data_6SIU
#
_model_server_result.job_id            e-cpVDFcA_c-NDeQ1ANHHQ 
_model_server_result.datetime_utc      '2024-12-03 02:34:46' 
_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          6siu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":201}' 
#
_entry.id    6SIU 
#
_exptl.entry_id    6SIU 
_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    2 
_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            6SIU 
_cell.length_a            92.241 
_cell.length_b            102.213 
_cell.length_c            129.273 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6SIU 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,M,N,O,P,Q,R,S,T,U,V,W,X 
_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
? 4 M N N 
? 4 Q 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
covale ? covale1 A SG CYS 274 A CYS 3755 1_555 S C56 LJN . D LJN 203 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.794 ? 
covale ? covale2 A SG CYS 274 A CYS 3755 1_555 S C56 LJN . D LJN 203 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.791 ? 
covale ? covale3 B SG CYS 274 B CYS 3755 1_555 O C56 LJN . C LJN 203 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.804 ? 
covale ? covale4 B SG CYS 274 B CYS 3755 1_555 O C56 LJN . C LJN 203 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.839 ? 
covale ? covale5 C OH TYR 33 C TYR 32 1_555 O P14 LJN . C LJN 203 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.673 ? 
covale ? covale6 C OH TYR 33 C TYR 32 1_555 O P14 LJN . C LJN 203 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.668 ? 
covale ? covale7 D OH TYR 33 D TYR 32 1_555 S P14 LJN . D LJN 203 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.66 ? 
covale ? covale8 D OH TYR 33 D TYR 32 1_555 S P14 LJN . D LJN 203 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.656 ? 
#
_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                     6SIU 
_atom_sites.fract_transf_matrix[1][1]    0.010841 
_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]    0.009783 
_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]    0.007736 
_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 SO4 A 1 3801 1 SO4 SO4 . 
F 3 SO4 A 1 3802 3 SO4 SO4 . 
G 3 SO4 A 1 3803 6 SO4 SO4 . 
H 3 SO4 A 1 3804 10 SO4 SO4 . 
I 3 SO4 B 1 3801 2 SO4 SO4 . 
J 3 SO4 B 1 3802 4 SO4 SO4 . 
K 3 SO4 B 1 3803 5 SO4 SO4 . 
L 3 SO4 B 1 3804 11 SO4 SO4 . 
M 4 GDP C 1 201 201 GDP GDP . 
N 5 GOL C 1 202 301 GOL GOL . 
O 6 LJN C 1 203 32 LJN YXC . 
P 3 SO4 C 1 204 7 SO4 SO4 . 
Q 4 GDP D 1 201 201 GDP GDP . 
R 5 GOL D 1 202 301 GOL GOL . 
S 6 LJN D 1 203 32 LJN YXC . 
T 3 SO4 D 1 204 8 SO4 SO4 . 
U 7 HOH A 1 3901 62 HOH HOH . 
U 7 HOH A 2 3902 31 HOH HOH . 
U 7 HOH A 3 3903 103 HOH HOH . 
U 7 HOH A 4 3904 66 HOH HOH . 
U 7 HOH A 5 3905 19 HOH HOH . 
U 7 HOH A 6 3906 15 HOH HOH . 
U 7 HOH A 7 3907 93 HOH HOH . 
U 7 HOH A 8 3908 7 HOH HOH . 
U 7 HOH A 9 3909 6 HOH HOH . 
U 7 HOH A 10 3910 104 HOH HOH . 
U 7 HOH A 11 3911 110 HOH HOH . 
U 7 HOH A 12 3912 2 HOH HOH . 
U 7 HOH A 13 3913 75 HOH HOH . 
U 7 HOH A 14 3914 5 HOH HOH . 
U 7 HOH A 15 3915 54 HOH HOH . 
U 7 HOH A 16 3916 44 HOH HOH . 
U 7 HOH A 17 3917 86 HOH HOH . 
U 7 HOH A 18 3918 87 HOH HOH . 
U 7 HOH A 19 3919 56 HOH HOH . 
U 7 HOH A 20 3920 108 HOH HOH . 
U 7 HOH A 21 3921 16 HOH HOH . 
U 7 HOH A 22 3922 10 HOH HOH . 
U 7 HOH A 23 3923 18 HOH HOH . 
U 7 HOH A 24 3924 65 HOH HOH . 
U 7 HOH A 25 3925 57 HOH HOH . 
U 7 HOH A 26 3926 40 HOH HOH . 
U 7 HOH A 27 3927 105 HOH HOH . 
