data_1SHZ
#
_model_server_result.job_id            iuxH0QILXvmXe2LPI6stWg 
_model_server_result.datetime_utc      '2024-11-22 12:58:40' 
_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          1shz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":475}' 
#
_entry.id    1SHZ 
#
_exptl.entry_id    1SHZ 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          96.91 
_cell.angle_gamma         90 
_cell.entry_id            1SHZ 
_cell.length_a            199.747 
_cell.length_b            105.274 
_cell.length_c            71.748 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1SHZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA tetrameric 4 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,E,F,G,K,L 1 1 
C,D,H,I,J,M,N 2 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N 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 G N N 
? 5 J 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 OG SER 26 A SER 62 1_555 E MG MG . A MG 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc2 A OG1 THR 167 A THR 203 1_555 E MG MG . A MG 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? 
metalc ? metalc3 E MG MG . A MG 377 1_555 F F3 ALF . A ALF 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc4 E MG MG . A MG 377 1_555 G O2B GDP . A GDP 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc5 E MG MG . A MG 377 1_555 K O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.108 ? 
metalc ? metalc6 F AL ALF . A ALF 378 1_555 G O2B GDP . A GDP 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.581 ? 
metalc ? metalc7 F AL ALF . A ALF 378 1_555 G O3B GDP . A GDP 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc8 F AL ALF . A ALF 378 1_555 K O HOH . A HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.866 ? 
metalc ? metalc9 C OG SER 26 D SER 62 1_555 H MG MG . D MG 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc10 C OG1 THR 167 D THR 203 1_555 H MG MG . D MG 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? 
metalc ? metalc11 H MG MG . D MG 377 1_555 I F3 ALF . D ALF 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc12 H MG MG . D MG 377 1_555 I AL ALF . D ALF 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.69 ? 
metalc ? metalc13 H MG MG . D MG 377 1_555 J O2B GDP . D GDP 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc14 H MG MG . D MG 377 1_555 M O HOH . D HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc15 I AL ALF . D ALF 378 1_555 J O3B GDP . D GDP 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc16 I AL ALF . D ALF 378 1_555 M O HOH . D HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
#
_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 87 n n 
PB O2B GDP sing 88 n n 
PB O3B GDP sing 89 n n 
PB O3A GDP sing 90 n n 
O2B HOB2 GDP sing 91 n n 
O3B HOB3 GDP sing 92 n n 
O3A PA GDP sing 93 n n 
PA O1A GDP doub 94 n n 
PA O2A GDP sing 95 n n 
PA O5' GDP sing 96 n n 
O2A HOA2 GDP sing 97 n n 
O5' C5' GDP sing 98 n n 
C5' C4' GDP sing 99 n n 
C5' H5' GDP sing 100 n n 
C5' "H5''" GDP sing 101 n n 
C4' O4' GDP sing 102 n n 
C4' C3' GDP sing 103 n n 
C4' H4' GDP sing 104 n n 
O4' C1' GDP sing 105 n n 
C3' O3' GDP sing 106 n n 
C3' C2' GDP sing 107 n n 
C3' H3' GDP sing 108 n n 
O3' HO3' GDP sing 109 n n 
C2' O2' GDP sing 110 n n 
C2' C1' GDP sing 111 n n 
C2' H2' GDP sing 112 n n 
O2' HO2' GDP sing 113 n n 
C1' N9 GDP sing 114 n n 
C1' H1' GDP sing 115 n n 
N9 C8 GDP sing 116 n y 
N9 C4 GDP sing 117 n y 
C8 N7 GDP doub 118 n y 
C8 H8 GDP sing 119 n n 
N7 C5 GDP sing 120 n y 
C5 C6 GDP sing 121 n n 
C5 C4 GDP doub 122 n y 
C6 O6 GDP doub 123 n n 
C6 N1 GDP sing 124 n n 
N1 C2 GDP sing 125 n n 
N1 HN1 GDP sing 126 n n 
C2 N2 GDP sing 127 n n 
C2 N3 GDP doub 128 n n 
N2 HN21 GDP sing 129 n n 
N2 HN22 GDP sing 130 n n 
N3 C4 GDP sing 131 n n 
#
_atom_sites.entry_id                     1SHZ 
_atom_sites.fract_transf_matrix[1][1]    0.005006 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000606 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009499 
_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]    0.01404 
_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 3 MG A 1 377 376 MG MG . 
F 4 ALF A 1 378 377 ALF ALF . 
G 5 GDP A 1 475 375 GDP GDP . 
