data_6UW5
#
_model_server_result.job_id            KGqlebYRC5HcC6ygqegxfA 
_model_server_result.datetime_utc      '2025-01-10 06:08:46' 
_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          6uw5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    6UW5 
#
_exptl.entry_id    6UW5 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.23 
_cell.angle_gamma         90 
_cell.entry_id            6UW5 
_cell.length_a            46.013 
_cell.length_b            73.647 
_cell.length_c            91.27 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6UW5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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,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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 H 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 OD2 ASP 45 B ASP 45 1_555 G CA CA . B CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc2 A OD1 ASP 57 B ASP 57 1_555 G CA CA . B CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc3 A OD2 ASP 57 B ASP 57 1_555 G CA CA . B CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc4 A O GLY 92 B GLY 92 1_555 I CA CA . A CA 402 2_656 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc5 A OE1 GLU 144 B GLU 144 1_555 E CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? 
metalc ? metalc6 A OE2 GLU 144 B GLU 144 1_555 E CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc7 A O GLN 188 B GLN 188 1_555 E CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc8 A OE1 GLN 221 B GLN 221 1_555 F CA CA . B CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? 
metalc ? metalc9 C O2B GDP . B GDP 401 1_555 G CA CA . B CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
metalc ? metalc10 D O6 FO1 . B FO1 402 1_555 G CA CA . B CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
metalc ? metalc11 E CA CA . B CA 403 1_555 J O HOH . B HOH 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc12 E CA CA . B CA 403 2_746 B O LEU 248 A LEU 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc13 E CA CA . B CA 403 2_746 B O GLY 250 A GLY 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc14 E CA CA . B CA 403 1_555 K O HOH . A HOH 552 2_756 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc15 F CA CA . B CA 404 1_555 J O HOH . B HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? 
metalc ? metalc16 F CA CA . B CA 404 1_555 J O HOH . B HOH 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? 
metalc ? metalc17 F CA CA . B CA 404 1_555 J O HOH . B HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc18 G CA CA . B CA 405 1_555 J O HOH . B HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? 
metalc ? metalc19 J O HOH . B HOH 524 2_646 I CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc20 J O HOH . B HOH 547 2_646 I CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc21 B O ASP 157 A ASP 157 1_555 I CA CA . A CA 402 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc22 B O GLY 245 A GLY 245 1_555 I CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
metalc ? metalc23 I CA CA . A CA 402 1_555 K O HOH . A HOH 558 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? 
#
_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 128 n n 
PB O2B GDP sing 129 n n 
PB O3B GDP sing 130 n n 
PB O3A GDP sing 131 n n 
O2B HOB2 GDP sing 132 n n 
O3B HOB3 GDP sing 133 n n 
O3A PA GDP sing 134 n n 
PA O1A GDP doub 135 n n 
PA O2A GDP sing 136 n n 
PA O5' GDP sing 137 n n 
O2A HOA2 GDP sing 138 n n 
O5' C5' GDP sing 139 n n 
C5' C4' GDP sing 140 n n 
C5' H5' GDP sing 141 n n 
C5' "H5''" GDP sing 142 n n 
C4' O4' GDP sing 143 n n 
C4' C3' GDP sing 144 n n 
C4' H4' GDP sing 145 n n 
O4' C1' GDP sing 146 n n 
C3' O3' GDP sing 147 n n 
C3' C2' GDP sing 148 n n 
C3' H3' GDP sing 149 n n 
O3' HO3' GDP sing 150 n n 
C2' O2' GDP sing 151 n n 
C2' C1' GDP sing 152 n n 
C2' H2' GDP sing 153 n n 
O2' HO2' GDP sing 154 n n 
C1' N9 GDP sing 155 n n 
C1' H1' GDP sing 156 n n 
N9 C8 GDP sing 157 n y 
N9 C4 GDP sing 158 n y 
C8 N7 GDP doub 159 n y 
C8 H8 GDP sing 160 n n 
N7 C5 GDP sing 161 n y 
C5 C6 GDP sing 162 n n 
C5 C4 GDP doub 163 n y 
C6 O6 GDP doub 164 n n 
C6 N1 GDP sing 165 n n 
N1 C2 GDP sing 166 n n 
N1 HN1 GDP sing 167 n n 
C2 N2 GDP sing 168 n n 
C2 N3 GDP doub 169 n n 
N2 HN21 GDP sing 170 n n 
N2 HN22 GDP sing 171 n n 
N3 C4 GDP sing 172 n n 
#
_atom_sites.entry_id                     6UW5 
_atom_sites.fract_transf_matrix[1][1]    0.021733 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001991 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013578 
_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]    0.011002 
_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 2 GDP B 1 401 401 GDP GDP . 
D 3 FO1 B 1 402 501 FO1 FO1 . 
E 4 CA B 1 403 2 CA CA . 
F 4 CA B 1 404 3 CA CA . 
G 4 CA B 1 405 4 CA CA . 
H 2 GDP A 1 401 401 GDP GDP . 
I 4 CA A 1 402 1 CA CA . 
J 5 HOH B 1 501 100 HOH HOH . 
