data_5YB1
#
_model_server_result.job_id            abOImU7tZgC_Jxh-_JC9Wg 
_model_server_result.datetime_utc      '2024-11-27 12:07:44' 
_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          5yb1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":608}' 
#
_entry.id    5YB1 
#
_exptl.entry_id    5YB1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              285.856 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ~{N},~{N},12-trimethyl-3$l^{3}-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),3,6,9,11-pentaen-4-amine 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         104.67 
_cell.angle_beta          101.43 
_cell.angle_gamma         89.97 
_cell.entry_id            5YB1 
_cell.length_a            38.492 
_cell.length_b            95.653 
_cell.length_c            96.642 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YB1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D,E,F,G,H,I,J,S 1 1 
B,K,L,M,N,O,P,Q,R,T 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
? 3 J N N 
? 3 R 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
disulf ? disulf1 A SG CYS 51 A CYS 53 1_555 A SG CYS 60 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 73 A CYS 75 1_555 A SG CYS 89 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf3 A SG CYS 88 A CYS 90 1_555 A SG CYS 99 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf4 A SG CYS 122 A CYS 124 1_555 A SG CYS 167 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf5 A SG CYS 166 A CYS 168 1_555 A SG CYS 175 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf6 A SG CYS 198 A CYS 200 1_555 A SG CYS 244 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf7 A SG CYS 243 A CYS 245 1_555 A SG CYS 251 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf8 A SG CYS 263 A CYS 265 1_555 A SG CYS 277 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf9 A SG CYS 276 A CYS 278 1_555 A SG CYS 287 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf10 A SG CYS 314 A CYS 316 1_555 A SG CYS 359 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf11 A SG CYS 358 A CYS 360 1_555 A SG CYS 367 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf12 A SG CYS 390 A CYS 392 1_555 A SG CYS 436 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf13 A SG CYS 435 A CYS 437 1_555 A SG CYS 446 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf14 A SG CYS 459 A CYS 461 1_555 A SG CYS 475 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf15 A SG CYS 474 A CYS 476 1_555 A SG CYS 485 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf16 A SG CYS 512 A CYS 514 1_555 A SG CYS 557 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf17 A SG CYS 556 A CYS 558 1_555 A SG CYS 565 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf18 B SG CYS 51 B CYS 53 1_555 B SG CYS 60 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf19 B SG CYS 73 B CYS 75 1_555 B SG CYS 89 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf20 B SG CYS 88 B CYS 90 1_555 B SG CYS 99 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf21 B SG CYS 122 B CYS 124 1_555 B SG CYS 167 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf22 B SG CYS 166 B CYS 168 1_555 B SG CYS 175 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf23 B SG CYS 198 B CYS 200 1_555 B SG CYS 244 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf24 B SG CYS 243 B CYS 245 1_555 B SG CYS 251 B CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf25 B SG CYS 263 B CYS 265 1_555 B SG CYS 277 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf26 B SG CYS 276 B CYS 278 1_555 B SG CYS 287 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf27 B SG CYS 314 B CYS 316 1_555 B SG CYS 359 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf28 B SG CYS 358 B CYS 360 1_555 B SG CYS 367 B CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf29 B SG CYS 390 B CYS 392 1_555 B SG CYS 436 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf30 B SG CYS 435 B CYS 437 1_555 B SG CYS 446 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf31 B SG CYS 459 B CYS 461 1_555 B SG CYS 475 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf32 B SG CYS 474 B CYS 476 1_555 B SG CYS 485 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf33 B SG CYS 512 B CYS 514 1_555 B SG CYS 557 B CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf34 B SG CYS 556 B CYS 558 1_555 B SG CYS 565 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc1 A NE2 HIS 144 A HIS 146 1_555 J CU1 8ZR . A 8ZR 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
metalc ? metalc2 B NE2 HIS 144 B HIS 146 1_555 R CU1 8ZR . B 8ZR 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? 
