data_2NGR
#
_model_server_result.job_id            ZuG_LuspWS3QeSqQ_bl70w 
_model_server_result.datetime_utc      '2024-11-25 10:08:56' 
_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          2ngr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":198}' 
#
_entry.id    2NGR 
#
_exptl.entry_id    2NGR 
_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    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         90 
_cell.entry_id            2NGR 
_cell.length_a            52.82 
_cell.length_b            67.69 
_cell.length_c            131.06 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2NGR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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                      4 
_struct_asym.id                             D 
_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 A SG CYS 105 A CYS 105 1_555 A SG CYS 188 A CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc1 A OG1 THR 17 A THR 17 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc3 D O2B GDP . A GDP 198 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? 
metalc ? metalc4 D O3B GDP . A GDP 198 1_555 E AL AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc5 D O2B GDP . A GDP 198 1_555 E AL AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.599 ? 
metalc ? metalc6 C MG MG . A MG 199 1_555 E F3 AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
metalc ? metalc7 C MG MG . A MG 199 1_555 E AL AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.391 ? 
metalc ? metalc8 C MG MG . A MG 199 1_555 F O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc9 C MG MG . A MG 199 1_555 F O HOH . A HOH 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc10 E AL AF3 . A AF3 200 1_555 F O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
#
_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                     2NGR 
_atom_sites.fract_transf_matrix[1][1]    0.018932 
_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]    0.014773 
_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]    0.00763 
_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
C 3 MG A 1 199 199 MG MG . 
D 4 GDP A 1 198 198 GDP GDP . 
E 5 AF3 A 1 200 200 AF3 AF3 . 
F 6 HOH A 1 505 505 HOH HOH . 
F 6 HOH A 2 507 507 HOH HOH . 
F 6 HOH A 3 509 509 HOH HOH . 
F 6 HOH A 4 510 510 HOH HOH . 
F 6 HOH A 5 512 512 HOH HOH . 
F 6 HOH A 6 517 517 HOH HOH . 
F 6 HOH A 7 518 518 HOH HOH . 
F 6 HOH A 8 519 519 HOH HOH . 
F 6 HOH A 9 520 520 HOH HOH . 
F 6 HOH A 10 522 522 HOH HOH . 
F 6 HOH A 11 523 523 HOH HOH . 
F 6 HOH A 12 524 524 HOH HOH . 
F 6 HOH A 13 525 525 HOH HOH . 
F 6 HOH A 14 526 526 HOH HOH . 
F 6 HOH A 15 528 528 HOH HOH . 
F 6 HOH A 16 529 529 HOH HOH . 
F 6 HOH A 17 530 530 HOH HOH . 
F 6 HOH A 18 531 531 HOH HOH . 
F 6 HOH A 19 532 532 HOH HOH . 
F 6 HOH A 20 533 533 HOH HOH . 
F 6 HOH A 21 534 534 HOH HOH . 
F 6 HOH A 22 535 535 HOH HOH . 
F 6 HOH A 23 536 536 HOH HOH . 
F 6 HOH A 24 537 537 HOH HOH . 
F 6 HOH A 25 538 538 HOH HOH . 
F 6 HOH A 26 539 539 HOH HOH . 
F 6 HOH A 27 540 540 HOH HOH . 
F 6 HOH A 28 541 541 HOH HOH . 
F 6 HOH A 29 542 542 HOH HOH . 
F 6 HOH A 30 544 544 HOH HOH . 
F 6 HOH A 31 545 545 HOH HOH . 
F 6 HOH A 32 546 546 HOH HOH . 
F 6 HOH A 33 547 547 HOH HOH . 
F 6 HOH A 34 548 548 HOH HOH . 
F 6 HOH A 35 549 549 HOH HOH . 
F 6 HOH A 36 550 550 HOH HOH . 
F 6 HOH A 37 552 552 HOH HOH . 
F 6 HOH A 38 553 553 HOH HOH . 
F 6 HOH A 39 561 561 HOH HOH . 
F 6 HOH A 40 562 562 HOH HOH . 
F 6 HOH A 41 563 563 HOH HOH . 
F 6 HOH A 42 564 564 HOH HOH . 
F 6 HOH A 43 565 565 HOH HOH . 
F 6 HOH A 44 567 567 HOH HOH . 
F 6 HOH A 45 569 569 HOH HOH . 
F 6 HOH A 46 570 570 HOH HOH . 
F 6 HOH A 47 571 571 HOH HOH . 
F 6 HOH A 48 572 572 HOH HOH . 
F 6 HOH A 49 573 573 HOH HOH . 
F 6 HOH A 50 574 574 HOH HOH . 
F 6 HOH A 51 575 575 HOH HOH . 
F 6 HOH A 52 576 576 HOH HOH . 
F 6 HOH A 53 577 577 HOH HOH . 
F 6 HOH A 54 578 578 HOH HOH . 
F 6 HOH A 55 579 579 HOH HOH . 
F 6 HOH A 56 580 580 HOH HOH . 
F 6 HOH A 57 581 581 HOH HOH . 
F 6 HOH A 58 582 582 HOH HOH . 
F 6 HOH A 59 583 583 HOH HOH . 
F 6 HOH A 60 584 584 HOH HOH . 
F 6 HOH A 61 594 594 HOH HOH . 
F 6 HOH A 62 598 598 HOH HOH . 
F 6 HOH A 63 599 599 HOH HOH . 
F 6 HOH A 64 600 600 HOH HOH . 
F 6 HOH A 65 601 601 HOH HOH . 
G 6 HOH B 1 501 501 HOH HOH . 
G 6 HOH B 2 502 502 HOH HOH . 
G 6 HOH B 3 503 503 HOH HOH . 
G 6 HOH B 4 504 504 HOH HOH . 
