data_9BXD
#
_model_server_result.job_id            p_AFWSvpbjpk2i_hJZbsTQ 
_model_server_result.datetime_utc      '2025-07-16 19:04:56' 
_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          9bxd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":512}' 
#
_entry.id    9BXD 
#
_exptl.entry_id    9BXD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    1 
_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            9BXD 
_cell.length_a            61.013 
_cell.length_b            65.837 
_cell.length_c            90.518 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9BXD 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             M 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 13 A CYS 54 1_555 A SG CYS 33 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? 
covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? 
covale ? covale8 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale9 A ND2 ASN 311 A ASN 448 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_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
C1 C2 MPD sing 342 n n 
C1 H11 MPD sing 343 n n 
C1 H12 MPD sing 344 n n 
C1 H13 MPD sing 345 n n 
C2 O2 MPD sing 346 n n 
C2 CM MPD sing 347 n n 
C2 C3 MPD sing 348 n n 
O2 HO2 MPD sing 349 n n 
CM HM1 MPD sing 350 n n 
CM HM2 MPD sing 351 n n 
CM HM3 MPD sing 352 n n 
C3 C4 MPD sing 353 n n 
C3 H31 MPD sing 354 n n 
C3 H32 MPD sing 355 n n 
C4 O4 MPD sing 356 n n 
C4 C5 MPD sing 357 n n 
C4 H4 MPD sing 358 n n 
O4 HO4 MPD sing 359 n n 
C5 H51 MPD sing 360 n n 
C5 H52 MPD sing 361 n n 
C5 H53 MPD sing 362 n n 
#
_atom_sites.entry_id                     9BXD 
_atom_sites.fract_transf_matrix[1][1]    0.01639 
_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]    0.015189 
_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]    0.011048 
_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
B 2 NAG A 1 501 501 NAG NAG . 
C 2 NAG A 1 502 502 NAG NAG . 
D 2 NAG A 1 503 503 NAG NAG . 
E 2 NAG A 1 504 504 NAG NAG . 
F 2 NAG A 1 505 505 NAG NAG . 
G 2 NAG A 1 506 506 NAG NAG . 
H 2 NAG A 1 507 507 NAG NAG . 
I 2 NAG A 1 508 508 NAG NAG . 
J 2 NAG A 1 509 510 NAG NAG . 
K 3 EPE A 1 510 512 EPE EPE . 
L 4 A1ATK A 1 511 1 A1ATK MW5 . 
M 5 MPD A 1 512 1 MPD MPD . 
N 6 HOH A 1 601 34 HOH HOH . 
N 6 HOH A 2 602 85 HOH HOH . 
N 6 HOH A 3 603 129 HOH HOH . 
N 6 HOH A 4 604 125 HOH HOH . 
N 6 HOH A 5 605 155 HOH HOH . 
N 6 HOH A 6 606 173 HOH HOH . 
N 6 HOH A 7 607 53 HOH HOH . 
N 6 HOH A 8 608 110 HOH HOH . 
N 6 HOH A 9 609 131 HOH HOH . 
N 6 HOH A 10 610 35 HOH HOH . 
N 6 HOH A 11 611 16 HOH HOH . 
N 6 HOH A 12 612 89 HOH HOH . 
N 6 HOH A 13 613 67 HOH HOH . 
N 6 HOH A 14 614 170 HOH HOH . 
N 6 HOH A 15 615 156 HOH HOH . 
N 6 HOH A 16 616 106 HOH HOH . 
N 6 HOH A 17 617 10 HOH HOH . 
N 6 HOH A 18 618 75 HOH HOH . 
N 6 HOH A 19 619 120 HOH HOH . 
N 6 HOH A 20 620 138 HOH HOH . 
N 6 HOH A 21 621 149 HOH HOH . 
N 6 HOH A 22 622 66 HOH HOH . 
N 6 HOH A 23 623 8 HOH HOH . 
N 6 HOH A 24 624 36 HOH HOH . 
N 6 HOH A 25 625 40 HOH HOH . 
N 6 HOH A 26 626 88 HOH HOH . 
N 6 HOH A 27 627 28 HOH HOH . 
N 6 HOH A 28 628 42 HOH HOH . 
N 6 HOH A 29 629 103 HOH HOH . 
N 6 HOH A 30 630 160 HOH HOH . 
N 6 HOH A 31 631 79 HOH HOH . 
N 6 HOH A 32 632 24 HOH HOH . 
N 6 HOH A 33 633 78 HOH HOH . 
N 6 HOH A 34 634 114 HOH HOH . 
N 6 HOH A 35 635 9 HOH HOH . 
N 6 HOH A 36 636 100 HOH HOH . 
N 6 HOH A 37 637 23 HOH HOH . 
N 6 HOH A 38 638 73 HOH HOH . 
