data_4X9M
#
_model_server_result.job_id            lnF_aYXipIYObK2Uo-WbmA 
_model_server_result.datetime_utc      '2025-02-05 06:04:07' 
_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          4x9m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    4X9M 
#
_exptl.entry_id    4X9M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              172.074 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SN-GLYCEROL-3-PHOSPHATE 
_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            4X9M 
_cell.length_a            111.59 
_cell.length_b            111.59 
_cell.length_c            111.59 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4X9M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        195 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 2 3' 
#
_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 
_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                      4 
_struct_asym.id                             D 
_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 328 A CYS 294 1_555 A SG CYS 328 A CYS 294 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc1 A NE2 HIS 93 A HIS 59 1_555 C NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc2 A NE2 HIS 93 A HIS 59 1_555 C NI NI . A NI 402 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc3 C NI NI . A NI 402 1_555 E O HOH . A HOH 679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc4 C NI NI . A NI 402 1_555 E O HOH . A HOH 679 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
#
_chem_comp.formula           'C3 H9 O6 P' 
_chem_comp.formula_weight    172.074 
_chem_comp.id                G3P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SN-GLYCEROL-3-PHOSPHATE 
_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
O1 C1 G3P sing 174 n n 
C1 C2 G3P sing 175 n n 
C2 O2 G3P sing 176 n n 
C2 C3 G3P sing 177 n n 
C3 O1P G3P sing 178 n n 
O1P P G3P sing 179 n n 
O4P P G3P sing 180 n n 
O2P P G3P doub 181 n n 
O3P P G3P sing 182 n n 
O1 HO1 G3P sing 183 n n 
C1 H11 G3P sing 184 n n 
C1 H12 G3P sing 185 n n 
C2 H2 G3P sing 186 n n 
O2 HO2 G3P sing 187 n n 
C3 H31 G3P sing 188 n n 
C3 H32 G3P sing 189 n n 
O3P HOP3 G3P sing 190 n n 
O4P HOP4 G3P sing 191 n n 
#
_atom_sites.entry_id                     4X9M 
_atom_sites.fract_transf_matrix[1][1]    0.008961 
_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]    0.008961 
_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]    0.008961 
_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 FAD A 1 401 600 FAD FAD . 
C 3 NI A 1 402 1 NI NI . 
D 4 G3P A 1 403 600 G3P G3P . 
E 5 HOH A 1 501 10 HOH HOH . 
E 5 HOH A 2 502 93 HOH HOH . 
E 5 HOH A 3 503 16 HOH HOH . 
E 5 HOH A 4 504 74 HOH HOH . 
E 5 HOH A 5 505 199 HOH HOH . 
E 5 HOH A 6 506 159 HOH HOH . 
E 5 HOH A 7 507 140 HOH HOH . 
E 5 HOH A 8 508 130 HOH HOH . 
E 5 HOH A 9 509 131 HOH HOH . 
E 5 HOH A 10 510 139 HOH HOH . 
E 5 HOH A 11 511 47 HOH HOH . 
E 5 HOH A 12 512 32 HOH HOH . 
E 5 HOH A 13 513 68 HOH HOH . 
E 5 HOH A 14 514 102 HOH HOH . 
E 5 HOH A 15 515 193 HOH HOH . 
E 5 HOH A 16 516 151 HOH HOH . 
E 5 HOH A 17 517 26 HOH HOH . 
E 5 HOH A 18 518 98 HOH HOH . 
E 5 HOH A 19 519 40 HOH HOH . 
E 5 HOH A 20 520 107 HOH HOH . 
E 5 HOH A 21 521 169 HOH HOH . 
E 5 HOH A 22 522 134 HOH HOH . 
E 5 HOH A 23 523 103 HOH HOH . 
E 5 HOH A 24 524 60 HOH HOH . 
E 5 HOH A 25 525 132 HOH HOH . 
E 5 HOH A 26 526 11 HOH HOH . 
E 5 HOH A 27 527 198 HOH HOH . 
