data_6YVT
#
_model_server_result.job_id            qXz4SuNgi8XOqwofSzFf6Q 
_model_server_result.datetime_utc      '2025-01-10 09:55:31' 
_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          6yvt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":501}' 
#
_entry.id    6YVT 
#
_exptl.entry_id    6YVT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              54.938 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MANGANESE (II) 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         90 
_cell.entry_id            6YVT 
_cell.length_a            84.456 
_cell.length_b            103.018 
_cell.length_c            196.028 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YVT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,H,U 1 1 
B,I,J,V 2 1 
C,K,L,W 3 1 
D,M,N,X 4 1 
E,O,P,Q,R,Y 5 1 
F,S,T,Z 6 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 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 S 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
metalc ? metalc1 A NE2 HIS 139 A HIS 313 1_555 G MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc2 A OD1 ASP 141 A ASP 315 1_555 G MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc3 A NE2 HIS 200 A HIS 374 1_555 G MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? 
metalc ? metalc4 G MN MN . A MN 501 1_555 H N18 PW2 . A PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc5 G MN MN . A MN 501 1_555 H O26 PW2 . A PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc6 B NE2 HIS 139 B HIS 313 1_555 I MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc7 B OD1 ASP 141 B ASP 315 1_555 I MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc8 B NE2 HIS 200 B HIS 374 1_555 I MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc9 I MN MN . B MN 501 1_555 J N18 PW2 . B PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc10 I MN MN . B MN 501 1_555 J O26 PW2 . B PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc11 I MN MN . B MN 501 1_555 V O HOH . B HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc12 C NE2 HIS 139 C HIS 313 1_555 K MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc13 C OD1 ASP 141 C ASP 315 1_555 K MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc14 C NE2 HIS 200 C HIS 374 1_555 K MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc15 K MN MN . C MN 501 1_555 L O26 PW2 . C PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc16 K MN MN . C MN 501 1_555 L N18 PW2 . C PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc17 K MN MN . C MN 501 1_555 W O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? 
metalc ? metalc18 D NE2 HIS 139 D HIS 313 1_555 M MN MN . D MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
metalc ? metalc19 D OD1 ASP 141 D ASP 315 1_555 M MN MN . D MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
metalc ? metalc20 D NE2 HIS 200 D HIS 374 1_555 M MN MN . D MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc21 M MN MN . D MN 501 1_555 N N18 PW2 . D PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc22 M MN MN . D MN 501 1_555 N O26 PW2 . D PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc23 M MN MN . D MN 501 1_555 X O HOH . D HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc24 E NE2 HIS 139 E HIS 313 1_555 O MN MN . E MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc25 E OD1 ASP 141 E ASP 315 1_555 O MN MN . E MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc26 E NE2 HIS 200 E HIS 374 1_555 O MN MN . E MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc27 O MN MN . E MN 501 1_555 P O26 PW2 . E PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc28 O MN MN . E MN 501 1_555 P N18 PW2 . E PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc29 O MN MN . E MN 501 1_555 Y O HOH . E HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc30 F NE2 HIS 139 F HIS 313 1_555 S MN MN . F MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc31 F OD1 ASP 141 F ASP 315 1_555 S MN MN . F MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc32 F NE2 HIS 200 F HIS 374 1_555 S MN MN . F MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc33 S MN MN . F MN 501 1_555 T O26 PW2 . F PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc34 S MN MN . F MN 501 1_555 T N18 PW2 . F PW2 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc35 S MN MN . F MN 501 1_555 Z O HOH . F HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? 
#
_chem_comp.formula           'Mn 2' 
_chem_comp.formula_weight    54.938 
_chem_comp.id                MN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MANGANESE (II) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     6YVT 
_atom_sites.fract_transf_matrix[1][1]    0.01184 
_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]    0.009707 
_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]    0.005101 
_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 2 MN A 1 501 501 MN MN . 
H 3 PW2 A 1 502 601 PW2 253 . 
I 2 MN B 1 501 501 MN MN . 
J 3 PW2 B 1 502 601 PW2 253 . 
K 2 MN C 1 501 501 MN MN . 
L 3 PW2 C 1 502 601 PW2 253 . 
M 2 MN D 1 501 501 MN MN . 
N 3 PW2 D 1 502 601 PW2 253 . 
O 2 MN E 1 501 501 MN MN . 