#
_chem_comp.formula           'C10 H14 Cu N4 S' 
_chem_comp.formula_weight    285.856 
_chem_comp.id                8ZR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ~{N},~{N},12-trimethyl-3$l^{3}-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),3,6,9,11-pentaen-4-amine 
_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
C10 C11 8ZR doub 1 n y 
C10 C9 8ZR sing 2 n y 
C11 C12 8ZR sing 3 n y 
C12 C13 8ZR doub 4 n y 
C13 C14 8ZR sing 5 n n 
C13 N15 8ZR sing 6 n y 
C2 N1 8ZR sing 7 n n 
C3 N1 8ZR sing 8 n n 
C4 N1 8ZR sing 9 n n 
C4 N6 8ZR sing 10 n n 
C4 S5 8ZR doub 11 n n 
C8 C9 8ZR sing 12 n n 
C8 N7 8ZR doub 13 n n 
C9 N15 8ZR doub 14 n y 
N15 CU1 8ZR sing 15 n n 
N6 N7 8ZR sing 16 n n 
N7 CU1 8ZR sing 17 n n 
S5 CU1 8ZR sing 18 n n 
C10 H10 8ZR sing 19 n n 
C11 H11 8ZR sing 20 n n 
C12 H12 8ZR sing 21 n n 
C14 H13 8ZR sing 22 n n 
C14 H14 8ZR sing 23 n n 
C14 H15 8ZR sing 24 n n 
C2 H22 8ZR sing 25 n n 
C2 H23 8ZR sing 26 n n 
C2 H21 8ZR sing 27 n n 
C3 H32 8ZR sing 28 n n 
C3 H31 8ZR sing 29 n n 
C3 H30 8ZR sing 30 n n 
C8 H2 8ZR sing 31 n n 
N6 H3 8ZR sing 32 n n 
#
_atom_sites.entry_id                     5YB1 
_atom_sites.fract_transf_matrix[1][1]    0.025979 
_atom_sites.fract_transf_matrix[1][2]    -0.000015 
_atom_sites.fract_transf_matrix[1][3]    0.005433 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010454 
_atom_sites.fract_transf_matrix[2][3]    0.002796 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.010928 
_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 PLM A 1 601 1 PLM PLM . 
D 2 PLM A 1 602 2 PLM PLM . 
E 2 PLM A 1 603 3 PLM PLM . 
F 2 PLM A 1 604 4 PLM PLM . 
G 2 PLM A 1 605 5 PLM PLM . 
H 2 PLM A 1 606 6 PLM PLM . 
I 2 PLM A 1 607 13 PLM PLM . 
J 3 8ZR A 1 608 2 8ZR CUL . 
K 2 PLM B 1 601 7 PLM PLM . 
L 2 PLM B 1 602 8 PLM PLM . 
M 2 PLM B 1 603 9 PLM PLM . 
N 2 PLM B 1 604 10 PLM PLM . 
O 2 PLM B 1 605 11 PLM PLM . 
P 2 PLM B 1 606 12 PLM PLM . 
Q 2 PLM B 1 607 14 PLM PLM . 
R 3 8ZR B 1 608 1 8ZR CUL . 
S 4 HOH A 1 701 32 HOH HOH . 
S 4 HOH A 2 702 13 HOH HOH . 
S 4 HOH A 3 703 11 HOH HOH . 
S 4 HOH A 4 704 34 HOH HOH . 
S 4 HOH A 5 705 1 HOH HOH . 
S 4 HOH A 6 706 6 HOH HOH . 
S 4 HOH A 7 707 19 HOH HOH . 
S 4 HOH A 8 708 2 HOH HOH . 
S 4 HOH A 9 709 14 HOH HOH . 
S 4 HOH A 10 710 7 HOH HOH . 
S 4 HOH A 11 711 10 HOH HOH . 
S 4 HOH A 12 712 25 HOH HOH . 
S 4 HOH A 13 713 30 HOH HOH . 
S 4 HOH A 14 714 8 HOH HOH . 
S 4 HOH A 15 715 33 HOH HOH . 
S 4 HOH A 16 716 21 HOH HOH . 
S 4 HOH A 17 717 28 HOH HOH . 
S 4 HOH A 18 718 29 HOH HOH . 
S 4 HOH A 19 719 26 HOH HOH . 
S 4 HOH A 20 720 24 HOH HOH . 
T 4 HOH B 1 701 16 HOH HOH . 
T 4 HOH B 2 702 12 HOH HOH . 
T 4 HOH B 3 703 31 HOH HOH . 
T 4 HOH B 4 704 35 HOH HOH . 
T 4 HOH B 5 705 15 HOH HOH . 
T 4 HOH B 6 706 5 HOH HOH . 
T 4 HOH B 7 707 17 HOH HOH . 
T 4 HOH B 8 708 36 HOH HOH . 
T 4 HOH B 9 709 4 HOH HOH . 
T 4 HOH B 10 710 22 HOH HOH . 
T 4 HOH B 11 711 3 HOH HOH . 