G 6 HOH B 5 506 506 HOH HOH . 
G 6 HOH B 6 508 508 HOH HOH . 
G 6 HOH B 7 511 511 HOH HOH . 
G 6 HOH B 8 513 513 HOH HOH . 
G 6 HOH B 9 514 514 HOH HOH . 
G 6 HOH B 10 515 515 HOH HOH . 
G 6 HOH B 11 516 516 HOH HOH . 
G 6 HOH B 12 521 521 HOH HOH . 
G 6 HOH B 13 527 527 HOH HOH . 
G 6 HOH B 14 543 543 HOH HOH . 
G 6 HOH B 15 551 551 HOH HOH . 
G 6 HOH B 16 554 554 HOH HOH . 
G 6 HOH B 17 555 555 HOH HOH . 
G 6 HOH B 18 556 556 HOH HOH . 
G 6 HOH B 19 557 557 HOH HOH . 
G 6 HOH B 20 558 558 HOH HOH . 
G 6 HOH B 21 559 559 HOH HOH . 
G 6 HOH B 22 560 560 HOH HOH . 
G 6 HOH B 23 566 566 HOH HOH . 
G 6 HOH B 24 568 568 HOH HOH . 
G 6 HOH B 25 585 585 HOH HOH . 
G 6 HOH B 26 586 586 HOH HOH . 
G 6 HOH B 27 587 587 HOH HOH . 
G 6 HOH B 28 588 588 HOH HOH . 
G 6 HOH B 29 589 589 HOH HOH . 
G 6 HOH B 30 590 590 HOH HOH . 
G 6 HOH B 31 591 591 HOH HOH . 
G 6 HOH B 32 592 592 HOH HOH . 
G 6 HOH B 33 593 593 HOH HOH . 
G 6 HOH B 34 595 595 HOH HOH . 
G 6 HOH B 35 596 596 HOH HOH . 
G 6 HOH B 36 597 597 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 . . . D 4 23.691 0.951 11.766 1 17.22 ? PB GDP 198 A 1 
HETATM 2 O O1B GDP . . . D 4 23.045 0.515 10.543 1 11.4 ? O1B GDP 198 A 1 
HETATM 3 O O2B GDP . . . D 4 23.747 2.399 12.066 1 19.86 ? O2B GDP 198 A 1 
HETATM 4 O O3B GDP . . . D 4 23.054 0.215 12.956 1 16.16 ? O3B GDP 198 A 1 
HETATM 5 O O3A GDP . . . D 4 25.201 0.393 11.769 1 22.66 ? O3A GDP 198 A 1 
HETATM 6 P PA GDP . . . D 4 26.6 1.155 12.026 1 17.13 ? PA GDP 198 A 1 
HETATM 7 O O1A GDP . . . D 4 26.791 2.184 10.973 1 20.96 ? O1A GDP 198 A 1 
HETATM 8 O O2A GDP . . . D 4 26.707 1.506 13.44 1 14.47 ? O2A GDP 198 A 1 
HETATM 9 O O5' GDP . . . D 4 27.572 -0.092 11.634 1 27.48 ? O5' GDP 198 A 1 
HETATM 10 C C5' GDP . . . D 4 27.432 -1.387 12.256 1 25.12 ? C5' GDP 198 A 1 
HETATM 11 C C4' GDP . . . D 4 28.814 -2.018 12.47 1 26.49 ? C4' GDP 198 A 1 
HETATM 12 O O4' GDP . . . D 4 29.349 -2.417 11.206 1 24.81 ? O4' GDP 198 A 1 
HETATM 13 C C3' GDP . . . D 4 29.833 -1.074 13.101 1 27.98 ? C3' GDP 198 A 1 
HETATM 14 O O3' GDP . . . D 4 30.374 -1.648 14.261 1 34.98 ? O3' GDP 198 A 1 
HETATM 15 C C2' GDP . . . D 4 30.89 -0.782 12.035 1 28.04 ? C2' GDP 198 A 1 
HETATM 16 O O2' GDP . . . D 4 32.252 -0.745 12.501 1 35.43 ? O2' GDP 198 A 1 
HETATM 17 C C1' GDP . . . D 4 30.645 -1.84 10.974 1 24.62 ? C1' GDP 198 A 1 
HETATM 18 N N9 GDP . . . D 4 30.666 -1.266 9.624 1 23.2 ? N9 GDP 198 A 1 
HETATM 19 C C8 GDP . . . D 4 29.872 -0.308 9.074 1 22.49 ? C8 GDP 198 A 1 
HETATM 20 N N7 GDP . . . D 4 30.124 0.003 7.848 1 23.37 ? N7 GDP 198 A 1 
HETATM 21 C C5 GDP . . . D 4 31.197 -0.821 7.529 1 21.38 ? C5 GDP 198 A 1 
HETATM 22 C C6 GDP . . . D 4 31.931 -0.942 6.297 1 21.27 ? C6 GDP 198 A 1 
HETATM 23 O O6 GDP . . . D 4 31.769 -0.332 5.247 1 19.66 ? O6 GDP 198 A 1 
HETATM 24 N N1 GDP . . . D 4 32.947 -1.898 6.394 1 23.59 ? N1 GDP 198 A 1 
HETATM 25 C C2 GDP . . . D 4 33.227 -2.647 7.521 1 23.65 ? C2 GDP 198 A 1 
HETATM 26 N N2 GDP . . . D 4 34.231 -3.506 7.416 1 29.29 ? N2 GDP 198 A 1 
HETATM 27 N N3 GDP . . . D 4 32.548 -2.545 8.678 1 24.26 ? N3 GDP 198 A 1 
HETATM 28 C C4 GDP . . . D 4 31.545 -1.613 8.611 1 24.14 ? C4 GDP 198 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#