N 6 HOH A 39 639 121 HOH HOH . 
N 6 HOH A 40 640 41 HOH HOH . 
N 6 HOH A 41 641 72 HOH HOH . 
N 6 HOH A 42 642 84 HOH HOH . 
N 6 HOH A 43 643 1 HOH HOH . 
N 6 HOH A 44 644 31 HOH HOH . 
N 6 HOH A 45 645 6 HOH HOH . 
N 6 HOH A 46 646 117 HOH HOH . 
N 6 HOH A 47 647 27 HOH HOH . 
N 6 HOH A 48 648 56 HOH HOH . 
N 6 HOH A 49 649 183 HOH HOH . 
N 6 HOH A 50 650 96 HOH HOH . 
N 6 HOH A 51 651 81 HOH HOH . 
N 6 HOH A 52 652 43 HOH HOH . 
N 6 HOH A 53 653 22 HOH HOH . 
N 6 HOH A 54 654 49 HOH HOH . 
N 6 HOH A 55 655 172 HOH HOH . 
N 6 HOH A 56 656 152 HOH HOH . 
N 6 HOH A 57 657 59 HOH HOH . 
N 6 HOH A 58 658 45 HOH HOH . 
N 6 HOH A 59 659 157 HOH HOH . 
N 6 HOH A 60 660 47 HOH HOH . 
N 6 HOH A 61 661 19 HOH HOH . 
N 6 HOH A 62 662 102 HOH HOH . 
N 6 HOH A 63 663 167 HOH HOH . 
N 6 HOH A 64 664 20 HOH HOH . 
N 6 HOH A 65 665 97 HOH HOH . 
N 6 HOH A 66 666 118 HOH HOH . 
N 6 HOH A 67 667 12 HOH HOH . 
N 6 HOH A 68 668 33 HOH HOH . 
N 6 HOH A 69 669 139 HOH HOH . 
N 6 HOH A 70 670 77 HOH HOH . 
N 6 HOH A 71 671 168 HOH HOH . 
N 6 HOH A 72 672 169 HOH HOH . 
N 6 HOH A 73 673 105 HOH HOH . 
N 6 HOH A 74 674 113 HOH HOH . 
N 6 HOH A 75 675 52 HOH HOH . 
N 6 HOH A 76 676 50 HOH HOH . 
N 6 HOH A 77 677 26 HOH HOH . 
N 6 HOH A 78 678 107 HOH HOH . 
N 6 HOH A 79 679 3 HOH HOH . 
N 6 HOH A 80 680 37 HOH HOH . 
N 6 HOH A 81 681 92 HOH HOH . 
N 6 HOH A 82 682 7 HOH HOH . 
N 6 HOH A 83 683 14 HOH HOH . 
N 6 HOH A 84 684 17 HOH HOH . 
N 6 HOH A 85 685 5 HOH HOH . 
N 6 HOH A 86 686 44 HOH HOH . 
N 6 HOH A 87 687 15 HOH HOH . 
N 6 HOH A 88 688 69 HOH HOH . 
N 6 HOH A 89 689 32 HOH HOH . 
N 6 HOH A 90 690 39 HOH HOH . 
N 6 HOH A 91 691 58 HOH HOH . 
N 6 HOH A 92 692 38 HOH HOH . 
N 6 HOH A 93 693 101 HOH HOH . 
N 6 HOH A 94 694 93 HOH HOH . 
N 6 HOH A 95 695 186 HOH HOH . 
N 6 HOH A 96 696 11 HOH HOH . 
N 6 HOH A 97 697 65 HOH HOH . 
N 6 HOH A 98 698 80 HOH HOH . 
N 6 HOH A 99 699 61 HOH HOH . 
N 6 HOH A 100 700 133 HOH HOH . 
N 6 HOH A 101 701 4 HOH HOH . 
N 6 HOH A 102 702 60 HOH HOH . 
N 6 HOH A 103 703 13 HOH HOH . 
N 6 HOH A 104 704 48 HOH HOH . 
N 6 HOH A 105 705 142 HOH HOH . 
N 6 HOH A 106 706 51 HOH HOH . 
N 6 HOH A 107 707 64 HOH HOH . 
N 6 HOH A 108 708 159 HOH HOH . 
N 6 HOH A 109 709 135 HOH HOH . 
N 6 HOH A 110 710 119 HOH HOH . 
N 6 HOH A 111 711 2 HOH HOH . 
N 6 HOH A 112 712 46 HOH HOH . 
N 6 HOH A 113 713 18 HOH HOH . 
N 6 HOH A 114 714 76 HOH HOH . 
N 6 HOH A 115 715 62 HOH HOH . 
N 6 HOH A 116 716 146 HOH HOH . 
N 6 HOH A 117 717 151 HOH HOH . 
N 6 HOH A 118 718 143 HOH HOH . 
