data_5M1D
#
_model_server_result.job_id            kPl_7lbnHt0ZZIPLFOwAIg 
_model_server_result.datetime_utc      '2024-11-24 20:09:36' 
_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          5m1d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":503}' 
#
_entry.id    5M1D 
#
_exptl.entry_id    5M1D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_entity.pdbx_number_of_molecules    3 
_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            5M1D 
_cell.length_a            194.199 
_cell.length_b            194.199 
_cell.length_c            107.598 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M1D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -53.799 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 I N N 
? 4 M 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 OD1 ASN 195 A ASN 175 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc2 A ND2 ASN 195 A ASN 175 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc3 A O ALA 251 A ALA 231 1_555 F NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc4 A OE1 GLU 261 A GLU 241 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc5 A OE2 GLU 261 A GLU 241 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? 
metalc ? metalc6 A OE2 GLU 261 A GLU 241 1_555 F NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc7 D MN MN . A MN 501 1_555 E O3P 4LU . A 4LU 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc8 E O4' 4LU . A 4LU 502 1_555 F NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? 
metalc ? metalc9 E O5' 4LU . A 4LU 502 1_555 F NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc10 E O3P 4LU . A 4LU 502 1_555 F NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? 
metalc ? metalc11 F NA NA . A NA 503 1_555 N O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc12 B OD1 ASN 195 B ASN 175 1_555 G MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? 
metalc ? metalc13 B O LEU 196 B LEU 176 1_555 I NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc14 B O ALA 251 B ALA 231 1_555 I NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc15 B OE1 GLU 261 B GLU 241 1_555 G MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc16 B OE2 GLU 261 B GLU 241 1_555 G MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc17 B OE1 GLU 261 B GLU 241 1_555 I NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc18 G MN MN . B MN 501 1_555 H O3P 4LU . B 4LU 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc19 G MN MN . B MN 501 1_555 O O HOH . B HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
metalc ? metalc20 G MN MN . B MN 501 1_555 O O HOH . B HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? 
metalc ? metalc21 H O5' 4LU . B 4LU 502 1_555 I NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc22 H O3P 4LU . B 4LU 502 1_555 I NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc23 I NA NA . B NA 503 1_555 O O HOH . B HOH 657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? 
metalc ? metalc24 C OD1 ASN 195 C ASN 175 1_555 K MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? 
metalc ? metalc25 C O ALA 251 C ALA 231 1_555 M NA NA . C NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc26 C OE1 GLU 261 C GLU 241 1_555 K MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? 
metalc ? metalc27 C OE2 GLU 261 C GLU 241 1_555 K MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? 
metalc ? metalc28 C OE2 GLU 261 C GLU 241 1_555 M NA NA . C NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc29 L O4' 4LU . C 4LU 502 1_555 M NA NA . C NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? 
metalc ? metalc30 L O5' 4LU . C 4LU 502 1_555 M NA NA . C NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? 
metalc ? metalc31 L O2P 4LU . C 4LU 502 1_555 M NA NA . C NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? 
metalc ? metalc32 L O3P 4LU . C 4LU 502 1_555 M NA NA . C NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? 
#
_chem_comp.formula           'Na 1' 
_chem_comp.formula_weight    22.99 
_chem_comp.id                NA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SODIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5M1D 
_atom_sites.fract_transf_matrix[1][1]    0.005149 
_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]    0.005149 
_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]    0.009294 
_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
D 2 MN A 1 501 501 MN MN . 
E 3 4LU A 1 502 502 4LU 4LU . 
F 4 NA A 1 503 503 NA NA . 
G 2 MN B 1 501 501 MN MN . 
H 3 4LU B 1 502 502 4LU 4LU . 
I 4 NA B 1 503 503 NA NA . 
J 5 SO4 B 1 504 504 SO4 SO4 . 
K 2 MN C 1 501 501 MN MN . 
L 3 4LU C 1 502 502 4LU 4LU . 
M 4 NA C 1 503 503 NA NA . 
N 6 HOH A 1 601 601 HOH HOH . 
N 6 HOH A 2 602 602 HOH HOH . 
N 6 HOH A 3 603 603 HOH HOH . 
