data_1KC3
#
_model_server_result.job_id            mFhizaVz0St8RMrOuXkgmQ 
_model_server_result.datetime_utc      '2025-02-05 07:02:27' 
_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          1kc3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":601}' 
#
_entry.id    1KC3 
#
_exptl.entry_id    1KC3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              548.33 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" 
_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            1KC3 
_cell.length_a            47.98 
_cell.length_b            72.261 
_cell.length_c            82.682 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KC3 
_symmetry.cell_setting             orthorhombic 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 B MG MG . A MG 501 1_555 E O HOH . A HOH 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc2 B MG MG . A MG 501 1_555 E O HOH . A HOH 908 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc3 B MG MG . A MG 501 1_555 E O HOH . A HOH 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc4 B MG MG . A MG 501 1_555 E O HOH . A HOH 909 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc5 B MG MG . A MG 501 1_555 E O HOH . A HOH 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc6 B MG MG . A MG 501 1_555 E O HOH . A HOH 910 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
#
_chem_comp.formula           'C16 H26 N2 O15 P2' 
_chem_comp.formula_weight    548.33 
_chem_comp.id                TRH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" 
_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
O4P P2 TRH sing 388 n n 
O4P H4PO TRH sing 389 n n 
P2 O3P TRH doub 390 n n 
P2 O1 TRH sing 391 n n 
P2 OPP TRH sing 392 n n 
O1 C1 TRH sing 393 n n 
C1 C2 TRH sing 394 n n 
C1 O5 TRH sing 395 n n 
C1 HC1 TRH sing 396 n n 
C2 O2 TRH sing 397 n n 
C2 C3 TRH sing 398 n n 
C2 HC2 TRH sing 399 n n 
O2 HO2 TRH sing 400 n n 
C3 O3 TRH sing 401 n n 
C3 C4 TRH sing 402 n n 
C3 HC3 TRH sing 403 n n 
O3 HO3 TRH sing 404 n n 
C4 O4 TRH sing 405 n n 
C4 C5 TRH sing 406 n n 
C4 HC4 TRH sing 407 n n 
O4 HO4 TRH sing 408 n n 
C5 O5 TRH sing 409 n n 
C5 C6 TRH sing 410 n n 
C5 HC5 TRH sing 411 n n 
C6 HC61 TRH sing 412 n n 
C6 HC62 TRH sing 413 n n 
C6 HC63 TRH sing 414 n n 
OPP P TRH sing 415 n n 
P O1P TRH sing 416 n n 
P O2P TRH doub 417 n n 
P O5' TRH sing 418 n n 
O1P H1PO TRH sing 419 n n 
O5' C5' TRH sing 420 n n 
C5' C4' TRH sing 421 n n 
C5' "H5'1" TRH sing 422 n n 
C5' "H5'2" TRH sing 423 n n 
C4' O4' TRH sing 424 n n 
C4' C3' TRH sing 425 n n 
C4' "H4'C" TRH sing 426 n n 
O4' C1' TRH sing 427 n n 
C3' O3' TRH sing 428 n n 
C3' C2' TRH sing 429 n n 
C3' "H3'C" TRH sing 430 n n 
O3' "H3'O" TRH sing 431 n n 
C2' C1' TRH sing 432 n n 
C2' "H2'1" TRH sing 433 n n 
C2' "H2'2" TRH sing 434 n n 
C1' N11 TRH sing 435 n n 
C1' "H1'C" TRH sing 436 n n 
N11 C21 TRH sing 437 n n 
N11 C61 TRH sing 438 n n 
C21 O21 TRH doub 439 n n 
C21 N31 TRH sing 440 n n 
N31 C41 TRH sing 441 n n 
N31 H31N TRH sing 442 n n 
C41 O41 TRH doub 443 n n 
C41 C51 TRH sing 444 n n 
C51 C5A TRH sing 445 n n 
C51 C61 TRH doub 446 n n 
C5A HCA1 TRH sing 447 n n 
C5A HCA2 TRH sing 448 n n 
C5A HCA3 TRH sing 449 n n 
C61 H61C TRH sing 450 n n 
#
_atom_sites.entry_id                     1KC3 
_atom_sites.fract_transf_matrix[1][1]    0.020842 
_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]    0.013839 
_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]    0.012095 
_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 MG A 1 501 501 MG MG . 
C 3 NDP A 1 901 901 NDP NDP . 
D 4 TRH A 1 601 601 TRH TRH . 
E 5 HOH A 1 902 1 HOH HOH . 
E 5 HOH A 2 903 2 HOH HOH . 
E 5 HOH A 3 904 3 HOH HOH . 
E 5 HOH A 4 905 4 HOH HOH . 
E 5 HOH A 5 906 5 HOH HOH . 
E 5 HOH A 6 907 6 HOH HOH . 
E 5 HOH A 7 908 7 HOH HOH . 
E 5 HOH A 8 909 8 HOH HOH . 
E 5 HOH A 9 910 9 HOH HOH . 