E 5 HOH A 28 528 79 HOH HOH . 
E 5 HOH A 29 529 186 HOH HOH . 
E 5 HOH A 30 530 80 HOH HOH . 
E 5 HOH A 31 531 101 HOH HOH . 
E 5 HOH A 32 532 156 HOH HOH . 
E 5 HOH A 33 533 113 HOH HOH . 
E 5 HOH A 34 534 146 HOH HOH . 
E 5 HOH A 35 535 177 HOH HOH . 
E 5 HOH A 36 536 14 HOH HOH . 
E 5 HOH A 37 537 97 HOH HOH . 
E 5 HOH A 38 538 9 HOH HOH . 
E 5 HOH A 39 539 55 HOH HOH . 
E 5 HOH A 40 540 144 HOH HOH . 
E 5 HOH A 41 541 184 HOH HOH . 
E 5 HOH A 42 542 121 HOH HOH . 
E 5 HOH A 43 543 175 HOH HOH . 
E 5 HOH A 44 544 77 HOH HOH . 
E 5 HOH A 45 545 66 HOH HOH . 
E 5 HOH A 46 546 81 HOH HOH . 
E 5 HOH A 47 547 157 HOH HOH . 
E 5 HOH A 48 548 61 HOH HOH . 
E 5 HOH A 49 549 17 HOH HOH . 
E 5 HOH A 50 550 135 HOH HOH . 
E 5 HOH A 51 551 20 HOH HOH . 
E 5 HOH A 52 552 195 HOH HOH . 
E 5 HOH A 53 553 23 HOH HOH . 
E 5 HOH A 54 554 2 HOH HOH . 
E 5 HOH A 55 555 171 HOH HOH . 
E 5 HOH A 56 556 33 HOH HOH . 
E 5 HOH A 57 557 43 HOH HOH . 
E 5 HOH A 58 558 189 HOH HOH . 
E 5 HOH A 59 559 187 HOH HOH . 
E 5 HOH A 60 560 51 HOH HOH . 
E 5 HOH A 61 561 71 HOH HOH . 
E 5 HOH A 62 562 176 HOH HOH . 
E 5 HOH A 63 563 190 HOH HOH . 
E 5 HOH A 64 564 45 HOH HOH . 
E 5 HOH A 65 565 28 HOH HOH . 
E 5 HOH A 66 566 196 HOH HOH . 
E 5 HOH A 67 567 99 HOH HOH . 
E 5 HOH A 68 568 180 HOH HOH . 
E 5 HOH A 69 569 136 HOH HOH . 
E 5 HOH A 70 570 120 HOH HOH . 
E 5 HOH A 71 571 25 HOH HOH . 
E 5 HOH A 72 572 129 HOH HOH . 
E 5 HOH A 73 573 56 HOH HOH . 
E 5 HOH A 74 574 165 HOH HOH . 
E 5 HOH A 75 575 41 HOH HOH . 
E 5 HOH A 76 576 15 HOH HOH . 
E 5 HOH A 77 577 185 HOH HOH . 
E 5 HOH A 78 578 54 HOH HOH . 
E 5 HOH A 79 579 85 HOH HOH . 
E 5 HOH A 80 580 109 HOH HOH . 
E 5 HOH A 81 581 173 HOH HOH . 
E 5 HOH A 82 582 35 HOH HOH . 
E 5 HOH A 83 583 44 HOH HOH . 
E 5 HOH A 84 584 52 HOH HOH . 
E 5 HOH A 85 585 125 HOH HOH . 
E 5 HOH A 86 586 37 HOH HOH . 
E 5 HOH A 87 587 53 HOH HOH . 
E 5 HOH A 88 588 38 HOH HOH . 
E 5 HOH A 89 589 155 HOH HOH . 
E 5 HOH A 90 590 90 HOH HOH . 
E 5 HOH A 91 591 18 HOH HOH . 
E 5 HOH A 92 592 118 HOH HOH . 
