data_2PMP
#
_model_server_result.job_id            4QVlhpFJ_Mff3Mbrs9CPxQ 
_model_server_result.datetime_utc      '2025-04-27 20:28:08' 
_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          2pmp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":700}' 
#
_entry.id    2PMP 
#
_exptl.entry_id    2PMP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              323.197 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-MONOPHOSPHATE" 
_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            2PMP 
_cell.length_a            135.795 
_cell.length_b            135.795 
_cell.length_c            135.795 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PMP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        214 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41 3 2' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 11 A ASP 11 1_555 B ZN ZN . A ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc2 A NE2 HIS 13 A HIS 13 1_555 B ZN ZN . A ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc3 A ND1 HIS 45 A HIS 45 1_555 B ZN ZN . A ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
#
_chem_comp.formula           'C9 H14 N3 O8 P' 
_chem_comp.formula_weight    323.197 
_chem_comp.id                C5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
O3P P C5P sing 70 n n 
O3P HOP3 C5P sing 71 n n 
P O1P C5P doub 72 n n 
P O2P C5P sing 73 n n 
P O5' C5P sing 74 n n 
O2P HOP2 C5P sing 75 n n 
O5' C5' C5P sing 76 n n 
C5' C4' C5P sing 77 n n 
C5' "H5'1" C5P sing 78 n n 
C5' "H5'2" C5P sing 79 n n 
C4' O4' C5P sing 80 n n 
C4' C3' C5P sing 81 n n 
C4' H4' C5P sing 82 n n 
O4' C1' C5P sing 83 n n 
C3' O3' C5P sing 84 n n 
C3' C2' C5P sing 85 n n 
C3' H3' C5P sing 86 n n 
O3' HO3' C5P sing 87 n n 
C2' O2' C5P sing 88 n n 
C2' C1' C5P sing 89 n n 
C2' "H2'1" C5P sing 90 n n 
O2' HO2' C5P sing 91 n n 
C1' N1 C5P sing 92 n n 
C1' H1' C5P sing 93 n n 
N1 C2 C5P sing 94 n n 
N1 C6 C5P sing 95 n n 
C2 N3 C5P sing 96 n n 
C2 O2 C5P doub 97 n n 
N3 C4 C5P doub 98 n n 
C4 C5 C5P sing 99 n n 
C4 N4 C5P sing 100 n n 
C5 C6 C5P doub 101 n n 
C5 H5 C5P sing 102 n n 
C6 H6 C5P sing 103 n n 
N4 HN41 C5P sing 104 n n 
N4 HN42 C5P sing 105 n n 
#
_atom_sites.entry_id                     2PMP 
_atom_sites.fract_transf_matrix[1][1]    0.007364 
_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]    0.007364 
_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]    0.007364 
_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
B 2 ZN A 1 500 500 ZN ZN . 
C 3 PO4 A 1 701 701 PO4 PO4 . 
D 4 CL A 1 702 702 CL CL . 
E 5 C5P A 1 700 700 C5P C5P . 
F 6 HOH A 1 703 1 HOH HOH . 
F 6 HOH A 2 704 2 HOH HOH . 
F 6 HOH A 3 705 3 HOH HOH . 
F 6 HOH A 4 706 4 HOH HOH . 
F 6 HOH A 5 707 5 HOH HOH . 
F 6 HOH A 6 708 6 HOH HOH . 
F 6 HOH A 7 709 7 HOH HOH . 
F 6 HOH A 8 710 8 HOH HOH . 
F 6 HOH A 9 711 9 HOH HOH . 
F 6 HOH A 10 712 10 HOH HOH . 
F 6 HOH A 11 713 11 HOH HOH . 
F 6 HOH A 12 714 12 HOH HOH . 
F 6 HOH A 13 715 13 HOH HOH . 
F 6 HOH A 14 716 14 HOH HOH . 
F 6 HOH A 15 717 15 HOH HOH . 
F 6 HOH A 16 718 16 HOH HOH . 
F 6 HOH A 17 719 17 HOH HOH . 
F 6 HOH A 18 720 18 HOH HOH . 
F 6 HOH A 19 721 19 HOH HOH . 
F 6 HOH A 20 722 20 HOH HOH . 
F 6 HOH A 21 723 21 HOH HOH . 
F 6 HOH A 22 724 22 HOH HOH . 
F 6 HOH A 23 725 23 HOH HOH . 
F 6 HOH A 24 726 24 HOH HOH . 
F 6 HOH A 25 727 25 HOH HOH . 
F 6 HOH A 26 728 26 HOH HOH . 
F 6 HOH A 27 729 27 HOH HOH . 
F 6 HOH A 28 730 28 HOH HOH . 
F 6 HOH A 29 731 29 HOH HOH . 
F 6 HOH A 30 732 30 HOH HOH . 
F 6 HOH A 31 733 31 HOH HOH . 
F 6 HOH A 32 734 32 HOH HOH . 
F 6 HOH A 33 735 33 HOH HOH . 
F 6 HOH A 34 736 34 HOH HOH . 