H 3 MG D 1 377 376 MG MG . 
I 4 ALF D 1 378 377 ALF ALF . 
J 5 GDP D 1 476 375 GDP GDP . 
K 6 HOH A 1 503 503 HOH HOH . 
K 6 HOH A 2 505 505 HOH HOH . 
K 6 HOH A 3 508 508 HOH HOH . 
K 6 HOH A 4 510 510 HOH HOH . 
K 6 HOH A 5 511 511 HOH HOH . 
K 6 HOH A 6 512 512 HOH HOH . 
K 6 HOH A 7 514 514 HOH HOH . 
K 6 HOH A 8 515 515 HOH HOH . 
K 6 HOH A 9 517 517 HOH HOH . 
K 6 HOH A 10 525 525 HOH HOH . 
K 6 HOH A 11 532 532 HOH HOH . 
K 6 HOH A 12 540 540 HOH HOH . 
K 6 HOH A 13 543 543 HOH HOH . 
K 6 HOH A 14 551 551 HOH HOH . 
K 6 HOH A 15 554 554 HOH HOH . 
K 6 HOH A 16 559 559 HOH HOH . 
K 6 HOH A 17 560 560 HOH HOH . 
K 6 HOH A 18 561 561 HOH HOH . 
K 6 HOH A 19 562 562 HOH HOH . 
K 6 HOH A 20 566 566 HOH HOH . 
K 6 HOH A 21 567 567 HOH HOH . 
K 6 HOH A 22 568 568 HOH HOH . 
K 6 HOH A 23 571 571 HOH HOH . 
K 6 HOH A 24 576 576 HOH HOH . 
K 6 HOH A 25 582 582 HOH HOH . 
L 6 HOH C 1 504 504 HOH HOH . 
L 6 HOH C 2 506 506 HOH HOH . 
L 6 HOH C 3 509 509 HOH HOH . 
L 6 HOH C 4 516 516 HOH HOH . 
L 6 HOH C 5 523 523 HOH HOH . 
L 6 HOH C 6 528 528 HOH HOH . 
L 6 HOH C 7 530 530 HOH HOH . 
L 6 HOH C 8 533 533 HOH HOH . 
L 6 HOH C 9 535 535 HOH HOH . 
L 6 HOH C 10 536 536 HOH HOH . 
L 6 HOH C 11 541 541 HOH HOH . 
L 6 HOH C 12 548 548 HOH HOH . 
L 6 HOH C 13 549 549 HOH HOH . 
L 6 HOH C 14 552 552 HOH HOH . 
L 6 HOH C 15 563 563 HOH HOH . 
L 6 HOH C 16 565 565 HOH HOH . 
L 6 HOH C 17 569 569 HOH HOH . 
L 6 HOH C 18 575 575 HOH HOH . 
L 6 HOH C 19 580 580 HOH HOH . 
L 6 HOH C 20 583 583 HOH HOH . 
M 6 HOH D 1 501 501 HOH HOH . 
M 6 HOH D 2 502 502 HOH HOH . 
M 6 HOH D 3 507 507 HOH HOH . 
M 6 HOH D 4 513 513 HOH HOH . 
M 6 HOH D 5 518 518 HOH HOH . 
M 6 HOH D 6 519 519 HOH HOH . 
M 6 HOH D 7 520 520 HOH HOH . 
M 6 HOH D 8 521 521 HOH HOH . 
M 6 HOH D 9 524 524 HOH HOH . 
M 6 HOH D 10 526 526 HOH HOH . 
M 6 HOH D 11 529 529 HOH HOH . 
M 6 HOH D 12 531 531 HOH HOH . 
M 6 HOH D 13 537 537 HOH HOH . 
M 6 HOH D 14 538 538 HOH HOH . 
M 6 HOH D 15 539 539 HOH HOH . 
M 6 HOH D 16 542 542 HOH HOH . 
M 6 HOH D 17 544 544 HOH HOH . 
M 6 HOH D 18 546 546 HOH HOH . 
M 6 HOH D 19 547 547 HOH HOH . 
M 6 HOH D 20 550 550 HOH HOH . 
M 6 HOH D 21 555 555 HOH HOH . 
M 6 HOH D 22 556 556 HOH HOH . 
M 6 HOH D 23 558 558 HOH HOH . 
M 6 HOH D 24 564 564 HOH HOH . 
M 6 HOH D 25 570 570 HOH HOH . 
M 6 HOH D 26 572 572 HOH HOH . 
M 6 HOH D 27 574 574 HOH HOH . 
M 6 HOH D 28 581 581 HOH HOH . 