E 5 HOH A 93 593 48 HOH HOH . 
E 5 HOH A 94 594 143 HOH HOH . 
E 5 HOH A 95 595 100 HOH HOH . 
E 5 HOH A 96 596 64 HOH HOH . 
E 5 HOH A 97 597 137 HOH HOH . 
E 5 HOH A 98 598 87 HOH HOH . 
E 5 HOH A 99 599 24 HOH HOH . 
E 5 HOH A 100 600 192 HOH HOH . 
E 5 HOH A 101 601 76 HOH HOH . 
E 5 HOH A 102 602 12 HOH HOH . 
E 5 HOH A 103 603 178 HOH HOH . 
E 5 HOH A 104 604 78 HOH HOH . 
E 5 HOH A 105 605 112 HOH HOH . 
E 5 HOH A 106 606 57 HOH HOH . 
E 5 HOH A 107 607 13 HOH HOH . 
E 5 HOH A 108 608 19 HOH HOH . 
E 5 HOH A 109 609 172 HOH HOH . 
E 5 HOH A 110 610 194 HOH HOH . 
E 5 HOH A 111 611 96 HOH HOH . 
E 5 HOH A 112 612 150 HOH HOH . 
E 5 HOH A 113 613 108 HOH HOH . 
E 5 HOH A 114 614 34 HOH HOH . 
E 5 HOH A 115 615 94 HOH HOH . 
E 5 HOH A 116 616 114 HOH HOH . 
E 5 HOH A 117 617 182 HOH HOH . 
E 5 HOH A 118 618 126 HOH HOH . 
E 5 HOH A 119 619 5 HOH HOH . 
E 5 HOH A 120 620 197 HOH HOH . 
E 5 HOH A 121 621 42 HOH HOH . 
E 5 HOH A 122 622 95 HOH HOH . 
E 5 HOH A 123 623 39 HOH HOH . 
E 5 HOH A 124 624 70 HOH HOH . 
E 5 HOH A 125 625 62 HOH HOH . 
E 5 HOH A 126 626 27 HOH HOH . 
E 5 HOH A 127 627 174 HOH HOH . 
E 5 HOH A 128 628 154 HOH HOH . 
E 5 HOH A 129 629 21 HOH HOH . 
E 5 HOH A 130 630 50 HOH HOH . 
E 5 HOH A 131 631 166 HOH HOH . 
E 5 HOH A 132 632 106 HOH HOH . 
E 5 HOH A 133 633 147 HOH HOH . 
E 5 HOH A 134 634 63 HOH HOH . 
E 5 HOH A 135 635 3 HOH HOH . 
E 5 HOH A 136 636 158 HOH HOH . 
E 5 HOH A 137 637 133 HOH HOH . 
E 5 HOH A 138 638 67 HOH HOH . 
E 5 HOH A 139 639 168 HOH HOH . 
E 5 HOH A 140 640 89 HOH HOH . 
E 5 HOH A 141 641 29 HOH HOH . 
E 5 HOH A 142 642 22 HOH HOH . 
E 5 HOH A 143 643 69 HOH HOH . 
E 5 HOH A 144 644 83 HOH HOH . 
E 5 HOH A 145 645 1 HOH HOH . 
E 5 HOH A 146 646 7 HOH HOH . 
E 5 HOH A 147 647 141 HOH HOH . 
E 5 HOH A 148 648 183 HOH HOH . 
E 5 HOH A 149 649 122 HOH HOH . 
E 5 HOH A 150 650 6 HOH HOH . 
E 5 HOH A 151 651 105 HOH HOH . 
E 5 HOH A 152 652 8 HOH HOH . 
E 5 HOH A 153 653 31 HOH HOH . 
E 5 HOH A 154 654 30 HOH HOH . 
E 5 HOH A 155 655 75 HOH HOH . 
E 5 HOH A 156 656 164 HOH HOH . 
E 5 HOH A 157 657 84 HOH HOH . 
E 5 HOH A 158 658 170 HOH HOH . 
