data_5TVM
#
_model_server_result.job_id            OZx4kr6UWVT7GaT2eayKnQ 
_model_server_result.datetime_utc      '2024-10-15 12:19:22' 
_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          5tvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    5TVM 
#
_exptl.entry_id    5TVM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              282.334 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 
_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          102.64 
_cell.angle_gamma         90 
_cell.entry_id            5TVM 
_cell.length_a            81.297 
_cell.length_b            96.708 
_cell.length_c            99.584 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5TVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,F,G,J,K,L,P 1 1 
C,D,E,H,I,M,N,O 2 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
? 4 G N N 
? 4 H N 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
covale ? covale1 B C PYR 1 B PYR 86 1_555 B N SER 2 B SER 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? 
covale ? covale2 D C PYR 1 D PYR 86 1_555 D N SER 2 D SER 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? 
#
_chem_comp.formula           'C11 H26 N2 O6' 
_chem_comp.formula_weight    282.334 
_chem_comp.id                B3P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 
_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
C1 C2 B3P sing 70 n n 
C1 C3 B3P sing 71 n n 
C1 H11 B3P sing 72 n n 
C1 H12 B3P sing 73 n n 
C2 N2 B3P sing 74 n n 
C2 H21 B3P sing 75 n n 
C2 H22 B3P sing 76 n n 
C3 N1 B3P sing 77 n n 
C3 H31 B3P sing 78 n n 
C3 H32 B3P sing 79 n n 
N1 C4 B3P sing 80 n n 
N1 HN1 B3P sing 81 n n 
C4 C5 B3P sing 82 n n 
C4 C6 B3P sing 83 n n 
C4 C7 B3P sing 84 n n 
C5 O4 B3P sing 85 n n 
C5 H51 B3P sing 86 n n 
C5 H52 B3P sing 87 n n 
C6 O5 B3P sing 88 n n 
C6 H61 B3P sing 89 n n 
C6 H62 B3P sing 90 n n 
C7 O6 B3P sing 91 n n 
C7 H71 B3P sing 92 n n 
C7 H72 B3P sing 93 n n 
N2 C8 B3P sing 94 n n 
N2 HN2 B3P sing 95 n n 
C8 C9 B3P sing 96 n n 
C8 C10 B3P sing 97 n n 
C8 C11 B3P sing 98 n n 
C9 O1 B3P sing 99 n n 
C9 H91 B3P sing 100 n n 
C9 H92 B3P sing 101 n n 
C10 O2 B3P sing 102 n n 
C10 H101 B3P sing 103 n n 
C10 H102 B3P sing 104 n n 
C11 O3 B3P sing 105 n n 
C11 H111 B3P sing 106 n n 
C11 H112 B3P sing 107 n n 
O1 HO1 B3P sing 108 n n 
O2 HO2 B3P sing 109 n n 
O3 HO3 B3P sing 110 n n 
O4 HO4 B3P sing 111 n n 
O5 HO5 B3P sing 112 n n 
O6 HO6 B3P sing 113 n n 
#
_atom_sites.entry_id                     5TVM 
_atom_sites.fract_transf_matrix[1][1]    0.012301 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002758 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01034 
_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]    0.010291 
_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
G 4 B3P B 1 401 1 B3P B3P . 
H 4 B3P D 1 401 2 B3P B3P . 
I 5 PUT E 1 401 3 PUT PUT . 
J 5 PUT F 1 401 4 PUT PUT . 
K 6 HOH A 1 101 102 HOH HOH . 
K 6 HOH A 2 102 116 HOH HOH . 
K 6 HOH A 3 103 153 HOH HOH . 
L 6 HOH B 1 501 98 HOH HOH . 
L 6 HOH B 2 502 119 HOH HOH . 
L 6 HOH B 3 503 7 HOH HOH . 
L 6 HOH B 4 504 86 HOH HOH . 
L 6 HOH B 5 505 117 HOH HOH . 
L 6 HOH B 6 506 115 HOH HOH . 
L 6 HOH B 7 507 112 HOH HOH . 