T 4 HOH B 12 712 9 HOH HOH . 
T 4 HOH B 13 713 23 HOH HOH . 
T 4 HOH B 14 714 18 HOH HOH . 
T 4 HOH B 15 715 20 HOH HOH . 
T 4 HOH B 16 716 27 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 C10 8ZR . . . J 3 2.284 8.847 8.744 1 110.36 ? C10 8ZR 608 A 1 
HETATM 2 C C11 8ZR . . . J 3 2.597 7.533 8.682 1 110.16 ? C11 8ZR 608 A 1 
HETATM 3 C C12 8ZR . . . J 3 1.612 6.608 8.62 1 110.02 ? C12 8ZR 608 A 1 
HETATM 4 C C13 8ZR . . . J 3 0.276 7.004 8.617 1 110.61 ? C13 8ZR 608 A 1 
HETATM 5 C C14 8ZR . . . J 3 -0.83 5.94 8.549 1 111.03 ? C14 8ZR 608 A 1 
HETATM 6 C C2 8ZR . . . J 3 -2.674 14.692 8.166 1 113.11 ? C2 8ZR 608 A 1 
HETATM 7 C C3 8ZR . . . J 3 -4.412 13.66 9.698 1 113.84 ? C3 8ZR 608 A 1 
HETATM 8 C C4 8ZR . . . J 3 -2.463 12.246 8.846 1 112.72 ? C4 8ZR 608 A 1 
HETATM 9 C C8 8ZR . . . J 3 0.72 10.623 8.809 1 111.85 ? C8 8ZR 608 A 1 
HETATM 10 C C9 8ZR . . . J 3 0.951 9.248 8.743 1 110.89 ? C9 8ZR 608 A 1 
HETATM 11 N N1 8ZR . . . J 3 -3.184 13.528 8.901 1 113.36 ? N1 8ZR 608 A 1 
HETATM 12 N N15 8ZR . . . J 3 -0.054 8.333 8.682 1 111 ? N15 8ZR 608 A 1 
HETATM 13 N N6 8ZR . . . J 3 -1.207 12.102 8.857 1 112.94 ? N6 8ZR 608 A 1 
HETATM 14 N N7 8ZR . . . J 3 -0.604 10.852 8.801 1 112.47 ? N7 8ZR 608 A 1 
HETATM 15 S S5 8ZR . . . J 3 -3.114 10.721 8.762 1 111.52 ? S5 8ZR 608 A 1 
HETATM 16 CU CU1 8ZR . . . J 3 -1.837 9.192 8.683 1 111.37 ? CU1 8ZR 608 A 1 
HETATM 17 H H10 8ZR . . . J 3 2.961 9.484 8.787 1 132.32 ? H10 8ZR 608 A 1 
HETATM 18 H H11 8ZR . . . J 3 3.487 7.266 8.681 1 132.07 ? H11 8ZR 608 A 1 
HETATM 19 H H12 8ZR . . . J 3 1.828 5.705 8.575 1 131.9 ? H12 8ZR 608 A 1 
HETATM 20 H H13 8ZR . . . J 3 -1.521 6.151 9.196 1 133.12 ? H13 8ZR 608 A 1 
HETATM 21 H H14 8ZR . . . J 3 -0.453 5.069 8.75 1 133.12 ? H14 8ZR 608 A 1 
HETATM 22 H H15 8ZR . . . J 3 -1.213 5.929 7.658 1 133.12 ? H15 8ZR 608 A 1 
HETATM 23 H H22 8ZR . . . J 3 -2.792 15.491 8.705 1 135.61 ? H22 8ZR 608 A 1 
HETATM 24 H H23 8ZR . . . J 3 -3.163 14.789 7.334 1 135.61 ? H23 8ZR 608 A 1 
HETATM 25 H H21 8ZR . . . J 3 -1.732 14.567 7.975 1 135.61 ? H21 8ZR 608 A 1 
HETATM 26 H H32 8ZR . . . J 3 -4.929 14.414 9.374 1 136.48 ? H32 8ZR 608 A 1 
HETATM 27 H H31 8ZR . . . J 3 -4.18 13.803 10.628 1 136.48 ? H31 8ZR 608 A 1 
HETATM 28 H H30 8ZR . . . J 3 -4.939 12.849 9.617 1 136.48 ? H30 8ZR 608 A 1 
HETATM 29 H H3 8ZR . . . J 3 -0.71 12.802 8.9 1 135.41 ? H3 8ZR 608 A 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           371 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           29 
#