data_6EG8
#
_model_server_result.job_id            y1v07kD904RSl6TAlPSeig 
_model_server_result.datetime_utc      '2024-11-23 21:55:35' 
_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          6eg8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":401}' 
#
_entry.id    6EG8 
#
_exptl.entry_id    6EG8 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          106.18 
_cell.angle_gamma         90 
_cell.entry_id            6EG8 
_cell.length_a            100.86 
_cell.length_b            100.81 
_cell.length_c            179.33 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6EG8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
PISA trimeric 3 author_and_software_defined_assembly 3 
PISA trimeric 3 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,I,M,N,U,W,Z 1 1 
B,G,L,S,T,V,CA 2 1 
D,E,K,Q,R,X,BA 3 1 
F,H,J,O,P,Y,AA 4 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
? 4 M N N 
? 4 O N N 
? 4 Q N N 
? 4 S 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 I OG SER 55 I SER 54 1_555 N MG MG . I MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc2 I OG1 THR 191 I THR 204 1_555 N MG MG . I MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? 
metalc ? metalc3 M O3B GDP . I GDP 401 1_555 N MG MG . I MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc4 N MG MG . I MG 402 1_555 Z O HOH . I HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? 
metalc ? metalc5 N MG MG . I MG 402 1_555 Z O HOH . I HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc6 J OG SER 55 J SER 54 1_555 P MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc7 J OG1 THR 191 J THR 204 1_555 P MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? 
metalc ? metalc8 O O3B GDP . J GDP 401 1_555 P MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc9 P MG MG . J MG 402 1_555 AA O HOH . J HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc10 P MG MG . J MG 402 1_555 AA O HOH . J HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc11 P MG MG . J MG 402 1_555 AA O HOH . J HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
metalc ? metalc12 K OG SER 55 K SER 54 1_555 R MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc13 K OG1 THR 191 K THR 204 1_555 R MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? 
metalc ? metalc14 Q O1B GDP . K GDP 401 1_555 R MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc15 R MG MG . K MG 402 1_555 BA O HOH . K HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? 
metalc ? metalc16 L OG SER 55 L SER 54 1_555 T MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc17 L OG1 THR 191 L THR 204 1_555 T MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? 
metalc ? metalc18 S O3B GDP . L GDP 401 1_555 T MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc19 T MG MG . L MG 402 1_555 CA O HOH . L HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc20 T MG MG . L MG 402 1_555 CA O HOH . L HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
#
_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 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     6EG8 
_atom_sites.fract_transf_matrix[1][1]    0.009915 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002876 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00992 
_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]    0.005806 
_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
M 4 GDP I 1 401 401 GDP GDP . 
N 5 MG I 1 402 1 MG MG . 
O 4 GDP J 1 401 401 GDP GDP . 
P 5 MG J 1 402 2 MG MG . 
Q 4 GDP K 1 401 401 GDP GDP . 
R 5 MG K 1 402 3 MG MG . 
S 4 GDP L 1 401 401 GDP GDP . 
T 5 MG L 1 402 4 MG MG . 
U 6 HOH A 1 401 54 HOH HOH . 
U 6 HOH A 2 402 60 HOH HOH . 
U 6 HOH A 3 403 55 HOH HOH . 
U 6 HOH A 4 404 61 HOH HOH . 
U 6 HOH A 5 405 59 HOH HOH . 
U 6 HOH A 6 406 28 HOH HOH . 
U 6 HOH A 7 407 57 HOH HOH . 
U 6 HOH A 8 408 29 HOH HOH . 
V 6 HOH B 1 401 48 HOH HOH . 
V 6 HOH B 2 402 1 HOH HOH . 
V 6 HOH B 3 403 41 HOH HOH . 
V 6 HOH B 4 404 42 HOH HOH . 
V 6 HOH B 5 405 43 HOH HOH . 
V 6 HOH B 6 406 37 HOH HOH . 
V 6 HOH B 7 407 45 HOH HOH . 
V 6 HOH B 8 408 47 HOH HOH . 
V 6 HOH B 9 409 30 HOH HOH . 
V 6 HOH B 10 410 31 HOH HOH . 
V 6 HOH B 11 411 46 HOH HOH . 
