data_5MLZ
#
_model_server_result.job_id            3KlJW183DeLWjAEwfGsVJg 
_model_server_result.datetime_utc      '2024-12-21 17:20:06' 
_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          5mlz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    5MLZ 
#
_exptl.entry_id    5MLZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_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            5MLZ 
_cell.length_a            90.87 
_cell.length_b            146.21 
_cell.length_c            95.35 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5MLZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,H,I,J,K,L 
_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                      2 
_struct_asym.id                             B 
_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
metalc ? metalc1 A OD2 ASP 113 A ASP 91 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc2 A OE1 GLN 115 A GLN 93 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? 
metalc ? metalc3 B O2B GDP . A GDP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc4 B O2A GDP . A GDP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
#
_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 70 n n 
PB O2B GDP sing 71 n n 
PB O3B GDP sing 72 n n 
PB O3A GDP sing 73 n n 
O2B HOB2 GDP sing 74 n n 
O3B HOB3 GDP sing 75 n n 
O3A PA GDP sing 76 n n 
PA O1A GDP doub 77 n n 
PA O2A GDP sing 78 n n 
PA O5' GDP sing 79 n n 
O2A HOA2 GDP sing 80 n n 
O5' C5' GDP sing 81 n n 
C5' C4' GDP sing 82 n n 
C5' H5' GDP sing 83 n n 
C5' "H5''" GDP sing 84 n n 
C4' O4' GDP sing 85 n n 
C4' C3' GDP sing 86 n n 
C4' H4' GDP sing 87 n n 
O4' C1' GDP sing 88 n n 
C3' O3' GDP sing 89 n n 
C3' C2' GDP sing 90 n n 
C3' H3' GDP sing 91 n n 
O3' HO3' GDP sing 92 n n 
C2' O2' GDP sing 93 n n 
C2' C1' GDP sing 94 n n 
C2' H2' GDP sing 95 n n 
O2' HO2' GDP sing 96 n n 
C1' N9 GDP sing 97 n n 
C1' H1' GDP sing 98 n n 
N9 C8 GDP sing 99 n y 
N9 C4 GDP sing 100 n y 
C8 N7 GDP doub 101 n y 
C8 H8 GDP sing 102 n n 
N7 C5 GDP sing 103 n y 
C5 C6 GDP sing 104 n n 
C5 C4 GDP doub 105 n y 
C6 O6 GDP doub 106 n n 
C6 N1 GDP sing 107 n n 
N1 C2 GDP sing 108 n n 
N1 HN1 GDP sing 109 n n 
C2 N2 GDP sing 110 n n 
C2 N3 GDP doub 111 n n 
N2 HN21 GDP sing 112 n n 
N2 HN22 GDP sing 113 n n 
N3 C4 GDP sing 114 n n 
#
_atom_sites.entry_id                     5MLZ 
_atom_sites.fract_transf_matrix[1][1]    0.011005 
_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]    0.006839 
_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]    0.010488 
_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
B 2 GDP A 1 401 500 GDP GDP . 
C 3 MG A 1 402 501 MG MG . 
D 4 CL A 1 403 502 CL CL . 
E 5 LDA A 1 404 600 LDA LDA . 
F 5 LDA A 1 405 601 LDA LDA . 
G 5 LDA A 1 406 602 LDA LDA . 
H 5 LDA A 1 407 603 LDA LDA . 
I 5 LDA A 1 408 604 LDA LDA . 
J 5 LDA A 1 409 605 LDA LDA . 
K 5 LDA A 1 410 606 LDA LDA . 
L 6 HOH A 1 501 1028 HOH HOH . 
L 6 HOH A 2 502 1045 HOH HOH . 
L 6 HOH A 3 503 1008 HOH HOH . 
L 6 HOH A 4 504 1042 HOH HOH . 
L 6 HOH A 5 505 1032 HOH HOH . 
L 6 HOH A 6 506 1020 HOH HOH . 
L 6 HOH A 7 507 1005 HOH HOH . 
L 6 HOH A 8 508 1040 HOH HOH . 
L 6 HOH A 9 509 1050 HOH HOH . 
L 6 HOH A 10 510 1003 HOH HOH . 
L 6 HOH A 11 511 1011 HOH HOH . 
L 6 HOH A 12 512 1022 HOH HOH . 
L 6 HOH A 13 513 1026 HOH HOH . 
L 6 HOH A 14 514 1010 HOH HOH . 
L 6 HOH A 15 515 1047 HOH HOH . 
L 6 HOH A 16 516 1004 HOH HOH . 
L 6 HOH A 17 517 1033 HOH HOH . 
L 6 HOH A 18 518 1015 HOH HOH . 
L 6 HOH A 19 519 1021 HOH HOH . 
L 6 HOH A 20 520 1024 HOH HOH . 
L 6 HOH A 21 521 1036 HOH HOH . 
L 6 HOH A 22 522 1038 HOH HOH . 
L 6 HOH A 23 523 1014 HOH HOH . 
L 6 HOH A 24 524 1037 HOH HOH . 
L 6 HOH A 25 525 1056 HOH HOH . 
L 6 HOH A 26 526 1013 HOH HOH . 
L 6 HOH A 27 527 1049 HOH HOH . 
L 6 HOH A 28 528 1029 HOH HOH . 
L 6 HOH A 29 529 1027 HOH HOH . 
L 6 HOH A 30 530 1006 HOH HOH . 
L 6 HOH A 31 531 1044 HOH HOH . 
L 6 HOH A 32 532 1019 HOH HOH . 