N 6 HOH A 4 604 604 HOH HOH . 
N 6 HOH A 5 605 605 HOH HOH . 
N 6 HOH A 6 606 606 HOH HOH . 
N 6 HOH A 7 607 607 HOH HOH . 
N 6 HOH A 8 608 608 HOH HOH . 
N 6 HOH A 9 609 609 HOH HOH . 
N 6 HOH A 10 610 610 HOH HOH . 
N 6 HOH A 11 611 611 HOH HOH . 
N 6 HOH A 12 612 612 HOH HOH . 
N 6 HOH A 13 613 613 HOH HOH . 
N 6 HOH A 14 614 614 HOH HOH . 
N 6 HOH A 15 615 615 HOH HOH . 
N 6 HOH A 16 616 616 HOH HOH . 
N 6 HOH A 17 617 617 HOH HOH . 
N 6 HOH A 18 618 618 HOH HOH . 
N 6 HOH A 19 619 619 HOH HOH . 
N 6 HOH A 20 620 620 HOH HOH . 
N 6 HOH A 21 621 621 HOH HOH . 
N 6 HOH A 22 622 622 HOH HOH . 
N 6 HOH A 23 623 623 HOH HOH . 
N 6 HOH A 24 624 624 HOH HOH . 
N 6 HOH A 25 625 625 HOH HOH . 
N 6 HOH A 26 626 626 HOH HOH . 
N 6 HOH A 27 627 627 HOH HOH . 
N 6 HOH A 28 628 628 HOH HOH . 
N 6 HOH A 29 629 629 HOH HOH . 
N 6 HOH A 30 630 630 HOH HOH . 
N 6 HOH A 31 631 631 HOH HOH . 
N 6 HOH A 32 632 632 HOH HOH . 
N 6 HOH A 33 633 633 HOH HOH . 
N 6 HOH A 34 634 634 HOH HOH . 
N 6 HOH A 35 635 635 HOH HOH . 
N 6 HOH A 36 636 636 HOH HOH . 
N 6 HOH A 37 637 637 HOH HOH . 
N 6 HOH A 38 638 638 HOH HOH . 
O 6 HOH B 1 601 601 HOH HOH . 
O 6 HOH B 2 602 602 HOH HOH . 
O 6 HOH B 3 603 603 HOH HOH . 
O 6 HOH B 4 604 604 HOH HOH . 
O 6 HOH B 5 605 605 HOH HOH . 
O 6 HOH B 6 606 606 HOH HOH . 
O 6 HOH B 7 607 607 HOH HOH . 
O 6 HOH B 8 608 608 HOH HOH . 
O 6 HOH B 9 609 609 HOH HOH . 
O 6 HOH B 10 610 610 HOH HOH . 
O 6 HOH B 11 611 611 HOH HOH . 
O 6 HOH B 12 612 612 HOH HOH . 
O 6 HOH B 13 613 613 HOH HOH . 
O 6 HOH B 14 614 614 HOH HOH . 
O 6 HOH B 15 615 615 HOH HOH . 
O 6 HOH B 16 616 616 HOH HOH . 
O 6 HOH B 17 617 617 HOH HOH . 
O 6 HOH B 18 618 618 HOH HOH . 
O 6 HOH B 19 619 619 HOH HOH . 
O 6 HOH B 20 620 620 HOH HOH . 
O 6 HOH B 21 621 621 HOH HOH . 
O 6 HOH B 22 622 622 HOH HOH . 
O 6 HOH B 23 623 623 HOH HOH . 
O 6 HOH B 24 624 624 HOH HOH . 
O 6 HOH B 25 625 625 HOH HOH . 
O 6 HOH B 26 626 626 HOH HOH . 
O 6 HOH B 27 627 627 HOH HOH . 
O 6 HOH B 28 628 628 HOH HOH . 
O 6 HOH B 29 629 629 HOH HOH . 
O 6 HOH B 30 630 630 HOH HOH . 
O 6 HOH B 31 631 631 HOH HOH . 
O 6 HOH B 32 632 632 HOH HOH . 
O 6 HOH B 33 633 633 HOH HOH . 
O 6 HOH B 34 634 634 HOH HOH . 
