data_3L7L
#
_model_server_result.job_id            yDouTcwnDy9YPJZ5g-FFPA 
_model_server_result.datetime_utc      '2025-07-31 02:29:29' 
_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          3l7l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":730}' 
#
_entry.id    3L7L 
#
_exptl.entry_id    3L7L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              477.255 
_entity.id                          4 
_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            3L7L 
_cell.length_a            222.88 
_cell.length_b            222.88 
_cell.length_c            100.75 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3L7L 
_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 1 1 
A,B,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,HA 2 1 
C,D,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,IA 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                      4 
_struct_asym.id                             CA 
_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                     3L7L 
_atom_sites.fract_transf_matrix[1][1]    0.004487 
_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]    0.004487 
_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]    0.009926 
_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 7 SO4 SO4 . 
G 3 CL A 1 732 6 CL CL . 
H 3 CL A 1 733 10 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 3 CL A 1 739 1 CL CL . 
O 2 SO4 B 1 730 2 SO4 SO4 . 
P 2 SO4 B 1 731 8 SO4 SO4 . 
Q 3 CL B 1 732 2 CL CL . 
R 3 CL B 1 733 7 CL CL . 
S 3 CL B 1 734 17 CL CL . 
T 3 CL B 1 735 24 CL CL . 
U 3 CL B 1 736 1 CL CL . 
V 2 SO4 C 1 730 5 SO4 SO4 . 
W 2 SO4 C 1 731 6 SO4 SO4 . 
X 3 CL C 1 732 4 CL CL . 
Y 3 CL C 1 733 8 CL CL . 
Z 3 CL C 1 734 12 CL CL . 
AA 3 CL C 1 735 19 CL CL . 
BA 3 CL C 1 736 21 CL CL . 
CA 4 C2G D 1 730 130 C2G C2G . 
DA 3 CL D 1 731 1 CL CL . 
EA 3 CL D 1 732 5 CL CL . 
FA 3 CL D 1 733 9 CL CL . 
GA 5 EDO D 1 734 1 EDO EDO . 
HA 6 HOH A 1 740 4 HOH HOH . 
HA 6 HOH A 2 741 5 HOH HOH . 
IA 6 HOH D 1 735 1 HOH HOH . 
IA 6 HOH D 2 736 3 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 . . . CA 4 -71.814 81.367 7.802 1 122.42 ? N1 C2G 730 D 1 
HETATM 2 C C2 C2G . . . CA 4 -71.822 82.463 8.887 1 122.45 ? C2 C2G 730 D 1 
HETATM 3 N N3 C2G . . . CA 4 -70.773 82.47 9.953 1 122.45 ? N3 C2G 730 D 1 
HETATM 4 C C4 C2G . . . CA 4 -69.714 81.43 9.99 1 122.93 ? C4 C2G 730 D 1 
HETATM 5 C C5 C2G . . . CA 4 -69.699 80.354 8.935 1 122.93 ? C5 C2G 730 D 1 
HETATM 6 C C6 C2G . . . CA 4 -70.759 80.344 7.862 1 122.81 ? C6 C2G 730 D 1 
HETATM 7 O O2 C2G . . . CA 4 -72.802 83.461 8.912 1 122.81 ? O2 C2G 730 D 1 
HETATM 8 N N4 C2G . . . CA 4 -68.694 81.408 11.021 1 122.38 ? N4 C2G 730 D 1 
HETATM 9 C C1' C2G . . . CA 4 -72.804 81.265 6.704 1 122.22 ? C1' C2G 730 D 1 
HETATM 10 C C2' C2G . . . CA 4 -72.183 81.675 5.352 1 123.1 ? C2' C2G 730 D 1 
HETATM 11 O O2' C2G . . . CA 4 -73.046 82.478 4.572 1 123.04 ? O2' C2G 730 D 1 
HETATM 12 C C3' C2G . . . CA 4 -71.812 80.378 4.659 1 122.26 ? C3' C2G 730 D 1 
HETATM 13 C C4' C2G . . . CA 4 -72.771 79.336 5.253 1 123.07 ? C4' C2G 730 D 1 
HETATM 14 O O4' C2G . . . CA 4 -73.221 79.855 6.552 1 122.89 ? O4' C2G 730 D 1 
HETATM 15 O O3' C2G . . . CA 4 -71.88 80.452 3.248 1 122.72 ? O3' C2G 730 D 1 
HETATM 16 C C5' C2G . . . CA 4 -72.083 77.964 5.441 1 122.27 ? C5' C2G 730 D 1 
HETATM 17 O O5' C2G . . . CA 4 -70.692 78.056 5.689 1 122.73 ? O5' C2G 730 D 1 
HETATM 18 P PA C2G . . . CA 4 -69.924 76.838 6.536 1 122.93 ? PA C2G 730 D 1 
HETATM 19 O O1A C2G . . . CA 4 -69.019 77.432 7.787 1 122.46 ? O1A C2G 730 D 1 
HETATM 20 O O2A C2G . . . CA 4 -69.066 76.007 5.678 1 122.23 ? O2A C2G 730 D 1 
HETATM 21 O O3A C2G . . . CA 4 -71.136 75.914 7.177 1 122.66 ? O3A C2G 730 D 1 
HETATM 22 P PB C2G . . . CA 4 -71.808 74.642 6.358 1 123.18 ? PB C2G 730 D 1 
HETATM 23 O O1B C2G . . . CA 4 -73.409 74.593 6.779 1 122.57 ? O1B C2G 730 D 1 
HETATM 24 O O2B C2G . . . CA 4 -71.098 73.415 6.742 1 122.33 ? O2B C2G 730 D 1 
HETATM 25 O O3B C2G . . . CA 4 -71.711 74.834 4.711 1 122.75 ? O3B C2G 730 D 1 
HETATM 26 O O1G C2G . . . CA 4 -72.102 73.631 0.589 1 122.38 ? O1G C2G 730 D 1 
HETATM 27 C C1G C2G . . . CA 4 -71.065 73.927 1.474 1 122.5 ? C1G C2G 730 D 1 
HETATM 28 C C2G C2G . . . CA 4 -71.497 73.367 2.833 1 122.36 ? C2G C2G 730 D 1 
HETATM 29 O O2G C2G . . . CA 4 -72.883 73.552 2.938 1 123.06 ? O2G C2G 730 D 1 
HETATM 30 C C3G C2G . . . CA 4 -70.762 74.133 3.947 1 122.49 ? C3G C2G 730 D 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           30 
#