PA GDP 605 A 1 
HETATM 7 O O1A GDP . . . H 6 44.379 -44.861 2.491 1 62.78 ? O1A GDP 605 A 1 
HETATM 8 O O2A GDP . . . H 6 44.672 -44.302 4.997 1 62.79 ? O2A GDP 605 A 1 
HETATM 9 O O5' GDP . . . H 6 42.545 -45.306 4.228 1 61.36 ? O5' GDP 605 A 1 
HETATM 10 C C5' GDP . . . H 6 41.529 -45.738 3.321 1 60.15 ? C5' GDP 605 A 1 
HETATM 11 C C4' GDP . . . H 6 40.181 -45.941 4.022 1 60.53 ? C4' GDP 605 A 1 
HETATM 12 O O4' GDP . . . H 6 40.24 -46.758 5.222 1 63.57 ? O4' GDP 605 A 1 
HETATM 13 C C3' GDP . . . H 6 39.524 -44.645 4.452 1 60.34 ? C3' GDP 605 A 1 
HETATM 14 O O3' GDP . . . H 6 39 -43.873 3.353 1 56.86 ? O3' GDP 605 A 1 
HETATM 15 C C2' GDP . . . H 6 38.503 -45.178 5.459 1 61.29 ? C2' GDP 605 A 1 
HETATM 16 O O2' GDP . . . H 6 37.293 -45.67 4.859 1 64.66 ? O2' GDP 605 A 1 
HETATM 17 C C1' GDP . . . H 6 39.261 -46.314 6.155 1 60.35 ? C1' GDP 605 A 1 
HETATM 18 N N9 GDP . . . H 6 39.839 -45.678 7.355 1 61.37 ? N9 GDP 605 A 1 
HETATM 19 C C8 GDP . . . H 6 41.043 -45.095 7.486 1 62.2 ? C8 GDP 605 A 1 
HETATM 20 N N7 GDP . . . H 6 41.19 -44.566 8.728 1 63.3 ? N7 GDP 605 A 1 
HETATM 21 C C5 GDP . . . H 6 40.054 -44.791 9.406 1 64.04 ? C5 GDP 605 A 1 
HETATM 22 C C6 GDP . . . H 6 39.518 -44.51 10.758 1 65.64 ? C6 GDP 605 A 1 
HETATM 23 O O6 GDP . . . H 6 40.185 -43.899 11.627 1 63.88 ? O6 GDP 605 A 1 
HETATM 24 N N1 GDP . . . H 6 38.271 -44.93 11.035 1 69.6 ? N1 GDP 605 A 1 
HETATM 25 C C2 GDP . . . H 6 37.504 -45.595 10.144 1 66.5 ? C2 GDP 605 A 1 
HETATM 26 N N2 GDP . . . H 6 36.256 -45.992 10.491 1 67.86 ? N2 GDP 605 A 1 
HETATM 27 N N3 GDP . . . H 6 37.934 -45.884 8.897 1 66.9 ? N3 GDP 605 A 1 
HETATM 28 C C4 GDP . . . H 6 39.168 -45.514 8.485 1 65.32 ? C4 GDP 605 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#