U 7 HOH A 28 3928 45 HOH HOH . 
U 7 HOH A 29 3929 106 HOH HOH . 
U 7 HOH A 30 3930 89 HOH HOH . 
U 7 HOH A 31 3931 109 HOH HOH . 
U 7 HOH A 32 3932 85 HOH HOH . 
V 7 HOH B 1 3901 77 HOH HOH . 
V 7 HOH B 2 3902 38 HOH HOH . 
V 7 HOH B 3 3903 94 HOH HOH . 
V 7 HOH B 4 3904 42 HOH HOH . 
V 7 HOH B 5 3905 102 HOH HOH . 
V 7 HOH B 6 3906 51 HOH HOH . 
V 7 HOH B 7 3907 20 HOH HOH . 
V 7 HOH B 8 3908 50 HOH HOH . 
V 7 HOH B 9 3909 35 HOH HOH . 
V 7 HOH B 10 3910 100 HOH HOH . 
V 7 HOH B 11 3911 9 HOH HOH . 
V 7 HOH B 12 3912 41 HOH HOH . 
V 7 HOH B 13 3913 32 HOH HOH . 
V 7 HOH B 14 3914 70 HOH HOH . 
V 7 HOH B 15 3915 21 HOH HOH . 
V 7 HOH B 16 3916 79 HOH HOH . 
V 7 HOH B 17 3917 1 HOH HOH . 
V 7 HOH B 18 3918 53 HOH HOH . 
V 7 HOH B 19 3919 29 HOH HOH . 
V 7 HOH B 20 3920 4 HOH HOH . 
V 7 HOH B 21 3921 49 HOH HOH . 
V 7 HOH B 22 3922 72 HOH HOH . 
V 7 HOH B 23 3923 78 HOH HOH . 
V 7 HOH B 24 3924 99 HOH HOH . 
V 7 HOH B 25 3925 92 HOH HOH . 
V 7 HOH B 26 3926 33 HOH HOH . 
V 7 HOH B 27 3927 55 HOH HOH . 
V 7 HOH B 28 3928 91 HOH HOH . 
V 7 HOH B 29 3929 34 HOH HOH . 
V 7 HOH B 30 3930 69 HOH HOH . 
V 7 HOH B 31 3931 74 HOH HOH . 
V 7 HOH B 32 3932 61 HOH HOH . 
V 7 HOH B 33 3933 8 HOH HOH . 
V 7 HOH B 34 3934 67 HOH HOH . 
V 7 HOH B 35 3935 52 HOH HOH . 
V 7 HOH B 36 3936 36 HOH HOH . 
V 7 HOH B 37 3937 60 HOH HOH . 
V 7 HOH B 38 3938 95 HOH HOH . 
V 7 HOH B 39 3939 68 HOH HOH . 
V 7 HOH B 40 3940 80 HOH HOH . 
V 7 HOH B 41 3941 96 HOH HOH . 
W 7 HOH C 1 301 27 HOH HOH . 
W 7 HOH C 2 302 3 HOH HOH . 
W 7 HOH C 3 303 47 HOH HOH . 
W 7 HOH C 4 304 81 HOH HOH . 
W 7 HOH C 5 305 107 HOH HOH . 
W 7 HOH C 6 306 26 HOH HOH . 
W 7 HOH C 7 307 39 HOH HOH . 
W 7 HOH C 8 308 14 HOH HOH . 
W 7 HOH C 9 309 46 HOH HOH . 
W 7 HOH C 10 310 73 HOH HOH . 
W 7 HOH C 11 311 17 HOH HOH . 
W 7 HOH C 12 312 30 HOH HOH . 
W 7 HOH C 13 313 23 HOH HOH . 
W 7 HOH C 14 314 28 HOH HOH . 
W 7 HOH C 15 315 25 HOH HOH . 
W 7 HOH C 16 316 58 HOH HOH . 
W 7 HOH C 17 317 97 HOH HOH . 
W 7 HOH C 18 318 59 HOH HOH . 
W 7 HOH C 19 319 63 HOH HOH . 
X 7 HOH D 1 301 76 HOH HOH . 
X 7 HOH D 2 302 48 HOH HOH . 
X 7 HOH D 3 303 24 HOH HOH . 
X 7 HOH D 4 304 83 HOH HOH . 
X 7 HOH D 5 305 82 HOH HOH . 
X 7 HOH D 6 306 98 HOH HOH . 
X 7 HOH D 7 307 90 HOH HOH . 
X 7 HOH D 8 308 64 HOH HOH . 