O 6 HOH B 35 635 635 HOH HOH . 
O 6 HOH B 36 636 636 HOH HOH . 
O 6 HOH B 37 637 637 HOH HOH . 
O 6 HOH B 38 638 638 HOH HOH . 
O 6 HOH B 39 639 639 HOH HOH . 
O 6 HOH B 40 640 640 HOH HOH . 
O 6 HOH B 41 641 641 HOH HOH . 
O 6 HOH B 42 642 642 HOH HOH . 
O 6 HOH B 43 643 643 HOH HOH . 
O 6 HOH B 44 644 644 HOH HOH . 
O 6 HOH B 45 645 645 HOH HOH . 
O 6 HOH B 46 646 646 HOH HOH . 
O 6 HOH B 47 647 647 HOH HOH . 
O 6 HOH B 48 648 648 HOH HOH . 
O 6 HOH B 49 649 649 HOH HOH . 
O 6 HOH B 50 650 650 HOH HOH . 
O 6 HOH B 51 651 651 HOH HOH . 
O 6 HOH B 52 652 652 HOH HOH . 
O 6 HOH B 53 653 653 HOH HOH . 
O 6 HOH B 54 654 654 HOH HOH . 
O 6 HOH B 55 655 655 HOH HOH . 
O 6 HOH B 56 656 656 HOH HOH . 
O 6 HOH B 57 657 657 HOH HOH . 
O 6 HOH B 58 658 658 HOH HOH . 
O 6 HOH B 59 659 659 HOH HOH . 
O 6 HOH B 60 660 660 HOH HOH . 
O 6 HOH B 61 661 661 HOH HOH . 
O 6 HOH B 62 662 662 HOH HOH . 
O 6 HOH B 63 663 663 HOH HOH . 
O 6 HOH B 64 664 664 HOH HOH . 
O 6 HOH B 65 665 665 HOH HOH . 
P 6 HOH C 1 601 601 HOH HOH . 
P 6 HOH C 2 602 602 HOH HOH . 
P 6 HOH C 3 603 603 HOH HOH . 
P 6 HOH C 4 604 604 HOH HOH . 
P 6 HOH C 5 605 605 HOH HOH . 
P 6 HOH C 6 606 606 HOH HOH . 
P 6 HOH C 7 607 607 HOH HOH . 
P 6 HOH C 8 608 608 HOH HOH . 
P 6 HOH C 9 609 609 HOH HOH . 
P 6 HOH C 10 610 610 HOH HOH . 
P 6 HOH C 11 611 611 HOH HOH . 
P 6 HOH C 12 612 612 HOH HOH . 
P 6 HOH C 13 613 613 HOH HOH . 
P 6 HOH C 14 614 614 HOH HOH . 
P 6 HOH C 15 615 615 HOH HOH . 
P 6 HOH C 16 616 616 HOH HOH . 
P 6 HOH C 17 617 617 HOH HOH . 
P 6 HOH C 18 618 618 HOH HOH . 
P 6 HOH C 19 619 619 HOH HOH . 
P 6 HOH C 20 620 620 HOH HOH . 
P 6 HOH C 21 621 621 HOH HOH . 
P 6 HOH C 22 622 622 HOH HOH . 
P 6 HOH C 23 623 623 HOH HOH . 
P 6 HOH C 24 624 624 HOH HOH . 
P 6 HOH C 25 625 625 HOH HOH . 
P 6 HOH C 26 626 626 HOH HOH . 
P 6 HOH C 27 627 627 HOH HOH . 
P 6 HOH C 28 628 628 HOH HOH . 
P 6 HOH C 29 629 629 HOH HOH . 
P 6 HOH C 30 630 630 HOH HOH . 
P 6 HOH C 31 631 631 HOH HOH . 
P 6 HOH C 32 632 632 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           NA 
_atom_site.label_atom_id         NA 
_atom_site.label_comp_id         NA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         F 
_atom_site.label_entity_id       4 
_atom_site.Cartn_x               66.879 
_atom_site.Cartn_y               -10.694 
_atom_site.Cartn_z               -9.238 
_atom_site.occupancy             0.5 
_atom_site.B_iso_or_equiv        60.48 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           503 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           1 
#