W 6 HOH C 1 101 63 HOH HOH . 
X 6 HOH D 1 401 64 HOH HOH . 
X 6 HOH D 2 402 65 HOH HOH . 
X 6 HOH D 3 403 18 HOH HOH . 
X 6 HOH D 4 404 68 HOH HOH . 
X 6 HOH D 5 405 27 HOH HOH . 
X 6 HOH D 6 406 67 HOH HOH . 
X 6 HOH D 7 407 70 HOH HOH . 
Y 6 HOH F 1 401 77 HOH HOH . 
Y 6 HOH F 2 402 76 HOH HOH . 
Y 6 HOH F 3 403 124 HOH HOH . 
Y 6 HOH F 4 404 74 HOH HOH . 
Y 6 HOH F 5 405 75 HOH HOH . 
Y 6 HOH F 6 406 80 HOH HOH . 
Y 6 HOH F 7 407 73 HOH HOH . 
Y 6 HOH F 8 408 33 HOH HOH . 
Z 6 HOH I 1 501 82 HOH HOH . 
Z 6 HOH I 2 502 83 HOH HOH . 
Z 6 HOH I 3 503 3 HOH HOH . 
Z 6 HOH I 4 504 122 HOH HOH . 
Z 6 HOH I 5 505 7 HOH HOH . 
Z 6 HOH I 6 506 123 HOH HOH . 
Z 6 HOH I 7 507 90 HOH HOH . 
Z 6 HOH I 8 508 9 HOH HOH . 
Z 6 HOH I 9 509 128 HOH HOH . 
Z 6 HOH I 10 510 6 HOH HOH . 
Z 6 HOH I 11 511 8 HOH HOH . 
Z 6 HOH I 12 512 88 HOH HOH . 
Z 6 HOH I 13 513 84 HOH HOH . 
Z 6 HOH I 14 514 32 HOH HOH . 
Z 6 HOH I 15 515 71 HOH HOH . 
AA 6 HOH J 1 501 119 HOH HOH . 
AA 6 HOH J 2 502 96 HOH HOH . 
AA 6 HOH J 3 503 93 HOH HOH . 
AA 6 HOH J 4 504 95 HOH HOH . 
AA 6 HOH J 5 505 13 HOH HOH . 
AA 6 HOH J 6 506 91 HOH HOH . 
AA 6 HOH J 7 507 11 HOH HOH . 
AA 6 HOH J 8 508 15 HOH HOH . 
AA 6 HOH J 9 509 35 HOH HOH . 
AA 6 HOH J 10 510 14 HOH HOH . 
AA 6 HOH J 11 511 92 HOH HOH . 
AA 6 HOH J 12 512 98 HOH HOH . 
AA 6 HOH J 13 513 121 HOH HOH . 
AA 6 HOH J 14 514 12 HOH HOH . 
AA 6 HOH J 15 515 10 HOH HOH . 
AA 6 HOH J 16 516 94 HOH HOH . 
BA 6 HOH K 1 501 104 HOH HOH . 
BA 6 HOH K 2 502 117 HOH HOH . 
BA 6 HOH K 3 503 16 HOH HOH . 
BA 6 HOH K 4 504 105 HOH HOH . 
BA 6 HOH K 5 505 116 HOH HOH . 
BA 6 HOH K 6 506 34 HOH HOH . 
BA 6 HOH K 7 507 20 HOH HOH . 
BA 6 HOH K 8 508 103 HOH HOH . 
BA 6 HOH K 9 509 106 HOH HOH . 
BA 6 HOH K 10 510 17 HOH HOH . 
BA 6 HOH K 11 511 101 HOH HOH . 
CA 6 HOH L 1 501 24 HOH HOH . 
CA 6 HOH L 2 502 126 HOH HOH . 
CA 6 HOH L 3 503 109 HOH HOH . 
CA 6 HOH L 4 504 23 HOH HOH . 
CA 6 HOH L 5 505 108 HOH HOH . 
CA 6 HOH L 6 506 127 HOH HOH . 
CA 6 HOH L 7 507 107 HOH HOH . 
CA 6 HOH L 8 508 21 HOH HOH . 