J 5 HOH B 2 502 83 HOH HOH . 
J 5 HOH B 3 503 44 HOH HOH . 
J 5 HOH B 4 504 41 HOH HOH . 
J 5 HOH B 5 505 105 HOH HOH . 
J 5 HOH B 6 506 18 HOH HOH . 
J 5 HOH B 7 507 115 HOH HOH . 
J 5 HOH B 8 508 108 HOH HOH . 
J 5 HOH B 9 509 33 HOH HOH . 
J 5 HOH B 10 510 39 HOH HOH . 
J 5 HOH B 11 511 85 HOH HOH . 
J 5 HOH B 12 512 2 HOH HOH . 
J 5 HOH B 13 513 109 HOH HOH . 
J 5 HOH B 14 514 99 HOH HOH . 
J 5 HOH B 15 515 49 HOH HOH . 
J 5 HOH B 16 516 15 HOH HOH . 
J 5 HOH B 17 517 128 HOH HOH . 
J 5 HOH B 18 518 19 HOH HOH . 
J 5 HOH B 19 519 23 HOH HOH . 
J 5 HOH B 20 520 29 HOH HOH . 
J 5 HOH B 21 521 78 HOH HOH . 
J 5 HOH B 22 522 31 HOH HOH . 
J 5 HOH B 23 523 57 HOH HOH . 
J 5 HOH B 24 524 124 HOH HOH . 
J 5 HOH B 25 525 17 HOH HOH . 
J 5 HOH B 26 526 80 HOH HOH . 
J 5 HOH B 27 527 7 HOH HOH . 
J 5 HOH B 28 528 43 HOH HOH . 
J 5 HOH B 29 529 122 HOH HOH . 
J 5 HOH B 30 530 98 HOH HOH . 
J 5 HOH B 31 531 64 HOH HOH . 
J 5 HOH B 32 532 27 HOH HOH . 
J 5 HOH B 33 533 103 HOH HOH . 
J 5 HOH B 34 534 88 HOH HOH . 
J 5 HOH B 35 535 107 HOH HOH . 
J 5 HOH B 36 536 56 HOH HOH . 
J 5 HOH B 37 537 59 HOH HOH . 
J 5 HOH B 38 538 63 HOH HOH . 
J 5 HOH B 39 539 28 HOH HOH . 
J 5 HOH B 40 540 112 HOH HOH . 
J 5 HOH B 41 541 24 HOH HOH . 
J 5 HOH B 42 542 110 HOH HOH . 
J 5 HOH B 43 543 97 HOH HOH . 
J 5 HOH B 44 544 114 HOH HOH . 
J 5 HOH B 45 545 118 HOH HOH . 
J 5 HOH B 46 546 93 HOH HOH . 
J 5 HOH B 47 547 116 HOH HOH . 
K 5 HOH A 1 501 68 HOH HOH . 
K 5 HOH A 2 502 40 HOH HOH . 
K 5 HOH A 3 503 11 HOH HOH . 
K 5 HOH A 4 504 37 HOH HOH . 
K 5 HOH A 5 505 55 HOH HOH . 
K 5 HOH A 6 506 126 HOH HOH . 
K 5 HOH A 7 507 30 HOH HOH . 
K 5 HOH A 8 508 9 HOH HOH . 
K 5 HOH A 9 509 16 HOH HOH . 
K 5 HOH A 10 510 35 HOH HOH . 
K 5 HOH A 11 511 53 HOH HOH . 
K 5 HOH A 12 512 65 HOH HOH . 
K 5 HOH A 13 513 92 HOH HOH . 
K 5 HOH A 14 514 127 HOH HOH . 
K 5 HOH A 15 515 117 HOH HOH . 
K 5 HOH A 16 516 45 HOH HOH . 
K 5 HOH A 17 517 12 HOH HOH . 
K 5 HOH A 18 518 8 HOH HOH . 
K 5 HOH A 19 519 96 HOH HOH . 
K 5 HOH A 20 520 102 HOH HOH . 
K 5 HOH A 21 521 6 HOH HOH . 
K 5 HOH A 22 522 14 HOH HOH . 
K 5 HOH A 23 523 61 HOH HOH . 
K 5 HOH A 24 524 22 HOH HOH . 
K 5 HOH A 25 525 3 HOH HOH . 
K 5 HOH A 26 526 20 HOH HOH . 
K 5 HOH A 27 527 32 HOH HOH . 
K 5 HOH A 28 528 66 HOH HOH . 
K 5 HOH A 29 529 91 HOH HOH . 
K 5 HOH A 30 530 60 HOH HOH . 
K 5 HOH A 31 531 51 HOH HOH . 
K 5 HOH A 32 532 50 HOH HOH . 
K 5 HOH A 33 533 90 HOH HOH . 
K 5 HOH A 34 534 10 HOH HOH . 
K 5 HOH A 35 535 42 HOH HOH . 
K 5 HOH A 36 536 21 HOH HOH . 
K 5 HOH A 37 537 76 HOH HOH . 
K 5 HOH A 38 538 46 HOH HOH . 