P 3 PW2 E 1 502 601 PW2 253 . 
Q 4 GOL E 1 503 701 GOL GOL . 
R 5 SO4 E 1 504 801 SO4 SO4 . 
S 2 MN F 1 501 501 MN MN . 
T 3 PW2 F 1 502 601 PW2 253 . 
U 6 HOH A 1 601 1043 HOH HOH . 
U 6 HOH A 2 602 1031 HOH HOH . 
U 6 HOH A 3 603 1044 HOH HOH . 
U 6 HOH A 4 604 1034 HOH HOH . 
U 6 HOH A 5 605 1003 HOH HOH . 
U 6 HOH A 6 606 1058 HOH HOH . 
V 6 HOH B 1 601 1015 HOH HOH . 
V 6 HOH B 2 602 1022 HOH HOH . 
V 6 HOH B 3 603 1045 HOH HOH . 
V 6 HOH B 4 604 1014 HOH HOH . 
V 6 HOH B 5 605 1046 HOH HOH . 
V 6 HOH B 6 606 1016 HOH HOH . 
V 6 HOH B 7 607 1013 HOH HOH . 
W 6 HOH C 1 601 1017 HOH HOH . 
W 6 HOH C 2 602 1021 HOH HOH . 
W 6 HOH C 3 603 1025 HOH HOH . 
W 6 HOH C 4 604 1026 HOH HOH . 
W 6 HOH C 5 605 1030 HOH HOH . 
W 6 HOH C 6 606 1020 HOH HOH . 
W 6 HOH C 7 607 1001 HOH HOH . 
W 6 HOH C 8 608 1008 HOH HOH . 
W 6 HOH C 9 609 1047 HOH HOH . 
X 6 HOH D 1 601 1037 HOH HOH . 
X 6 HOH D 2 602 1004 HOH HOH . 
X 6 HOH D 3 603 1039 HOH HOH . 
X 6 HOH D 4 604 1024 HOH HOH . 
X 6 HOH D 5 605 1035 HOH HOH . 
X 6 HOH D 6 606 1005 HOH HOH . 
X 6 HOH D 7 607 1049 HOH HOH . 
X 6 HOH D 8 608 1036 HOH HOH . 
X 6 HOH D 9 609 1029 HOH HOH . 
X 6 HOH D 10 610 1048 HOH HOH . 
X 6 HOH D 11 611 1038 HOH HOH . 
X 6 HOH D 12 612 1023 HOH HOH . 
X 6 HOH D 13 613 1027 HOH HOH . 
Y 6 HOH E 1 601 1054 HOH HOH . 
Y 6 HOH E 2 602 1051 HOH HOH . 
Y 6 HOH E 3 603 1018 HOH HOH . 
Y 6 HOH E 4 604 1009 HOH HOH . 
Y 6 HOH E 5 605 1010 HOH HOH . 
Y 6 HOH E 6 606 1041 HOH HOH . 
Y 6 HOH E 7 607 1002 HOH HOH . 
Y 6 HOH E 8 608 1028 HOH HOH . 
Y 6 HOH E 9 609 1006 HOH HOH . 
Y 6 HOH E 10 610 1011 HOH HOH . 
Y 6 HOH E 11 611 1050 HOH HOH . 
Y 6 HOH E 12 612 1053 HOH HOH . 
Y 6 HOH E 13 613 1019 HOH HOH . 
Y 6 HOH E 14 614 1052 HOH HOH . 
Z 6 HOH F 1 601 1056 HOH HOH . 
Z 6 HOH F 2 602 1033 HOH HOH . 
Z 6 HOH F 3 603 1040 HOH HOH . 
Z 6 HOH F 4 604 1042 HOH HOH . 
Z 6 HOH F 5 605 1007 HOH HOH . 
Z 6 HOH F 6 606 1057 HOH HOH . 
Z 6 HOH F 7 607 1032 HOH HOH . 
Z 6 HOH F 8 608 1055 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           MN 
_atom_site.label_atom_id         MN 
_atom_site.label_comp_id         MN 
_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       2 
_atom_site.Cartn_x               -32.275 
_atom_site.Cartn_y               -18.001 
_atom_site.Cartn_z               -54.476 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        29.45 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          MN 
_atom_site.auth_comp_id          MN 
_atom_site.auth_seq_id           501 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#