data_3TCM
#
_model_server_result.job_id            Tly7AFKmE7PPMu8phljHIg 
_model_server_result.datetime_utc      '2024-10-31 11:18:27' 
_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          3tcm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    3TCM 
#
_exptl.entry_id    3TCM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              333.234 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE 
_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            3TCM 
_cell.length_a            119.859 
_cell.length_b            126.973 
_cell.length_c            75.663 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TCM 
_symmetry.cell_setting             ? 
_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 
_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,F 
_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
? 2 C N N 
? 2 D N N 
#
_struct_conn.conn_type_id                   disulf 
_struct_conn.details                        ? 
_struct_conn.id                             disulf1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             69 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              51 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            A 
_struct_conn.ptnr2_label_atom_id            SG 
_struct_conn.ptnr2_label_comp_id            CYS 
_struct_conn.ptnr2_label_seq_id             471 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             CYS 
_struct_conn.ptnr2_auth_seq_id              453 
_struct_conn.ptnr2_symmetry                 1_555 
_struct_conn.pdbx_ptnr1_PDB_ins_code        ? 
_struct_conn.pdbx_ptnr1_label_alt_id        A 
_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                2.152 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C11 H16 N3 O7 P' 
_chem_comp.formula_weight    333.234 
_chem_comp.id                DCS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE 
#
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 DCS doub 83 n y 
N1 C6 DCS sing 84 n y 
C2 C2A DCS sing 85 n n 
C2 C3 DCS sing 86 n y 
C2A H2A1 DCS sing 87 n n 
C2A H2A2 DCS sing 88 n n 
C2A H2A3 DCS sing 89 n n 
C3 O3 DCS sing 90 n n 
C3 C4 DCS doub 91 n y 
O3 HO3 DCS sing 92 n n 
C4 C4A DCS sing 93 n n 
C4 C5 DCS sing 94 n y 
C4A N DCS sing 95 n n 
C4A H4A1 DCS sing 96 n n 
C4A H4A2 DCS sing 97 n n 
C5 C6 DCS doub 98 n y 
C5 C5A DCS sing 99 n n 
C6 H6 DCS sing 100 n n 
C5A O4P DCS sing 101 n n 
C5A H5A1 DCS sing 102 n n 
C5A H5A2 DCS sing 103 n n 
O4P P DCS sing 104 n n 
P O1P DCS doub 105 n n 
P O2P DCS sing 106 n n 
P O3P DCS sing 107 n n 
O2P HOP2 DCS sing 108 n n 
O3P HOP3 DCS sing 109 n n 
N CA DCS sing 110 n n 
N HN DCS sing 111 n n 
CA C DCS sing 112 n n 
CA CB DCS sing 113 n n 
CA HA DCS sing 114 n n 
C O DCS doub 115 n n 
C ND DCS sing 116 n n 
ND OG DCS sing 117 n n 
ND HND DCS sing 118 n n 
OG CB DCS sing 119 n n 
CB HB1 DCS sing 120 n n 
CB HB2 DCS sing 121 n n 
#
_atom_sites.entry_id                     3TCM 
_atom_sites.fract_transf_matrix[1][1]    0.008343 
_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]    0.007876 
_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]    0.013216 
_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
C 2 DCS A 1 501 501 DCS DCS . 
D 2 DCS B 1 502 502 DCS DCS . 
E 3 HOH A 1 483 7 HOH HOH . 
E 3 HOH A 2 484 11 HOH HOH . 
E 3 HOH A 3 485 20 HOH HOH . 
E 3 HOH A 4 486 25 HOH HOH . 
E 3 HOH A 5 487 27 HOH HOH . 
E 3 HOH A 6 488 37 HOH HOH . 
E 3 HOH A 7 489 44 HOH HOH . 
E 3 HOH A 8 490 45 HOH HOH . 
E 3 HOH A 9 491 46 HOH HOH . 
E 3 HOH A 10 492 48 HOH HOH . 
E 3 HOH A 11 493 54 HOH HOH . 
E 3 HOH A 12 494 71 HOH HOH . 
E 3 HOH A 13 495 73 HOH HOH . 
E 3 HOH A 14 496 77 HOH HOH . 
E 3 HOH A 15 497 85 HOH HOH . 
E 3 HOH A 16 498 87 HOH HOH . 
E 3 HOH A 17 499 91 HOH HOH . 
E 3 HOH A 18 500 27 HOH HOH . 
E 3 HOH A 19 502 31 HOH HOH . 
E 3 HOH A 20 503 34 HOH HOH . 
E 3 HOH A 21 504 35 HOH HOH . 
E 3 HOH A 22 505 43 HOH HOH . 
E 3 HOH A 23 506 47 HOH HOH . 
E 3 HOH A 24 507 51 HOH HOH . 
E 3 HOH A 25 508 71 HOH HOH . 
E 3 HOH A 26 509 75 HOH HOH . 
E 3 HOH A 27 510 81 HOH HOH . 
E 3 HOH A 28 511 97 HOH HOH . 
