data_3L7K
#
_model_server_result.job_id            GN8kY-kcP11vyHhJrsQZ1g 
_model_server_result.datetime_utc      '2025-08-01 13:42:05' 
_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          3l7k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"EA","auth_seq_id":730}' 
#
_entry.id    3L7K 
#
_exptl.entry_id    3L7K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              477.255 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER" 
_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            3L7K 
_cell.length_a            222.04 
_cell.length_b            222.04 
_cell.length_c            100.91 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3L7K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
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 tetrameric 4 software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA 1 1 
A,B,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,KA,LA 2 1 
C,D,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,MA,NA 3 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                      5 
_struct_asym.id                             EA 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C12 H21 N3 O13 P2' 
_chem_comp.formula_weight    477.255 
_chem_comp.id                C2G 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "CYTIDINE 5'-DIPHOSPHOGLYCEROL" 
#
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
N1 C2 C2G sing 70 n y 
N1 C6 C2G sing 71 n y 
N1 C1' C2G sing 72 n n 
C2 N3 C2G sing 73 n y 
C2 O2 C2G doub 74 n n 
N3 C4 C2G doub 75 n y 
C4 C5 C2G sing 76 n y 
C4 N4 C2G sing 77 n n 
C5 C6 C2G doub 78 n y 
C5 HC5 C2G sing 79 n n 
C6 HC6 C2G sing 80 n n 
N4 HN41 C2G sing 81 n n 
N4 HN42 C2G sing 82 n n 
C1' C2' C2G sing 83 n n 
C1' O4' C2G sing 84 n n 
C1' HC1 C2G sing 85 n n 
C2' O2' C2G sing 86 n n 
C2' C3' C2G sing 87 n n 
C2' HC2 C2G sing 88 n n 
O2' HO2 C2G sing 89 n n 
C3' C4' C2G sing 90 n n 
C3' O3' C2G sing 91 n n 
C3' HC3 C2G sing 92 n n 
C4' O4' C2G sing 93 n n 
C4' C5' C2G sing 94 n n 
C4' HC4 C2G sing 95 n n 
O3' HO3 C2G sing 96 n n 
C5' O5' C2G sing 97 n n 
C5' HC51 C2G sing 98 n n 
C5' HC52 C2G sing 99 n n 
O5' PA C2G sing 100 n n 
PA O1A C2G doub 101 n n 
PA O2A C2G sing 102 n n 
PA O3A C2G sing 103 n n 
O2A H2A C2G sing 104 n n 
O3A PB C2G sing 105 n n 
PB O1B C2G doub 106 n n 
PB O2B C2G sing 107 n n 
PB O3B C2G sing 108 n n 
O2B H2B C2G sing 109 n n 
O3B C3G C2G sing 110 n n 
O1G C1G C2G sing 111 n n 
O1G H1G C2G sing 112 n n 
C1G C2G C2G sing 113 n n 
C1G H1G1 C2G sing 114 n n 
C1G H1G2 C2G sing 115 n n 
C2G O2G C2G sing 116 n n 
C2G C3G C2G sing 117 n n 
C2G H2G C2G sing 118 n n 
O2G HOG C2G sing 119 n n 
C3G H3G1 C2G sing 120 n n 
C3G H3G2 C2G sing 121 n n 
#
_atom_sites.entry_id                     3L7K 
_atom_sites.fract_transf_matrix[1][1]    0.004504 
_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]    0.004504 
_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]    0.00991 
_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 2 SO4 A 1 730 1 SO4 SO4 . 
F 2 SO4 A 1 731 2 SO4 SO4 . 
G 2 SO4 A 1 732 7 SO4 SO4 . 
H 3 CL A 1 733 6 CL CL . 
I 3 CL A 1 734 14 CL CL . 
J 3 CL A 1 735 16 CL CL . 
K 3 CL A 1 736 20 CL CL . 
L 3 CL A 1 737 22 CL CL . 
M 3 CL A 1 738 23 CL CL . 
N 4 EDT A 1 739 2 EDT EDT . 
O 3 CL A 1 740 1 CL CL . 
P 3 CL A 1 741 1 CL CL . 
Q 3 CL A 1 742 1 CL CL . 
R 2 SO4 B 1 730 8 SO4 SO4 . 
S 3 CL B 1 731 1 CL CL . 
T 3 CL B 1 732 2 CL CL . 
U 3 CL B 1 733 7 CL CL . 
V 3 CL B 1 734 17 CL CL . 
W 3 CL B 1 735 24 CL CL . 
X 3 CL B 1 736 1 CL CL . 
Y 2 SO4 C 1 730 6 SO4 SO4 . 
Z 3 CL C 1 731 4 CL CL . 
AA 3 CL C 1 732 8 CL CL . 
BA 3 CL C 1 733 12 CL CL . 
CA 3 CL C 1 734 19 CL CL . 
DA 3 CL C 1 735 21 CL CL . 
EA 5 C2G D 1 730 130 C2G C2G . 
FA 2 SO4 D 1 731 5 SO4 SO4 . 
