data_3I6B # _model_server_result.job_id D1C64MiX79orYdLJNkMO0g _model_server_result.datetime_utc '2024-11-09 09:27:21' _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 3i6b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":900}' # _entry.id 3I6B # _exptl.entry_id 3I6B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 238.192 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' _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 3I6B _cell.length_a 64.964 _cell.length_b 144.104 _cell.length_c 145.854 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I6B _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA octameric 8 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 2 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 N 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 O ASP 34 A ASP 34 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc2 E MG MG . A MG 201 1_555 F O1 PO4 . A PO4 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc3 C O ASP 34 C ASP 34 1_555 J MG MG . C MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc4 C OD1 ASP 125 C ASP 125 1_555 J MG MG . C MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc5 J MG MG . C MG 204 1_555 K O3 PO4 . C PO4 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc6 L MG MG . D MG 203 1_555 M O2 PO4 . D PO4 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? # _chem_comp.formula 'C8 H14 O8' _chem_comp.formula_weight 238.192 _chem_comp.id KDO _chem_comp.mon_nstd_flag . _chem_comp.name '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms '3-deoxy-d-manno-oct-2-ulopyranosonic acid;2-keto-3-deoxy-D-mannooctanoic acid;3-deoxy-alpha-D-manno-oct-2-ulosonic acid;3-deoxy-D-manno-oct-2-ulosonic acid;3-deoxy-manno-oct-2-ulosonic acid' # 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 O1A KDO doub 173 n n C1 O1B KDO sing 174 n n C1 C2 KDO sing 175 n n O1B HO1B KDO sing 176 n n C2 O2 KDO sing 177 n n C2 C3 KDO sing 178 n n C2 O6 KDO sing 179 n n O2 HO2 KDO sing 180 n n C3 C4 KDO sing 181 n n C3 H31 KDO sing 182 n n C3 H32 KDO sing 183 n n C4 O4 KDO sing 184 n n C4 C5 KDO sing 185 n n C4 H4 KDO sing 186 n n O4 HO4 KDO sing 187 n n C5 O5 KDO sing 188 n n C5 C6 KDO sing 189 n n C5 H5 KDO sing 190 n n O5 HO5 KDO sing 191 n n C6 O6 KDO sing 192 n n C6 C7 KDO sing 193 n n C6 H6 KDO sing 194 n n C7 O7 KDO sing 195 n n C7 C8 KDO sing 196 n n C7 H7 KDO sing 197 n n O7 HO7 KDO sing 198 n n C8 O8 KDO sing 199 n n C8 H81 KDO sing 200 n n C8 H82 KDO sing 201 n n O8 HO8 KDO sing 202 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version KDO DKdopa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 KDO a-D-Kdop 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 KDO Kdo 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3I6B _atom_sites.fract_transf_matrix[1][1] 0.015393 _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] 0.006939 _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] 0.006856 _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 E 2 MG A 1 201 201 MG MG . F 3 PO4 A 1 800 800 PO4 PO4 . G 2 MG B 1 202 202 MG MG . H 3 PO4 B 1 800 800 PO4 PO4 . I 4 KDO B 1 900 900 KDO KDO . J 2 MG C 1 204 204 MG MG . K 3 PO4 C 1 800 800 PO4 PO4 . L 2 MG D 1 203 203 MG MG . M 3 PO4 D 1 800 800 PO4 PO4 . N 4 KDO D 1 900 900 KDO KDO . O 5 HOH A 1 506 506 HOH HOH . O 5 HOH A 2 519 519 HOH HOH . O 5 HOH A 3 520 520 HOH HOH . O 5 HOH A 4 525 525 HOH HOH . O 5 HOH A 5 534 534 HOH HOH . O 5 HOH A 6 535 535 HOH HOH . O 5 HOH A 7 537 537 HOH HOH . O 5 HOH A 8 539 539 HOH HOH . O 