E 5 HOH A 10 911 10 HOH HOH . 
E 5 HOH A 11 912 11 HOH HOH . 
E 5 HOH A 12 913 12 HOH HOH . 
E 5 HOH A 13 914 13 HOH HOH . 
E 5 HOH A 14 915 14 HOH HOH . 
E 5 HOH A 15 916 15 HOH HOH . 
E 5 HOH A 16 917 16 HOH HOH . 
E 5 HOH A 17 918 17 HOH HOH . 
E 5 HOH A 18 919 18 HOH HOH . 
E 5 HOH A 19 920 19 HOH HOH . 
E 5 HOH A 20 921 20 HOH HOH . 
E 5 HOH A 21 922 21 HOH HOH . 
E 5 HOH A 22 923 22 HOH HOH . 
E 5 HOH A 23 924 23 HOH HOH . 
E 5 HOH A 24 925 24 HOH HOH . 
E 5 HOH A 25 926 25 HOH HOH . 
E 5 HOH A 26 927 26 HOH HOH . 
E 5 HOH A 27 928 27 HOH HOH . 
E 5 HOH A 28 929 28 HOH HOH . 
E 5 HOH A 29 930 29 HOH HOH . 
E 5 HOH A 30 931 30 HOH HOH . 
E 5 HOH A 31 932 31 HOH HOH . 
E 5 HOH A 32 933 32 HOH HOH . 
E 5 HOH A 33 934 33 HOH HOH . 
E 5 HOH A 34 935 34 HOH HOH . 
E 5 HOH A 35 936 35 HOH HOH . 
E 5 HOH A 36 937 36 HOH HOH . 
E 5 HOH A 37 938 37 HOH HOH . 
E 5 HOH A 38 939 38 HOH HOH . 
E 5 HOH A 39 940 39 HOH HOH . 
E 5 HOH A 40 941 40 HOH HOH . 
E 5 HOH A 41 942 41 HOH HOH . 
E 5 HOH A 42 943 42 HOH HOH . 
E 5 HOH A 43 944 43 HOH HOH . 
E 5 HOH A 44 945 44 HOH HOH . 
E 5 HOH A 45 946 45 HOH HOH . 
E 5 HOH A 46 947 46 HOH HOH . 
E 5 HOH A 47 948 47 HOH HOH . 
E 5 HOH A 48 949 48 HOH HOH . 
E 5 HOH A 49 950 49 HOH HOH . 
E 5 HOH A 50 951 50 HOH HOH . 
E 5 HOH A 51 952 51 HOH HOH . 
E 5 HOH A 52 953 52 HOH HOH . 
E 5 HOH A 53 954 53 HOH HOH . 
E 5 HOH A 54 955 54 HOH HOH . 
E 5 HOH A 55 956 55 HOH HOH . 
E 5 HOH A 56 957 56 HOH HOH . 
E 5 HOH A 57 958 57 HOH HOH . 
E 5 HOH A 58 959 58 HOH HOH . 
E 5 HOH A 59 960 59 HOH HOH . 
E 5 HOH A 60 961 60 HOH HOH . 
E 5 HOH A 61 962 61 HOH HOH . 
E 5 HOH A 62 963 62 HOH HOH . 
E 5 HOH A 63 964 63 HOH HOH . 
E 5 HOH A 64 965 64 HOH HOH . 
E 5 HOH A 65 966 65 HOH HOH . 
E 5 HOH A 66 967 66 HOH HOH . 
E 5 HOH A 67 968 67 HOH HOH . 
E 5 HOH A 68 969 68 HOH HOH . 
E 5 HOH A 69 970 69 HOH HOH . 
E 5 HOH A 70 971 70 HOH HOH . 
E 5 HOH A 71 972 71 HOH HOH . 
E 5 HOH A 72 973 72 HOH HOH . 
E 5 HOH A 73 974 73 HOH HOH . 
E 5 HOH A 74 975 74 HOH HOH . 
E 5 HOH A 75 976 75 HOH HOH . 
E 5 HOH A 76 977 76 HOH HOH . 
E 5 HOH A 77 978 77 HOH HOH . 
E 5 HOH A 78 979 78 HOH HOH . 
E 5 HOH A 79 980 79 HOH HOH . 
E 5 HOH A 80 981 80 HOH HOH . 
E 5 HOH A 81 982 81 HOH HOH . 
E 5 HOH A 82 983 82 HOH HOH . 
E 5 HOH A 83 984 83 HOH HOH . 
E 5 HOH A 84 985 84 HOH HOH . 
E 5 HOH A 85 986 85 HOH HOH . 
E 5 HOH A 86 987 86 HOH HOH . 
E 5 HOH A 87 988 87 HOH HOH . 
E 5 HOH A 88 989 88 HOH HOH . 
E 5 HOH A 89 990 89 HOH HOH . 
E 5 HOH A 90 991 90 HOH HOH . 
E 5 HOH A 91 992 91 HOH HOH . 
E 5 HOH A 92 993 92 HOH HOH . 