X 7 HOH D 9 309 37 HOH HOH . 
X 7 HOH D 10 310 12 HOH HOH . 
X 7 HOH D 11 311 22 HOH HOH . 
X 7 HOH D 12 312 88 HOH HOH . 
X 7 HOH D 13 313 13 HOH HOH . 
X 7 HOH D 14 314 43 HOH HOH . 
X 7 HOH D 15 315 71 HOH HOH . 
X 7 HOH D 16 316 84 HOH HOH . 
X 7 HOH D 17 317 11 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 . . . M 4 -18.713 -7.096 -40.449 1 30.57 ? PB GDP 201 C 1 
HETATM 2 O O1B GDP . . . M 4 -18.229 -7.476 -41.829 1 29.01 ? O1B GDP 201 C 1 
HETATM 3 O O2B GDP . . . M 4 -17.547 -6.765 -39.547 1 36.41 ? O2B GDP 201 C 1 
HETATM 4 O O3B GDP . . . M 4 -19.518 -8.219 -39.836 1 37.17 ? O3B GDP 201 C 1 
HETATM 5 O O3A GDP . . . M 4 -19.682 -5.824 -40.548 1 37.72 ? O3A GDP 201 C 1 
HETATM 6 P PA GDP . . . M 4 -19.105 -4.339 -40.746 1 30.06 ? PA GDP 201 C 1 
HETATM 7 O O1A GDP . . . M 4 -17.896 -4.324 -41.641 1 36.89 ? O1A GDP 201 C 1 
HETATM 8 O O2A GDP . . . M 4 -18.775 -3.726 -39.406 1 33.66 ? O2A GDP 201 C 1 
HETATM 9 O O5' GDP . . . M 4 -20.394 -3.647 -41.405 1 28.59 ? O5' GDP 201 C 1 
HETATM 10 C C5' GDP . . . M 4 -20.692 -3.782 -42.792 1 34.7 ? C5' GDP 201 C 1 
HETATM 11 C C4' GDP . . . M 4 -21.666 -2.678 -43.196 1 44.11 ? C4' GDP 201 C 1 
HETATM 12 O O4' GDP . . . M 4 -22.802 -2.658 -42.328 1 50.18 ? O4' GDP 201 C 1 
HETATM 13 C C3' GDP . . . M 4 -21.03 -1.306 -43.1 1 40.9 ? C3' GDP 201 C 1 
HETATM 14 O O3' GDP . . . M 4 -21.337 -0.589 -44.295 1 37.67 ? O3' GDP 201 C 1 
HETATM 15 C C2' GDP . . . M 4 -21.714 -0.609 -41.947 1 49.57 ? C2' GDP 201 C 1 
HETATM 16 O O2' GDP . . . M 4 -21.933 0.766 -42.261 1 61.55 ? O2' GDP 201 C 1 
HETATM 17 C C1' GDP . . . M 4 -23.04 -1.337 -41.829 1 53.61 ? C1' GDP 201 C 1 
HETATM 18 N N9 GDP . . . M 4 -23.561 -1.381 -40.436 1 64.95 ? N9 GDP 201 C 1 
HETATM 19 C C8 GDP . . . M 4 -22.985 -1.98 -39.377 1 61.37 ? C8 GDP 201 C 1 
HETATM 20 N N7 GDP . . . M 4 -23.745 -1.841 -38.259 1 54.39 ? N7 GDP 201 C 1 
HETATM 21 C C5 GDP . . . M 4 -24.851 -1.144 -38.599 1 57.53 ? C5 GDP 201 C 1 
HETATM 22 C C6 GDP . . . M 4 -26.075 -0.643 -37.922 1 48.96 ? C6 GDP 201 C 1 
HETATM 23 O O6 GDP . . . M 4 -26.286 -0.835 -36.702 1 42.49 ? O6 GDP 201 C 1 
HETATM 24 N N1 GDP . . . M 4 -26.965 0.039 -38.654 1 47.34 ? N1 GDP 201 C 1 
HETATM 25 C C2 GDP . . . M 4 -26.791 0.275 -39.97 1 54.65 ? C2 GDP 201 C 1 
HETATM 26 N N2 GDP . . . M 4 -27.737 0.972 -40.644 1 50.75 ? N2 GDP 201 C 1 
HETATM 27 N N3 GDP . . . M 4 -25.7 -0.156 -40.653 1 59.61 ? N3 GDP 201 C 1 
HETATM 28 C C4 GDP . . . M 4 -24.72 -0.852 -40.036 1 61.49 ? C4 GDP 201 C 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#