K 5 HOH A 39 539 52 HOH HOH . 
K 5 HOH A 40 540 54 HOH HOH . 
K 5 HOH A 41 541 34 HOH HOH . 
K 5 HOH A 42 542 82 HOH HOH . 
K 5 HOH A 43 543 74 HOH HOH . 
K 5 HOH A 44 544 70 HOH HOH . 
K 5 HOH A 45 545 25 HOH HOH . 
K 5 HOH A 46 546 79 HOH HOH . 
K 5 HOH A 47 547 36 HOH HOH . 
K 5 HOH A 48 548 38 HOH HOH . 
K 5 HOH A 49 549 106 HOH HOH . 
K 5 HOH A 50 550 104 HOH HOH . 
K 5 HOH A 51 551 67 HOH HOH . 
K 5 HOH A 52 552 111 HOH HOH . 
K 5 HOH A 53 553 62 HOH HOH . 
K 5 HOH A 54 554 86 HOH HOH . 
K 5 HOH A 55 555 13 HOH HOH . 
K 5 HOH A 56 556 4 HOH HOH . 
K 5 HOH A 57 557 69 HOH HOH . 
K 5 HOH A 58 558 121 HOH HOH . 
K 5 HOH A 59 559 84 HOH HOH . 
K 5 HOH A 60 560 81 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 2 25.043 5.942 52.597 1 87.93 ? PB GDP 401 A 1 
HETATM 2 O O1B GDP . . . H 2 25.794 6.641 51.476 1 71.14 -1 O1B GDP 401 A 1 
HETATM 3 O O2B GDP . . . H 2 23.561 5.821 52.281 1 75.63 ? O2B GDP 401 A 1 
HETATM 4 O O3B GDP . . . H 2 25.595 4.537 52.793 1 91.82 ? O3B GDP 401 A 1 
HETATM 5 O O3A GDP . . . H 2 25.281 6.789 53.961 1 82.85 ? O3A GDP 401 A 1 
HETATM 6 P PA GDP . . . H 2 24.183 7.375 55.022 1 91.47 ? PA GDP 401 A 1 
HETATM 7 O O1A GDP . . . H 2 23.489 8.607 54.476 1 87.64 ? O1A GDP 401 A 1 
HETATM 8 O O2A GDP . . . H 2 24.905 7.697 56.317 1 67.88 -1 O2A GDP 401 A 1 
HETATM 9 O O5' GDP . . . H 2 22.967 6.332 55.256 1 74.1 ? O5' GDP 401 A 1 
HETATM 10 C C5' GDP . . . H 2 23.061 4.961 55.654 1 62.21 ? C5' GDP 401 A 1 
HETATM 11 C C4' GDP . . . H 2 22.358 4.852 56.997 1 51.46 ? C4' GDP 401 A 1 
HETATM 12 O O4' GDP . . . H 2 21.044 5.366 56.834 1 58.04 ? O4' GDP 401 A 1 
HETATM 13 C C3' GDP . . . H 2 22.164 3.398 57.373 1 56.48 ? C3' GDP 401 A 1 
HETATM 14 O O3' GDP . . . H 2 23.133 2.992 58.353 1 74.6 ? O3' GDP 401 A 1 
HETATM 15 C C2' GDP . . . H 2 20.758 3.286 57.934 1 52.51 ? C2' GDP 401 A 1 
HETATM 16 O O2' GDP . . . H 2 20.754 2.857 59.3 1 46.28 ? O2' GDP 401 A 1 
HETATM 17 C C1' GDP . . . H 2 20.186 4.689 57.739 1 55.97 ? C1' GDP 401 A 1 
HETATM 18 N N9 GDP . . . H 2 18.849 4.667 57.123 1 45.05 ? N9 GDP 401 A 1 
HETATM 19 C C8 GDP . . . H 2 18.524 4.376 55.849 1 45.71 ? C8 GDP 401 A 1 
HETATM 20 N N7 GDP . . . H 2 17.184 4.438 55.664 1 48.73 ? N7 GDP 401 A 1 
HETATM 21 C C5 GDP . . . H 2 16.649 4.734 56.865 1 49.36 ? C5 GDP 401 A 1 
HETATM 22 C C6 GDP . . . H 2 15.296 4.934 57.407 1 42.34 ? C6 GDP 401 A 1 
HETATM 23 O O6 GDP . . . H 2 14.293 4.834 56.673 1 49.65 ? O6 GDP 401 A 1 
HETATM 24 N N1 GDP . . . H 2 15.188 5.223 58.709 1 43.07 ? N1 GDP 401 A 1 
HETATM 25 C C2 GDP . . . H 2 16.251 5.348 59.535 1 40.2 ? C2 GDP 401 A 1 
HETATM 26 N N2 GDP . . . H 2 16.038 5.659 60.845 1 38.36 ? N2 GDP 401 A 1 
HETATM 27 N N3 GDP . . . H 2 17.524 5.187 59.103 1 37.13 ? N3 GDP 401 A 1 
HETATM 28 C C4 GDP . . . H 2 17.758 4.886 57.813 1 44.98 ? C4 GDP 401 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#