M 6 HOH D 29 584 584 HOH HOH . 
N 6 HOH F 1 522 522 HOH HOH . 
N 6 HOH F 2 527 527 HOH HOH . 
N 6 HOH F 3 534 534 HOH HOH . 
N 6 HOH F 4 545 545 HOH HOH . 
N 6 HOH F 5 553 553 HOH HOH . 
N 6 HOH F 6 557 557 HOH HOH . 
N 6 HOH F 7 573 573 HOH HOH . 
N 6 HOH F 8 577 577 HOH HOH . 
N 6 HOH F 9 578 578 HOH HOH . 
N 6 HOH F 10 579 579 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 . . . G 5 49.978 2.884 27.906 1 35.96 ? PB GDP 475 A 1 
HETATM 2 O O1B GDP . . . G 5 51.148 1.911 28.018 1 56.05 ? O1B GDP 475 A 1 
HETATM 3 O O2B GDP . . . G 5 49.858 3.981 28.887 1 35.8 ? O2B GDP 475 A 1 
HETATM 4 O O3B GDP . . . G 5 49.786 3.504 26.562 1 45.27 ? O3B GDP 475 A 1 
HETATM 5 O O3A GDP . . . G 5 48.631 1.928 28.064 1 48.59 ? O3A GDP 475 A 1 
HETATM 6 P PA GDP . . . G 5 47.342 2.559 28.781 1 42.74 ? PA GDP 475 A 1 
HETATM 7 O O1A GDP . . . G 5 47.807 2.784 30.154 1 32.92 ? O1A GDP 475 A 1 
HETATM 8 O O2A GDP . . . G 5 46.729 3.772 28.247 1 40.43 ? O2A GDP 475 A 1 
HETATM 9 O O5' GDP . . . G 5 46.294 1.389 28.674 1 47.76 ? O5' GDP 475 A 1 
HETATM 10 C C5' GDP . . . G 5 45.77 0.935 27.509 1 38.66 ? C5' GDP 475 A 1 
HETATM 11 C C4' GDP . . . G 5 44.267 0.667 27.633 1 29.73 ? C4' GDP 475 A 1 
HETATM 12 O O4' GDP . . . G 5 43.984 -0.607 28.176 1 28.12 ? O4' GDP 475 A 1 
HETATM 13 C C3' GDP . . . G 5 43.473 1.618 28.425 1 25.62 ? C3' GDP 475 A 1 
HETATM 14 O O3' GDP . . . G 5 42.163 1.568 27.965 1 24.27 ? O3' GDP 475 A 1 
HETATM 15 C C2' GDP . . . G 5 43.421 0.892 29.793 1 28.15 ? C2' GDP 475 A 1 
HETATM 16 O O2' GDP . . . G 5 42.13 1.029 30.374 1 24.05 ? O2' GDP 475 A 1 
HETATM 17 C C1' GDP . . . G 5 43.387 -0.56 29.5 1 22.81 ? C1' GDP 475 A 1 
HETATM 18 N N9 GDP . . . G 5 44.168 -1.557 30.37 1 33.38 ? N9 GDP 475 A 1 
HETATM 19 C C8 GDP . . . G 5 45.423 -1.551 30.884 1 46.45 ? C8 GDP 475 A 1 
HETATM 20 N N7 GDP . . . G 5 45.843 -2.629 31.447 1 44.86 ? N7 GDP 475 A 1 
HETATM 21 C C5 GDP . . . G 5 44.752 -3.443 31.318 1 49.12 ? C5 GDP 475 A 1 
HETATM 22 C C6 GDP . . . G 5 44.572 -4.79 31.752 1 55.39 ? C6 GDP 475 A 1 
HETATM 23 O O6 GDP . . . G 5 45.379 -5.495 32.365 1 57.94 ? O6 GDP 475 A 1 
HETATM 24 N N1 GDP . . . G 5 43.291 -5.267 31.396 1 54.96 ? N1 GDP 475 A 1 
HETATM 25 C C2 GDP . . . G 5 42.316 -4.537 30.709 1 50.3 ? C2 GDP 475 A 1 
HETATM 26 N N2 GDP . . . G 5 41.18 -5.088 30.387 1 48.99 ? N2 GDP 475 A 1 
HETATM 27 N N3 GDP . . . G 5 42.482 -3.288 30.326 1 48.85 ? N3 GDP 475 A 1 
HETATM 28 C C4 GDP . . . G 5 43.725 -2.805 30.67 1 42.79 ? C4 GDP 475 A 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#