N 6 HOH A 119 719 30 HOH HOH . 
N 6 HOH A 120 720 82 HOH HOH . 
N 6 HOH A 121 721 136 HOH HOH . 
N 6 HOH A 122 722 122 HOH HOH . 
N 6 HOH A 123 723 57 HOH HOH . 
N 6 HOH A 124 724 29 HOH HOH . 
N 6 HOH A 125 725 127 HOH HOH . 
N 6 HOH A 126 726 141 HOH HOH . 
N 6 HOH A 127 727 132 HOH HOH . 
N 6 HOH A 128 728 134 HOH HOH . 
N 6 HOH A 129 729 70 HOH HOH . 
N 6 HOH A 130 730 185 HOH HOH . 
N 6 HOH A 131 731 21 HOH HOH . 
N 6 HOH A 132 732 128 HOH HOH . 
N 6 HOH A 133 733 124 HOH HOH . 
N 6 HOH A 134 734 55 HOH HOH . 
N 6 HOH A 135 735 63 HOH HOH . 
N 6 HOH A 136 736 184 HOH HOH . 
N 6 HOH A 137 737 162 HOH HOH . 
N 6 HOH A 138 738 180 HOH HOH . 
N 6 HOH A 139 739 99 HOH HOH . 
N 6 HOH A 140 740 164 HOH HOH . 
N 6 HOH A 141 741 115 HOH HOH . 
N 6 HOH A 142 742 25 HOH HOH . 
N 6 HOH A 143 743 68 HOH HOH . 
N 6 HOH A 144 744 90 HOH HOH . 
N 6 HOH A 145 745 54 HOH HOH . 
N 6 HOH A 146 746 161 HOH HOH . 
N 6 HOH A 147 747 166 HOH HOH . 
N 6 HOH A 148 748 179 HOH HOH . 
N 6 HOH A 149 749 104 HOH HOH . 
N 6 HOH A 150 750 74 HOH HOH . 
N 6 HOH A 151 751 177 HOH HOH . 
N 6 HOH A 152 752 95 HOH HOH . 
N 6 HOH A 153 753 165 HOH HOH . 
N 6 HOH A 154 754 175 HOH HOH . 
N 6 HOH A 155 755 147 HOH HOH . 
N 6 HOH A 156 756 181 HOH HOH . 
N 6 HOH A 157 757 176 HOH HOH . 
N 6 HOH A 158 758 91 HOH HOH . 
N 6 HOH A 159 759 153 HOH HOH . 
N 6 HOH A 160 760 145 HOH HOH . 
N 6 HOH A 161 761 109 HOH HOH . 
N 6 HOH A 162 762 116 HOH HOH . 
N 6 HOH A 163 763 86 HOH HOH . 
N 6 HOH A 164 764 163 HOH HOH . 
N 6 HOH A 165 765 111 HOH HOH . 
N 6 HOH A 166 766 137 HOH HOH . 
N 6 HOH A 167 767 174 HOH HOH . 
N 6 HOH A 168 768 150 HOH HOH . 
N 6 HOH A 169 769 123 HOH HOH . 
N 6 HOH A 170 770 130 HOH HOH . 
N 6 HOH A 171 771 83 HOH HOH . 
N 6 HOH A 172 772 98 HOH HOH . 
N 6 HOH A 173 773 148 HOH HOH . 
N 6 HOH A 174 774 94 HOH HOH . 
N 6 HOH A 175 775 71 HOH HOH . 
N 6 HOH A 176 776 158 HOH HOH . 
N 6 HOH A 177 777 140 HOH HOH . 
N 6 HOH A 178 778 154 HOH HOH . 
N 6 HOH A 179 779 144 HOH HOH . 
N 6 HOH A 180 780 178 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 C1 MPD . . . M 5 -16.508 23.804 10.452 1 62.91 ? C1 MPD 512 A 1 
HETATM 2 C C2 MPD . . . M 5 -15.058 23.942 10.001 1 73.63 ? C2 MPD 512 A 1 
HETATM 3 O O2 MPD . . . M 5 -15.014 24.191 8.568 1 77.48 ? O2 MPD 512 A 1 
HETATM 4 C CM MPD . . . M 5 -14.361 22.625 10.274 1 67.45 ? CM MPD 512 A 1 
HETATM 5 C C3 MPD . . . M 5 -14.362 25.084 10.737 1 63.55 ? C3 MPD 512 A 1 
HETATM 6 C C4 MPD . . . M 5 -13.043 25.489 10.08 1 74.02 ? C4 MPD 512 A 1 
HETATM 7 O O4 MPD . . . M 5 -13.023 26.884 9.932 1 64.95 ? O4 MPD 512 A 1 
HETATM 8 C C5 MPD . . . M 5 -11.817 25.066 10.888 1 60.47 ? C5 MPD 512 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           386 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#