data_6DYB
#
_model_server_result.job_id            EoF5pPVA6zbG42xU6Ce8Cw 
_model_server_result.datetime_utc      '2024-12-15 05:48:40' 
_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          6dyb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":202}' 
#
_entry.id    6DYB 
#
_exptl.entry_id    6DYB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CALCIUM ION' 
_entity.pdbx_number_of_molecules    6 
_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         120 
_cell.entry_id            6DYB 
_cell.length_a            73.008 
_cell.length_b            73.008 
_cell.length_c            143.994 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DYB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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,K 1 1 
B,H,I,J,L 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 D N N 
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 I N N 
? 3 J 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 96 A CYS 96 1_555 B SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
covale ? covale1 A SG CYS 98 A CYS 98 1_555 C CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.774 ? 
covale ? covale2 A SG CYS 101 A CYS 101 1_555 C CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.771 ? 
covale ? covale3 B SG CYS 98 C CYS 98 1_555 H CAB HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? 
covale ? covale4 B SG CYS 101 C CYS 101 1_555 H CAC HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? 
metalc ? metalc1 A OE1 GLU 4 A GLU 4 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc2 A OE1 GLU 4 A GLU 4 1_555 D CA CA . A CA 202 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? 
metalc ? metalc3 A OE2 GLU 4 A GLU 4 1_555 D CA CA . A CA 202 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? 
metalc ? metalc4 A OE2 GLU 4 A GLU 4 1_555 F CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? 
metalc ? metalc5 A OD1 ASP 5 A ASP 5 1_555 E CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc6 A OD1 ASP 5 A ASP 5 1_555 E CA CA . A CA 203 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? 
metalc ? metalc7 A OD2 ASP 5 A ASP 5 1_555 E CA CA . A CA 203 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc8 A SD MET 7 A MET 7 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc9 A OE2 GLU 8 A GLU 8 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc10 A OE1 GLU 8 A GLU 8 1_555 E CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc11 A OD2 ASP 50 A ASP 50 1_555 D CA CA . A CA 202 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc12 A OD2 ASP 50 A ASP 50 1_555 F CA CA . A CA 204 10_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? 
metalc ? metalc13 A OD1 ASP 50 A ASP 50 1_555 G CA CA . A CA 205 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? 
metalc ? metalc14 A NE2 HIS 102 A HIS 102 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc15 C O1A HEC . A HEC 201 1_555 D CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? 
metalc ? metalc16 E CA CA . A CA 203 1_555 K O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc17 E CA CA . A CA 203 1_555 K O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? 
metalc ? metalc18 E CA CA . A CA 203 1_555 K O HOH . A HOH 304 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? 
metalc ? metalc19 F CA CA . A CA 204 1_555 K O HOH . A HOH 306 10_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc20 G CA CA . A CA 205 1_555 K O HOH . A HOH 306 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? 
metalc ? metalc21 B OE2 GLU 4 C GLU 4 1_555 I CA CA . C CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? 
metalc ? metalc22 B OE2 GLU 4 C GLU 4 1_555 I CA CA . C CA 202 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? 
metalc ? metalc23 B OE1 GLU 4 C GLU 4 1_555 J CA CA . C CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? 
metalc ? metalc24 B SD MET 7 C MET 7 1_555 H FE HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? 
metalc ? metalc25 B OE1 GLU 8 C GLU 8 1_555 J CA CA . C CA 203 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc26 B OE2 GLU 8 C GLU 8 1_555 J CA CA . C CA 203 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? 
metalc ? metalc27 B NE2 HIS 102 C HIS 102 1_555 H FE HEC . C HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc28 H O1A HEC . C HEC 201 1_555 I CA CA . C CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc29 H O1A HEC . C HEC 201 1_555 I CA CA . C CA 202 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
#
_chem_comp.formula           'Ca 2' 
_chem_comp.formula_weight    40.078 
_chem_comp.id                CA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CALCIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     6DYB 
_atom_sites.fract_transf_matrix[1][1]    0.013697 
_atom_sites.fract_transf_matrix[1][2]    0.007908 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015816 
_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]    0.006945 
_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 HEC A 1 201 1 HEC HEC . 
D 3 CA A 1 202 3 CA CA . 
E 3 CA A 1 203 4 CA CA . 
F 3 CA A 1 204 6 CA CA . 
G 3 CA A 1 205 7 CA CA . 
H 2 HEC C 1 201 2 HEC HEC . 
I 3 CA C 1 202 2 CA CA . 
J 3 CA C 1 203 5 CA CA . 
K 4 HOH A 1 301 15 HOH HOH . 
K 4 HOH A 2 302 13 HOH HOH . 
K 4 HOH A 3 303 4 HOH HOH . 
K 4 HOH A 4 304 5 HOH HOH . 
K 4 HOH A 5 305 7 HOH HOH . 
K 4 HOH A 6 306 8 HOH HOH . 
K 4 HOH A 7 307 6 HOH HOH . 
K 4 HOH A 8 308 9 HOH HOH . 
L 4 HOH C 1 301 12 HOH HOH . 
L 4 HOH C 2 302 11 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           CA 
_atom_site.label_atom_id         CA 
_atom_site.label_comp_id         CA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         I 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               3.993 
_atom_site.Cartn_y               -44.456 
_atom_site.Cartn_z               -11.999 
_atom_site.occupancy             0.5 
_atom_site.B_iso_or_equiv        99.43 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           202 
_atom_site.auth_asym_id          C 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#