L 6 HOH B 8 508 145 HOH HOH . 
L 6 HOH B 9 509 11 HOH HOH . 
L 6 HOH B 10 510 122 HOH HOH . 
L 6 HOH B 11 511 39 HOH HOH . 
L 6 HOH B 12 512 109 HOH HOH . 
L 6 HOH B 13 513 155 HOH HOH . 
L 6 HOH B 14 514 144 HOH HOH . 
L 6 HOH B 15 515 156 HOH HOH . 
L 6 HOH B 16 516 108 HOH HOH . 
L 6 HOH B 17 517 159 HOH HOH . 
L 6 HOH B 18 518 157 HOH HOH . 
L 6 HOH B 19 519 154 HOH HOH . 
L 6 HOH B 20 520 75 HOH HOH . 
L 6 HOH B 21 521 123 HOH HOH . 
L 6 HOH B 22 522 124 HOH HOH . 
L 6 HOH B 23 523 46 HOH HOH . 
L 6 HOH B 24 524 96 HOH HOH . 
L 6 HOH B 25 525 62 HOH HOH . 
M 6 HOH C 1 101 141 HOH HOH . 
M 6 HOH C 2 102 131 HOH HOH . 
M 6 HOH C 3 103 140 HOH HOH . 
M 6 HOH C 4 104 152 HOH HOH . 
M 6 HOH C 5 105 45 HOH HOH . 
N 6 HOH D 1 501 149 HOH HOH . 
N 6 HOH D 2 502 130 HOH HOH . 
N 6 HOH D 3 503 31 HOH HOH . 
N 6 HOH D 4 504 99 HOH HOH . 
N 6 HOH D 5 505 137 HOH HOH . 
N 6 HOH D 6 506 162 HOH HOH . 
N 6 HOH D 7 507 139 HOH HOH . 
N 6 HOH D 8 508 55 HOH HOH . 
N 6 HOH D 9 509 132 HOH HOH . 
N 6 HOH D 10 510 3 HOH HOH . 
N 6 HOH D 11 511 47 HOH HOH . 
N 6 HOH D 12 512 136 HOH HOH . 
N 6 HOH D 13 513 133 HOH HOH . 
N 6 HOH D 14 514 88 HOH HOH . 
O 6 HOH E 1 501 51 HOH HOH . 
O 6 HOH E 2 502 14 HOH HOH . 
O 6 HOH E 3 503 100 HOH HOH . 
O 6 HOH E 4 504 127 HOH HOH . 
O 6 HOH E 5 505 74 HOH HOH . 
O 6 HOH E 6 506 58 HOH HOH . 
O 6 HOH E 7 507 79 HOH HOH . 
O 6 HOH E 8 508 38 HOH HOH . 
O 6 HOH E 9 509 41 HOH HOH . 
O 6 HOH E 10 510 160 HOH HOH . 
O 6 HOH E 11 511 87 HOH HOH . 
O 6 HOH E 12 512 134 HOH HOH . 
O 6 HOH E 13 513 101 HOH HOH . 
O 6 HOH E 14 514 19 HOH HOH . 
O 6 HOH E 15 515 94 HOH HOH . 
O 6 HOH E 16 516 15 HOH HOH . 
O 6 HOH E 17 517 18 HOH HOH . 
O 6 HOH E 18 518 93 HOH HOH . 
O 6 HOH E 19 519 27 HOH HOH . 
O 6 HOH E 20 520 16 HOH HOH . 
O 6 HOH E 21 521 22 HOH HOH . 
O 6 HOH E 22 522 151 HOH HOH . 
O 6 HOH E 23 523 148 HOH HOH . 
O 6 HOH E 24 524 150 HOH HOH . 
O 6 HOH E 25 525 77 HOH HOH . 
O 6 HOH E 26 526 8 HOH HOH . 
O 6 HOH E 27 527 42 HOH HOH . 
O 6 HOH E 28 528 97 HOH HOH . 
O 6 HOH E 29 529 65 HOH HOH . 
