data_6Y4M
#
_model_server_result.job_id            zba6VlQEJxbNPqPNS6598g 
_model_server_result.datetime_utc      '2024-11-24 23:52:16' 
_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          6y4m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":1003}' 
#
_entry.id    6Y4M 
#
_exptl.entry_id    6Y4M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CALCIUM ION' 
_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            6Y4M 
_cell.length_a            103.961 
_cell.length_b            152.59 
_cell.length_c            185.989 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Y4M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 
_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
? 7 I N N 
? 7 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
covale ? covale1 M C31 O9B . B O9B 1004 1_555 T N VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
covale ? covale2 N C5 O9H . B O9H 1005 1_555 O NBI OH5 . B OH5 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale3 N N3 O9H . B O9H 1005 1_555 T C VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? 
metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? 
metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? 
metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc7 G O1G GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc8 G O1B GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc9 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc10 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc11 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc12 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc13 K MG MG . B MG 1002 1_555 Y O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? 
metalc ? metalc14 K MG MG . B MG 1002 1_555 Z O HOH . C HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? 
metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? 
metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc17 C O THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? 
metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc19 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? 
metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc22 P O1G GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? 
metalc ? metalc23 P O1B GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc24 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc25 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc26 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc27 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc28 U O1G GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? 
metalc ? metalc29 U O1B GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc30 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc31 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc32 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc33 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
#
_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                     6Y4M 
_atom_sites.fract_transf_matrix[1][1]    0.009619 
_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]    0.006554 
_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]    0.005377 
_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 5 GTP A 1 1001 1001 GTP GTP . 
H 6 MG A 1 1002 1002 MG MO6 . 
I 7 CA A 1 1003 1003 CA CA . 
J 8 GDP B 1 1001 1001 GDP GDP . 
K 6 MG B 1 1002 1002 MG MG . 
L 9 MES B 1 1003 1004 MES MES . 
M 10 O9B B 1 1004 2001 O9B ABB . 
N 11 O9H B 1 1005 2001 O9H ABB . 
O 12 OH5 B 1 1006 2001 OH5 ABB . 
P 5 GTP C 1 1001 1001 GTP GTP . 
Q 6 MG C 1 1002 1002 MG MO6 . 
R 7 CA C 1 1003 1003 CA CA . 
S 13 PGE C 1 1004 1004 PGE PGE . 
T 14 VAL C 1 1005 2001 VAL ABB . 
U 5 GTP D 1 1001 1001 GTP GTP . 
V 6 MG D 1 1002 1002 MG MO6 . 
W 15 ACP F 1 401 401 ACP ACP . 
X 16 HOH A 1 1101 1002 HOH MO6 . 
X 16 HOH A 2 1102 1002 HOH MO6 . 
X 16 HOH A 3 1103 1002 HOH MO6 . 
X 16 HOH A 4 1104 11 HOH HOH . 
X 16 HOH A 5 1105 1002 HOH MO6 . 
X 16 HOH A 6 1106 8 HOH HOH . 
X 16 HOH A 7 1107 10 HOH HOH . 
X 16 HOH A 8 1108 13 HOH HOH . 
X 16 HOH A 9 1109 7 HOH HOH . 
Y 16 HOH B 1 1101 20 HOH HOH . 
Y 16 HOH B 2 1102 18 HOH HOH . 
Y 16 HOH B 3 1103 5 HOH HOH . 
Y 16 HOH B 4 1104 16 HOH HOH . 
Y 16 HOH B 5 1105 4 HOH HOH . 
Y 16 HOH B 6 1106 14 HOH HOH . 
Y 16 HOH B 7 1107 6 HOH HOH . 
Y 16 HOH B 8 1108 21 HOH HOH . 
Y 16 HOH B 9 1109 1 HOH HOH . 
Y 16 HOH B 10 1110 9 HOH HOH . 
Y 16 HOH B 11 1111 19 HOH HOH . 
Z 16 HOH C 1 1101 1002 HOH MO6 . 
Z 16 HOH C 2 1102 1002 HOH MO6 . 
Z 16 HOH C 3 1103 1002 HOH MO6 . 
Z 16 HOH C 4 1104 15 HOH HOH . 
Z 16 HOH C 5 1105 1002 HOH MO6 . 
Z 16 HOH C 6 1106 2 HOH HOH . 
Z 16 HOH C 7 1107 3 HOH HOH . 
AA 16 HOH D 1 1101 1002 HOH MO6 . 
AA 16 HOH D 2 1102 17 HOH HOH . 
AA 16 HOH D 3 1103 1002 HOH MO6 . 
AA 16 HOH D 4 1104 1002 HOH MO6 . 
AA 16 HOH D 5 1105 1002 HOH MO6 . 
BA 16 HOH E 1 201 12 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         R 
_atom_site.label_entity_id       7 
_atom_site.Cartn_x               -14.338 
_atom_site.Cartn_y               22.992 
_atom_site.Cartn_z               -11.531 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        86.83 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           1003 
_atom_site.auth_asym_id          C 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              38 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           253 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           1 
#