E 3 HOH A 29 512 100 HOH HOH . 
F 3 HOH B 1 483 2 HOH HOH . 
F 3 HOH B 2 484 4 HOH HOH . 
F 3 HOH B 3 485 12 HOH HOH . 
F 3 HOH B 4 486 17 HOH HOH . 
F 3 HOH B 5 487 23 HOH HOH . 
F 3 HOH B 6 488 26 HOH HOH . 
F 3 HOH B 7 489 28 HOH HOH . 
F 3 HOH B 8 490 32 HOH HOH . 
F 3 HOH B 9 491 35 HOH HOH . 
F 3 HOH B 10 492 38 HOH HOH . 
F 3 HOH B 11 493 40 HOH HOH . 
F 3 HOH B 12 494 55 HOH HOH . 
F 3 HOH B 13 495 58 HOH HOH . 
F 3 HOH B 14 496 69 HOH HOH . 
F 3 HOH B 15 497 76 HOH HOH . 
F 3 HOH B 16 498 78 HOH HOH . 
F 3 HOH B 17 499 80 HOH HOH . 
F 3 HOH B 18 500 82 HOH HOH . 
F 3 HOH B 19 501 90 HOH HOH . 
F 3 HOH B 20 503 106 HOH HOH . 
F 3 HOH B 21 504 110 HOH HOH . 
F 3 HOH B 22 505 4 HOH HOH . 
F 3 HOH B 23 506 9 HOH HOH . 
F 3 HOH B 24 507 12 HOH HOH . 
F 3 HOH B 25 508 15 HOH HOH . 
F 3 HOH B 26 509 21 HOH HOH . 
F 3 HOH B 27 510 39 HOH HOH . 
F 3 HOH B 28 511 73 HOH HOH . 
F 3 HOH B 29 512 77 HOH HOH . 
F 3 HOH B 30 513 78 HOH HOH . 
F 3 HOH B 31 514 79 HOH HOH . 
F 3 HOH B 32 515 95 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 DCS . . . D 2 -44.642 -39.162 22.807 1 26.1 ? N1 DCS 502 B 1 
HETATM 2 C C2 DCS . . . D 2 -45.889 -39.665 22.824 1 28.95 ? C2 DCS 502 B 1 
HETATM 3 C C2A DCS . . . D 2 -46.074 -41.133 23.027 1 29.69 ? C2A DCS 502 B 1 
HETATM 4 C C3 DCS . . . D 2 -47.09 -38.808 22.67 1 32 ? C3 DCS 502 B 1 
HETATM 5 O O3 DCS . . . D 2 -48.347 -39.376 22.716 1 29.16 ? O3 DCS 502 B 1 
HETATM 6 C C4 DCS . . . D 2 -46.816 -37.354 22.465 1 34.13 ? C4 DCS 502 B 1 
HETATM 7 C C4A DCS . . . D 2 -47.919 -36.35 22.251 1 38.85 ? C4A DCS 502 B 1 
HETATM 8 C C5 DCS . . . D 2 -45.381 -36.938 22.466 1 31.62 ? C5 DCS 502 B 1 
HETATM 9 C C6 DCS . . . D 2 -44.377 -37.867 22.639 1 27.49 ? C6 DCS 502 B 1 
HETATM 10 C C5A DCS . . . D 2 -44.957 -35.503 22.265 1 32.02 ? C5A DCS 502 B 1 
HETATM 11 O O4P DCS . . . D 2 -45.463 -34.793 23.369 1 32.94 ? O4P DCS 502 B 1 
HETATM 12 P P DCS . . . D 2 -45.192 -33.25 23.546 1 33.36 ? P DCS 502 B 1 
HETATM 13 O O1P DCS . . . D 2 -44.53 -33.188 24.887 1 34.29 ? O1P DCS 502 B 1 
HETATM 14 O O2P DCS . . . D 2 -44.266 -32.838 22.444 1 34.86 ? O2P DCS 502 B 1 
HETATM 15 O O3P DCS . . . D 2 -46.603 -32.754 23.447 1 33.11 ? O3P DCS 502 B 1 
HETATM 16 N N DCS . . . D 2 -49.158 -37.023 21.879 1 40.6 ? N DCS 502 B 1 
HETATM 17 C CA DCS . . . D 2 -50.041 -36.607 20.797 1 41.85 ? CA DCS 502 B 1 
HETATM 18 C C DCS . . . D 2 -51.165 -37.575 20.525 1 42.18 ? C DCS 502 B 1 
HETATM 19 O O DCS . . . D 2 -51.114 -38.767 20.749 1 43.03 ? O DCS 502 B 1 
HETATM 20 N ND DCS . . . D 2 -52.205 -36.951 20.032 1 42.17 ? ND DCS 502 B 1 
HETATM 21 O OG DCS . . . D 2 -52.039 -35.639 20.331 1 44.29 ? OG DCS 502 B 1 
HETATM 22 C CB DCS . . . D 2 -50.799 -35.301 20.992 1 41.77 ? CB DCS 502 B 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#