E 5 HOH A 159 659 65 HOH HOH . 
E 5 HOH A 160 660 138 HOH HOH . 
E 5 HOH A 161 661 104 HOH HOH . 
E 5 HOH A 162 662 88 HOH HOH . 
E 5 HOH A 163 663 92 HOH HOH . 
E 5 HOH A 164 664 148 HOH HOH . 
E 5 HOH A 165 665 119 HOH HOH . 
E 5 HOH A 166 666 46 HOH HOH . 
E 5 HOH A 167 667 123 HOH HOH . 
E 5 HOH A 168 668 110 HOH HOH . 
E 5 HOH A 169 669 145 HOH HOH . 
E 5 HOH A 170 670 124 HOH HOH . 
E 5 HOH A 171 671 4 HOH HOH . 
E 5 HOH A 172 672 117 HOH HOH . 
E 5 HOH A 173 673 152 HOH HOH . 
E 5 HOH A 174 674 116 HOH HOH . 
E 5 HOH A 175 675 82 HOH HOH . 
E 5 HOH A 176 676 162 HOH HOH . 
E 5 HOH A 177 677 191 HOH HOH . 
E 5 HOH A 178 678 153 HOH HOH . 
E 5 HOH A 179 679 302 HOH HOH . 
E 5 HOH A 180 680 179 HOH HOH . 
E 5 HOH A 181 681 115 HOH HOH . 
E 5 HOH A 182 682 72 HOH HOH . 
E 5 HOH A 183 683 36 HOH HOH . 
E 5 HOH A 184 684 86 HOH HOH . 
E 5 HOH A 185 685 128 HOH HOH . 
E 5 HOH A 186 686 160 HOH HOH . 
E 5 HOH A 187 687 59 HOH HOH . 
E 5 HOH A 188 688 111 HOH HOH . 
E 5 HOH A 189 689 142 HOH HOH . 
E 5 HOH A 190 690 149 HOH HOH . 
E 5 HOH A 191 691 163 HOH HOH . 
E 5 HOH A 192 692 301 HOH HOH . 
E 5 HOH A 193 693 73 HOH HOH . 
E 5 HOH A 194 694 188 HOH HOH . 
E 5 HOH A 195 695 91 HOH HOH . 
E 5 HOH A 196 696 167 HOH HOH . 
E 5 HOH A 197 697 127 HOH HOH . 
E 5 HOH A 198 698 181 HOH HOH . 
E 5 HOH A 199 699 58 HOH HOH . 
E 5 HOH A 200 700 49 HOH HOH . 
E 5 HOH A 201 701 161 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 O O1 G3P . . . D 4 6.784 -18.402 39.935 0 22.55 ? O1 G3P 403 A 1 
HETATM 2 C C1 G3P . . . D 4 7.427 -19.436 39.182 0 22.55 ? C1 G3P 403 A 1 
HETATM 3 C C2 G3P . . . D 4 8.816 -19.698 39.75 0 22.55 ? C2 G3P 403 A 1 
HETATM 4 O O2 G3P . . . D 4 9.304 -20.96 39.276 0 22.55 ? O2 G3P 403 A 1 
HETATM 5 C C3 G3P . . . D 4 9.768 -18.585 39.324 0 22.55 ? C3 G3P 403 A 1 
HETATM 6 O O1P G3P . . . D 4 11.006 -18.717 40.02 0 22.55 ? O1P G3P 403 A 1 
HETATM 7 O O4P G3P . . . D 4 13.387 -18.308 40.47 0 22.55 ? O4P G3P 403 A 1 
HETATM 8 O O2P G3P . . . D 4 12.365 -17.749 38.214 0 22.55 ? O2P G3P 403 A 1 
HETATM 9 O O3P G3P . . . D 4 11.743 -16.384 40.263 0 22.55 ? O3P G3P 403 A 1 
HETATM 10 P P G3P . . . D 4 12.223 -17.708 39.718 0 22.55 ? P G3P 403 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           10 
#