L 6 HOH A 33 533 1043 HOH HOH . 
L 6 HOH A 34 534 1051 HOH HOH . 
L 6 HOH A 35 535 1002 HOH HOH . 
L 6 HOH A 36 536 1046 HOH HOH . 
L 6 HOH A 37 537 1007 HOH HOH . 
L 6 HOH A 38 538 1039 HOH HOH . 
L 6 HOH A 39 539 1023 HOH HOH . 
L 6 HOH A 40 540 1031 HOH HOH . 
L 6 HOH A 41 541 1012 HOH HOH . 
L 6 HOH A 42 542 1017 HOH HOH . 
L 6 HOH A 43 543 1025 HOH HOH . 
L 6 HOH A 44 544 1041 HOH HOH . 
L 6 HOH A 45 545 1009 HOH HOH . 
L 6 HOH A 46 546 1001 HOH HOH . 
L 6 HOH A 47 547 1053 HOH HOH . 
L 6 HOH A 48 548 1035 HOH HOH . 
L 6 HOH A 49 549 1048 HOH HOH . 
L 6 HOH A 50 550 1057 HOH HOH . 
L 6 HOH A 51 551 1055 HOH HOH . 
L 6 HOH A 52 552 1018 HOH HOH . 
L 6 HOH A 53 553 1058 HOH HOH . 
L 6 HOH A 54 554 1054 HOH HOH . 
L 6 HOH A 55 555 1034 HOH HOH . 
L 6 HOH A 56 556 1030 HOH HOH . 
L 6 HOH A 57 557 1016 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 . . . B 2 1.756 19.435 -1.029 1 65.52 ? PB GDP 401 A 1 
HETATM 2 O O1B GDP . . . B 2 2.976 18.59 -1.302 1 68.41 ? O1B GDP 401 A 1 
HETATM 3 O O2B GDP . . . B 2 1.982 20.246 0.224 1 56.15 ? O2B GDP 401 A 1 
HETATM 4 O O3B GDP . . . B 2 0.548 18.546 -0.854 1 71.26 ? O3B GDP 401 A 1 
HETATM 5 O O3A GDP . . . B 2 1.522 20.436 -2.266 1 65.26 ? O3A GDP 401 A 1 
HETATM 6 P PA GDP . . . B 2 0.156 21.277 -2.369 1 64.65 ? PA GDP 401 A 1 
HETATM 7 O O1A GDP . . . B 2 -0.911 20.486 -3.086 1 69.96 ? O1A GDP 401 A 1 
HETATM 8 O O2A GDP . . . B 2 -0.307 21.692 -0.994 1 48.9 ? O2A GDP 401 A 1 
HETATM 9 O O5' GDP . . . B 2 0.613 22.54 -3.251 1 60.84 ? O5' GDP 401 A 1 
HETATM 10 C C5' GDP . . . B 2 1.199 23.667 -2.606 1 60.16 ? C5' GDP 401 A 1 
HETATM 11 C C4' GDP . . . B 2 0.696 24.942 -3.26 1 59.26 ? C4' GDP 401 A 1 
HETATM 12 O O4' GDP . . . B 2 1.031 24.929 -4.647 1 58.25 ? O4' GDP 401 A 1 
HETATM 13 C C3' GDP . . . B 2 -0.819 25.004 -3.166 1 63.1 ? C3' GDP 401 A 1 
HETATM 14 O O3' GDP . . . B 2 -1.215 26.308 -2.731 1 68.8 ? O3' GDP 401 A 1 
HETATM 15 C C2' GDP . . . B 2 -1.305 24.759 -4.579 1 66.57 ? C2' GDP 401 A 1 
HETATM 16 O O2' GDP . . . B 2 -2.465 25.533 -4.873 1 71.58 ? O2' GDP 401 A 1 
HETATM 17 C C1' GDP . . . B 2 -0.133 25.225 -5.419 1 61.83 ? C1' GDP 401 A 1 
HETATM 18 N N9 GDP . . . B 2 -0.066 24.558 -6.739 1 63.1 ? N9 GDP 401 A 1 
HETATM 19 C C8 GDP . . . B 2 0.153 23.254 -6.993 1 65.14 ? C8 GDP 401 A 1 
HETATM 20 N N7 GDP . . . B 2 0.166 23.02 -8.333 1 64.42 ? N7 GDP 401 A 1 
HETATM 21 C C5 GDP . . . B 2 -0.041 24.199 -8.952 1 57.43 ? C5 GDP 401 A 1 
HETATM 22 C C6 GDP . . . B 2 -0.146 24.679 -10.348 1 61.95 ? C6 GDP 401 A 1 
HETATM 23 O O6 GDP . . . B 2 -0.033 23.894 -11.314 1 65 ? O6 GDP 401 A 1 
HETATM 24 N N1 GDP . . . B 2 -0.364 25.987 -10.543 1 64.62 ? N1 GDP 401 A 1 
HETATM 25 C C2 GDP . . . B 2 -0.489 26.863 -9.527 1 59.54 ? C2 GDP 401 A 1 
HETATM 26 N N2 GDP . . . B 2 -0.71 28.168 -9.817 1 70.43 ? N2 GDP 401 A 1 
HETATM 27 N N3 GDP . . . B 2 -0.408 26.494 -8.228 1 57.15 ? N3 GDP 401 A 1 
HETATM 28 C C4 GDP . . . B 2 -0.187 25.204 -7.893 1 60.11 ? C4 GDP 401 A 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           46 
_model_server_stats.create_model_time_ms    56 
_model_server_stats.query_time_ms           1102 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#