P 6 HOH F 1 501 48 HOH HOH . 
P 6 HOH F 2 502 37 HOH HOH . 
P 6 HOH F 3 503 105 HOH HOH . 
P 6 HOH F 4 504 125 HOH HOH . 
P 6 HOH F 5 505 107 HOH HOH . 
P 6 HOH F 6 506 103 HOH HOH . 
P 6 HOH F 7 507 163 HOH HOH . 
P 6 HOH F 8 508 161 HOH HOH . 
P 6 HOH F 9 509 126 HOH HOH . 
P 6 HOH F 10 510 164 HOH HOH . 
P 6 HOH F 11 511 21 HOH HOH . 
P 6 HOH F 12 512 104 HOH HOH . 
P 6 HOH F 13 513 114 HOH HOH . 
P 6 HOH F 14 514 106 HOH HOH . 
P 6 HOH F 15 515 110 HOH HOH . 
P 6 HOH F 16 516 57 HOH HOH . 
P 6 HOH F 17 517 26 HOH HOH . 
P 6 HOH F 18 518 91 HOH HOH . 
P 6 HOH F 19 519 158 HOH HOH . 
P 6 HOH F 20 520 32 HOH HOH . 
P 6 HOH F 21 521 111 HOH HOH . 
P 6 HOH F 22 522 43 HOH HOH . 
P 6 HOH F 23 523 53 HOH HOH . 
P 6 HOH F 24 524 34 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 C C1 B3P . . . H 4 62.974 57.685 152.305 1 64.14 ? C1 B3P 401 D 1 
HETATM 2 C C2 B3P . . . H 4 63.037 57.549 150.818 1 64.04 ? C2 B3P 401 D 1 
HETATM 3 C C3 B3P . . . H 4 61.751 58.464 152.66 1 64.49 ? C3 B3P 401 D 1 
HETATM 4 N N1 B3P . . . H 4 61.754 58.75 154.114 1 66.05 ? N1 B3P 401 D 1 
HETATM 5 C C4 B3P . . . H 4 60.913 59.93 154.389 1 66.93 ? C4 B3P 401 D 1 
HETATM 6 C C5 B3P . . . H 4 60.627 60.098 155.885 1 69.15 ? C5 B3P 401 D 1 
HETATM 7 C C6 B3P . . . H 4 61.575 61.229 153.818 1 63.25 ? C6 B3P 401 D 1 
HETATM 8 C C7 B3P . . . H 4 59.495 59.728 153.657 1 68.51 ? C7 B3P 401 D 1 
HETATM 9 N N2 B3P . . . H 4 62.132 56.46 150.383 1 63.06 ? N2 B3P 401 D 1 
HETATM 10 C C8 B3P . . . H 4 62.166 56.349 148.915 1 61.47 ? C8 B3P 401 D 1 
HETATM 11 C C9 B3P . . . H 4 61.376 55.139 148.409 1 61.63 ? C9 B3P 401 D 1 
HETATM 12 C C10 B3P . . . H 4 63.634 56.281 148.395 1 60.99 ? C10 B3P 401 D 1 
HETATM 13 C C11 B3P . . . H 4 61.478 57.656 148.295 1 61.46 ? C11 B3P 401 D 1 
HETATM 14 O O1 B3P . . . H 4 61.9 54.019 149.017 1 62.55 ? O1 B3P 401 D 1 
HETATM 15 O O2 B3P . . . H 4 64.225 55.213 149.023 1 62.05 ? O2 B3P 401 D 1 
HETATM 16 O O3 B3P . . . H 4 61.545 57.55 146.918 1 62.63 ? O3 B3P 401 D 1 
HETATM 17 O O4 B3P . . . H 4 61.692 59.563 156.571 1 70.31 ? O4 B3P 401 D 1 
HETATM 18 O O5 B3P . . . H 4 62.791 61.367 154.445 1 60.97 ? O5 B3P 401 D 1 
HETATM 19 O O6 B3P . . . H 4 58.976 58.51 154.06 1 69.91 ? O6 B3P 401 D 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           19 
#