E 5 HOH A 93 994 93 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 O4P TRH . . . D 4 3.908 -21.229 12.812 1 70.81 ? O4P TRH 601 A 1 
HETATM 2 P P2 TRH . . . D 4 2.982 -22.411 13.121 1 70.4 ? P2 TRH 601 A 1 
HETATM 3 O O3P TRH . . . D 4 3.701 -23.658 13.599 1 69.29 ? O3P TRH 601 A 1 
HETATM 4 O O1 TRH . . . D 4 1.854 -22.017 14.218 1 68.88 ? O1 TRH 601 A 1 
HETATM 5 C C1 TRH . . . D 4 2.171 -21.974 15.588 1 64.72 ? C1 TRH 601 A 1 
HETATM 6 C C2 TRH . . . D 4 1.034 -21.327 16.352 1 62.68 ? C2 TRH 601 A 1 
HETATM 7 O O2 TRH . . . D 4 0.955 -19.94 16.057 1 62.11 ? O2 TRH 601 A 1 
HETATM 8 C C3 TRH . . . D 4 1.377 -21.606 17.808 1 61.86 ? C3 TRH 601 A 1 
HETATM 9 O O3 TRH . . . D 4 0.447 -21.111 18.724 1 56.52 ? O3 TRH 601 A 1 
HETATM 10 C C4 TRH . . . D 4 2.768 -21.085 18.145 1 63.09 ? C4 TRH 601 A 1 
HETATM 11 O O4 TRH . . . D 4 2.995 -21.479 19.519 1 63.46 ? O4 TRH 601 A 1 
HETATM 12 C C5 TRH . . . D 4 3.917 -21.378 17.136 1 63.24 ? C5 TRH 601 A 1 
HETATM 13 O O5 TRH . . . D 4 3.392 -21.26 15.816 1 63.5 ? O5 TRH 601 A 1 
HETATM 14 C C6 TRH . . . D 4 5.106 -20.413 17.108 1 61.4 ? C6 TRH 601 A 1 
HETATM 15 O OPP TRH . . . D 4 1.975 -22.726 11.917 1 72.11 ? OPP TRH 601 A 1 
HETATM 16 P P TRH . . . D 4 1.087 -21.564 11.259 1 72 ? P TRH 601 A 1 
HETATM 17 O O1P TRH . . . D 4 1.973 -21.107 10.105 1 72.14 ? O1P TRH 601 A 1 
HETATM 18 O O2P TRH . . . D 4 0.519 -20.649 12.321 1 72.83 ? O2P TRH 601 A 1 
HETATM 19 O O5' TRH . . . D 4 -0.201 -22.278 10.645 1 72.63 ? O5' TRH 601 A 1 
HETATM 20 C C5' TRH . . . D 4 -1.354 -22.678 11.375 1 73.77 ? C5' TRH 601 A 1 
HETATM 21 C C4' TRH . . . D 4 -2.241 -23.512 10.441 1 75.67 ? C4' TRH 601 A 1 
HETATM 22 O O4' TRH . . . D 4 -2.014 -23.289 9.012 1 76.99 ? O4' TRH 601 A 1 
HETATM 23 C C3' TRH . . . D 4 -2.071 -25.034 10.572 1 75.56 ? C3' TRH 601 A 1 
HETATM 24 O O3' TRH . . . D 4 -2.707 -25.643 11.709 1 74.85 ? O3' TRH 601 A 1 
HETATM 25 C C2' TRH . . . D 4 -2.671 -25.473 9.248 1 75.63 ? C2' TRH 601 A 1 
HETATM 26 C C1' TRH . . . D 4 -2.837 -24.23 8.345 1 76.25 ? C1' TRH 601 A 1 
HETATM 27 N N11 TRH . . . D 4 -2.591 -24.771 6.985 1 77.27 ? N11 TRH 601 A 1 
HETATM 28 C C21 TRH . . . D 4 -3.662 -25.114 6.219 1 78.25 ? C21 TRH 601 A 1 
HETATM 29 O O21 TRH . . . D 4 -4.802 -24.908 6.596 1 77.89 ? O21 TRH 601 A 1 
HETATM 30 N N31 TRH . . . D 4 -3.58 -25.693 5.008 1 79.84 ? N31 TRH 601 A 1 
HETATM 31 C C41 TRH . . . D 4 -2.391 -26.016 4.473 1 79.22 ? C41 TRH 601 A 1 
HETATM 32 O O41 TRH . . . D 4 -2.32 -26.549 3.338 1 76.61 ? O41 TRH 601 A 1 
HETATM 33 C C51 TRH . . . D 4 -1.177 -25.694 5.284 1 78.68 ? C51 TRH 601 A 1 
HETATM 34 C C5A TRH . . . D 4 0.178 -26.035 4.743 1 77.85 ? C5A TRH 601 A 1 
HETATM 35 C C61 TRH . . . D 4 -1.346 -25.069 6.539 1 77.89 ? C61 TRH 601 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           35 
#