F 6 HOH A 35 737 35 HOH HOH . 
F 6 HOH A 36 738 36 HOH HOH . 
F 6 HOH A 37 739 37 HOH HOH . 
F 6 HOH A 38 740 38 HOH HOH . 
F 6 HOH A 39 741 39 HOH HOH . 
F 6 HOH A 40 742 40 HOH HOH . 
F 6 HOH A 41 743 41 HOH HOH . 
F 6 HOH A 42 744 42 HOH HOH . 
F 6 HOH A 43 745 43 HOH HOH . 
F 6 HOH A 44 746 44 HOH HOH . 
F 6 HOH A 45 747 45 HOH HOH . 
F 6 HOH A 46 748 46 HOH HOH . 
F 6 HOH A 47 749 47 HOH HOH . 
F 6 HOH A 48 750 48 HOH HOH . 
F 6 HOH A 49 751 49 HOH HOH . 
F 6 HOH A 50 752 50 HOH HOH . 
F 6 HOH A 51 753 51 HOH HOH . 
F 6 HOH A 52 754 52 HOH HOH . 
F 6 HOH A 53 755 53 HOH HOH . 
F 6 HOH A 54 756 54 HOH HOH . 
F 6 HOH A 55 757 55 HOH HOH . 
F 6 HOH A 56 758 56 HOH HOH . 
F 6 HOH A 57 759 57 HOH HOH . 
F 6 HOH A 58 760 58 HOH HOH . 
F 6 HOH A 59 761 59 HOH HOH . 
F 6 HOH A 60 762 60 HOH HOH . 
F 6 HOH A 61 763 61 HOH HOH . 
F 6 HOH A 62 764 62 HOH HOH . 
F 6 HOH A 63 765 63 HOH HOH . 
F 6 HOH A 64 766 64 HOH HOH . 
F 6 HOH A 65 767 65 HOH HOH . 
F 6 HOH A 66 768 66 HOH HOH . 
F 6 HOH A 67 769 67 HOH HOH . 
F 6 HOH A 68 770 68 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 O O3P C5P . . . E 5 -21.503 1.137 -7.168 1 35.93 ? O3P C5P 700 A 1 
HETATM 2 P P C5P . . . E 5 -20.107 1.237 -6.742 1 35.26 ? P C5P 700 A 1 
HETATM 3 O O1P C5P . . . E 5 -19.337 -0.047 -6.849 1 34.78 ? O1P C5P 700 A 1 
HETATM 4 O O2P C5P . . . E 5 -19.515 2.375 -7.544 1 35.23 ? O2P C5P 700 A 1 
HETATM 5 O O5' C5P . . . E 5 -20.282 1.633 -5.212 1 34.64 ? O5' C5P 700 A 1 
HETATM 6 C C5' C5P . . . E 5 -20.897 2.882 -4.923 1 34.23 ? C5' C5P 700 A 1 
HETATM 7 C C4' C5P . . . E 5 -20.956 3.093 -3.431 1 33.18 ? C4' C5P 700 A 1 
HETATM 8 O O4' C5P . . . E 5 -21.861 2.178 -2.805 1 32.37 ? O4' C5P 700 A 1 
HETATM 9 C C3' C5P . . . E 5 -19.626 2.887 -2.746 1 33.61 ? C3' C5P 700 A 1 
HETATM 10 O O3' C5P . . . E 5 -18.735 4.009 -2.915 1 32.3 ? O3' C5P 700 A 1 
HETATM 11 C C2' C5P . . . E 5 -20.102 2.618 -1.326 1 33.64 ? C2' C5P 700 A 1 
HETATM 12 O O2' C5P . . . E 5 -20.465 3.853 -0.679 1 32.54 ? O2' C5P 700 A 1 
HETATM 13 C C1' C5P . . . E 5 -21.39 1.802 -1.515 1 32.77 ? C1' C5P 700 A 1 
HETATM 14 N N1 C5P . . . E 5 -21.356 0.327 -1.461 1 32.45 ? N1 C5P 700 A 1 
HETATM 15 C C2 C5P . . . E 5 -21.816 -0.297 -0.301 1 33.19 ? C2 C5P 700 A 1 
HETATM 16 N N3 C5P . . . E 5 -21.883 -1.643 -0.209 1 34.22 ? N3 C5P 700 A 1 
HETATM 17 C C4 C5P . . . E 5 -21.451 -2.423 -1.235 1 33.58 ? C4 C5P 700 A 1 
HETATM 18 C C5 C5P . . . E 5 -20.958 -1.839 -2.389 1 32.05 ? C5 C5P 700 A 1 
HETATM 19 C C6 C5P . . . E 5 -20.947 -0.454 -2.49 1 33.1 ? C6 C5P 700 A 1 
HETATM 20 O O2 C5P . . . E 5 -22.215 0.401 0.639 1 34.22 ? O2 C5P 700 A 1 
HETATM 21 N N4 C5P . . . E 5 -21.513 -3.757 -1.105 1 32.53 ? N4 C5P 700 A 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           35 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           21 
#