CA 6 HOH L 9 509 110 HOH HOH . 
CA 6 HOH L 10 510 26 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 . . . S 4 -26.238 -4.273 -88.125 1 19.18 ? PB GDP 401 L 1 
HETATM 2 O O1B GDP . . . S 4 -24.762 -4.434 -87.85 1 21.41 -1 O1B GDP 401 L 1 
HETATM 3 O O2B GDP . . . S 4 -26.98 -5.441 -87.521 1 20.23 ? O2B GDP 401 L 1 
HETATM 4 O O3B GDP . . . S 4 -26.743 -2.984 -87.522 1 19.21 ? O3B GDP 401 L 1 
HETATM 5 O O3A GDP . . . S 4 -26.473 -4.271 -89.716 1 21.36 ? O3A GDP 401 L 1 
HETATM 6 P PA GDP . . . S 4 -26.954 -2.942 -90.484 1 19.32 ? PA GDP 401 L 1 
HETATM 7 O O1A GDP . . . S 4 -26.031 -1.788 -90.176 1 19.33 ? O1A GDP 401 L 1 
HETATM 8 O O2A GDP . . . S 4 -28.382 -2.597 -90.134 1 19.35 -1 O2A GDP 401 L 1 
HETATM 9 O O5' GDP . . . S 4 -26.831 -3.369 -92.03 1 19.35 ? O5' GDP 401 L 1 
HETATM 10 C C5' GDP . . . S 4 -25.768 -2.828 -92.807 1 23.37 ? C5' GDP 401 L 1 
HETATM 11 C C4' GDP . . . S 4 -26.093 -2.887 -94.291 1 28.77 ? C4' GDP 401 L 1 
HETATM 12 O O4' GDP . . . S 4 -26.83 -4.067 -94.609 1 29.3 ? O4' GDP 401 L 1 
HETATM 13 C C3' GDP . . . S 4 -26.947 -1.709 -94.729 1 31.52 ? C3' GDP 401 L 1 
HETATM 14 O O3' GDP . . . S 4 -26.13 -0.731 -95.378 1 34.03 ? O3' GDP 401 L 1 
HETATM 15 C C2' GDP . . . S 4 -27.953 -2.287 -95.704 1 31.58 ? C2' GDP 401 L 1 
HETATM 16 O O2' GDP . . . S 4 -27.711 -1.768 -97.013 1 32.69 ? O2' GDP 401 L 1 
HETATM 17 C C1' GDP . . . S 4 -27.707 -3.787 -95.702 1 28.78 ? C1' GDP 401 L 1 
HETATM 18 N N9 GDP . . . S 4 -28.985 -4.527 -95.555 1 25.15 ? N9 GDP 401 L 1 
HETATM 19 C C8 GDP . . . S 4 -29.645 -4.752 -94.405 1 25.29 ? C8 GDP 401 L 1 
HETATM 20 N N7 GDP . . . S 4 -30.779 -5.467 -94.626 1 26.3 ? N7 GDP 401 L 1 
HETATM 21 C C5 GDP . . . S 4 -30.851 -5.713 -95.947 1 24.5 ? C5 GDP 401 L 1 
HETATM 22 C C6 GDP . . . S 4 -31.788 -6.416 -96.855 1 24.11 ? C6 GDP 401 L 1 
HETATM 23 O O6 GDP . . . S 4 -32.819 -6.971 -96.417 1 24.62 ? O6 GDP 401 L 1 
HETATM 24 N N1 GDP . . . S 4 -31.494 -6.439 -98.161 1 23.18 ? N1 GDP 401 L 1 
HETATM 25 C C2 GDP . . . S 4 -30.391 -5.85 -98.659 1 22.53 ? C2 GDP 401 L 1 
HETATM 26 N N2 GDP . . . S 4 -30.166 -5.915 -99.991 1 19.61 ? N2 GDP 401 L 1 
HETATM 27 N N3 GDP . . . S 4 -29.491 -5.191 -97.888 1 22.34 ? N3 GDP 401 L 1 
HETATM 28 C C4 GDP . . . S 4 -29.666 -5.092 -96.551 1 23.75 ? C4 GDP 401 L 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           363 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#