GA 3 CL D 1 732 5 CL CL . 
HA 3 CL D 1 733 9 CL CL . 
IA 6 EDO D 1 734 1 EDO EDO . 
JA 4 EDT D 1 735 1 EDT EDT . 
KA 7 HOH A 1 743 6 HOH HOH . 
LA 7 HOH B 1 737 3 HOH HOH . 
LA 7 HOH B 2 738 4 HOH HOH . 
LA 7 HOH B 3 739 7 HOH HOH . 
MA 7 HOH C 1 736 5 HOH HOH . 
MA 7 HOH C 2 737 8 HOH HOH . 
NA 7 HOH D 1 736 1 HOH HOH . 
NA 7 HOH D 2 737 2 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 N N1 C2G . . . EA 5 -71.397 81.181 7.843 1 121 ? N1 C2G 730 D 1 
HETATM 2 C C2 C2G . . . EA 5 -71.497 82.064 9.091 1 121.35 ? C2 C2G 730 D 1 
HETATM 3 N N3 C2G . . . EA 5 -70.422 82.013 10.126 1 121.65 ? N3 C2G 730 D 1 
HETATM 4 C C4 C2G . . . EA 5 -69.257 81.111 9.959 1 122.11 ? C4 C2G 730 D 1 
HETATM 5 C C5 C2G . . . EA 5 -69.153 80.237 8.738 1 121.8 ? C5 C2G 730 D 1 
HETATM 6 C C6 C2G . . . EA 5 -70.243 80.287 7.702 1 121.38 ? C6 C2G 730 D 1 
HETATM 7 O O2 C2G . . . EA 5 -72.591 82.915 9.274 1 121.73 ? O2 C2G 730 D 1 
HETATM 8 N N4 C2G . . . EA 5 -68.204 81.027 10.953 1 121.86 ? N4 C2G 730 D 1 
HETATM 9 C C1' C2G . . . EA 5 -72.425 81.154 6.79 1 120.51 ? C1' C2G 730 D 1 
HETATM 10 C C2' C2G . . . EA 5 -71.87 81.654 5.445 1 121.41 ? C2' C2G 730 D 1 
HETATM 11 O O2' C2G . . . EA 5 -72.855 82.347 4.719 1 121.29 ? O2' C2G 730 D 1 
HETATM 12 C C3' C2G . . . EA 5 -71.438 80.407 4.704 1 120.3 ? C3' C2G 730 D 1 
HETATM 13 C C4' C2G . . . EA 5 -72.402 79.331 5.234 1 120.85 ? C4' C2G 730 D 1 
HETATM 14 O O4' C2G . . . EA 5 -72.823 79.753 6.576 1 120.83 ? O4' C2G 730 D 1 
HETATM 15 O O3' C2G . . . EA 5 -71.517 80.569 3.302 1 120.6 ? O3' C2G 730 D 1 
HETATM 16 C C5' C2G . . . EA 5 -71.77 77.921 5.298 1 119.96 ? C5' C2G 730 D 1 
HETATM 17 O O5' C2G . . . EA 5 -70.375 77.949 5.518 1 120.68 ? O5' C2G 730 D 1 
HETATM 18 P PA C2G . . . EA 5 -69.643 76.598 6.157 1 120.87 ? PA C2G 730 D 1 
HETATM 19 O O1A C2G . . . EA 5 -68.541 76.973 7.337 1 120.78 ? O1A C2G 730 D 1 
HETATM 20 O O2A C2G . . . EA 5 -68.968 75.831 5.109 1 120.06 ? O2A C2G 730 D 1 
HETATM 21 O O3A C2G . . . EA 5 -70.859 75.693 6.824 1 120.33 ? O3A C2G 730 D 1 
HETATM 22 P PB C2G . . . EA 5 -71.309 74.194 6.27 1 120.45 ? PB C2G 730 D 1 
HETATM 23 O O1B C2G . . . EA 5 -72.793 73.894 6.937 1 119.65 ? O1B C2G 730 D 1 
HETATM 24 O O2B C2G . . . EA 5 -70.301 73.205 6.701 1 119.56 ? O2B C2G 730 D 1 
HETATM 25 O O3B C2G . . . EA 5 -71.509 74.14 4.621 1 119.9 ? O3B C2G 730 D 1 
HETATM 26 O O1G C2G . . . EA 5 -71.808 73.78 0.453 1 118.83 ? O1G C2G 730 D 1 
HETATM 27 C C1G C2G . . . EA 5 -70.777 73.484 1.347 1 119.25 ? C1G C2G 730 D 1 
HETATM 28 C C2G C2G . . . EA 5 -71.379 72.836 2.605 1 119.15 ? C2G C2G 730 D 1 
HETATM 29 O O2G C2G . . . EA 5 -72.745 73.16 2.697 1 119.65 ? O2G C2G 730 D 1 
HETATM 30 C C3G C2G . . . EA 5 -70.619 73.408 3.816 1 119.62 ? C3G C2G 730 D 1 
#
_model_server_stats.io_time_ms              36 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           424 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           30 
#