5 HOH A 9 541 541 HOH HOH . O 5 HOH A 10 544 544 HOH HOH . O 5 HOH A 11 554 554 HOH HOH . O 5 HOH A 12 556 556 HOH HOH . O 5 HOH A 13 557 557 HOH HOH . O 5 HOH A 14 558 558 HOH HOH . O 5 HOH A 15 560 560 HOH HOH . O 5 HOH A 16 562 562 HOH HOH . O 5 HOH A 17 568 568 HOH HOH . O 5 HOH A 18 569 569 HOH HOH . O 5 HOH A 19 570 570 HOH HOH . O 5 HOH A 20 573 573 HOH HOH . O 5 HOH A 21 583 583 HOH HOH . O 5 HOH A 22 584 584 HOH HOH . O 5 HOH A 23 586 586 HOH HOH . O 5 HOH A 24 591 591 HOH HOH . O 5 HOH A 25 593 593 HOH HOH . O 5 HOH A 26 595 595 HOH HOH . O 5 HOH A 27 596 596 HOH HOH . O 5 HOH A 28 597 597 HOH HOH . O 5 HOH A 29 604 604 HOH HOH . O 5 HOH A 30 606 606 HOH HOH . O 5 HOH A 31 610 610 HOH HOH . O 5 HOH A 32 618 618 HOH HOH . O 5 HOH A 33 628 628 HOH HOH . O 5 HOH A 34 630 630 HOH HOH . O 5 HOH A 35 631 631 HOH HOH . O 5 HOH A 36 633 633 HOH HOH . O 5 HOH A 37 650 650 HOH HOH . O 5 HOH A 38 657 657 HOH HOH . O 5 HOH A 39 663 663 HOH HOH . O 5 HOH A 40 666 666 HOH HOH . O 5 HOH A 41 667 667 HOH HOH . O 5 HOH A 42 678 678 HOH HOH . O 5 HOH A 43 693 693 HOH HOH . O 5 HOH A 44 694 694 HOH HOH . O 5 HOH A 45 697 697 HOH HOH . O 5 HOH A 46 699 699 HOH HOH . O 5 HOH A 47 700 700 HOH HOH . O 5 HOH A 48 702 702 HOH HOH . P 5 HOH B 1 502 502 HOH HOH . P 5 HOH B 2 504 504 HOH HOH . P 5 HOH B 3 507 507 HOH HOH . P 5 HOH B 4 511 511 HOH HOH . P 5 HOH B 5 513 513 HOH HOH . P 5 HOH B 6 516 516 HOH HOH . P 5 HOH B 7 518 518 HOH HOH . P 5 HOH B 8 527 527 HOH HOH . P 5 HOH B 9 531 531 HOH HOH . P 5 HOH B 10 536 536 HOH HOH . P 5 HOH B 11 538 538 HOH HOH . P 5 HOH B 12 543 543 HOH HOH . P 5 HOH B 13 547 547 HOH HOH . P 5 HOH B 14 552 552 HOH HOH . P 5 HOH B 15 553 553 HOH HOH . P 5 HOH B 16 559 559 HOH HOH . P 5 HOH B 17 566 566 HOH HOH . P 5 HOH B 18 572 572 HOH HOH . P 5 HOH B 19 579 579 HOH HOH . P 5 HOH B 20 580 580 HOH HOH . P 5 HOH B 21 582 582 HOH HOH . P 5 HOH B 22 588 588 HOH HOH . P 5 HOH B 23 589 589 HOH HOH . P 5 HOH B 24 592 592 HOH HOH . P 5 HOH B 25 594 594 HOH HOH . P 5 HOH B 26 601 601 HOH HOH . P 5 HOH B 27 602 602 HOH HOH . P 5 HOH B 28 612 612 HOH HOH . P 5 HOH B 29 615 615 HOH HOH . P 5 HOH B 30 616 616 HOH HOH . P 5 HOH B 31 623 623 HOH HOH . P 5 HOH B 32 632 632 HOH HOH . P 5 HOH B 33 636 636 HOH HOH . P 5 HOH B 34 647 647 HOH HOH . P 5 HOH B 35 648 648 HOH HOH . P 5 HOH B 36 649 649 HOH HOH . P 5 HOH B 37 651 651 HOH HOH . P 5 HOH B 38 653 653 HOH HOH . P 5 HOH B 39 655 655 HOH HOH . P 5 HOH B 40 656 656 HOH HOH . P 5 HOH B 41 659 659 HOH HOH . P 5 HOH B 42 671 671 HOH HOH . P 5 HOH B 43 672 672 HOH HOH . P 5 HOH B 44 673 673 HOH HOH . P 5 HOH B 45 675 675 HOH HOH . P 5 HOH B 46 676 676 HOH HOH . P 5 HOH B 47 679 679 HOH HOH . P 5 HOH B 48 687 687 HOH HOH . P 5 HOH B 49 688 688 HOH HOH . P 5 HOH B 50 696 696 HOH HOH . P 5 HOH B 51 701 701 HOH HOH . Q 5 HOH C 1 517 517 HOH HOH . Q 5 HOH C 2 521 521 HOH HOH . Q 5 HOH C 3 524 524 HOH HOH . Q 5 HOH C 4 532 532 HOH HOH . Q 5 HOH C 5 546 546 HOH HOH . Q 5 HOH C 6 548 548 HOH HOH . Q 5 HOH C 7 549 549 HOH HOH . Q 5 HOH C 8 550 550 HOH HOH . Q 5 HOH C 9 551 551 HOH HOH . Q 5 HOH C 10 564 564 HOH HOH . Q 5 HOH C 11 565 565 HOH HOH . Q 5 HOH C 12 567 567 HOH HOH . Q 5 HOH C 13 571 571 HOH HOH . Q 5 HOH C 14 575 575 HOH HOH . Q 5 HOH C 15 576 576 HOH HOH . Q 5 HOH C 16 581 581 HOH HOH . Q 5 HOH C 17 599 599 HOH HOH . Q 5 HOH C 18 605 605 HOH HOH . Q 5 HOH C 19 611 611 HOH HOH . Q 5 HOH C 20 613 613 HOH HOH . Q 5 HOH C 21 614 614 HOH HOH . Q 5 HOH C 22 617 617 HOH HOH . Q 5 HOH C 23 620 620 HOH HOH . Q 5 HOH C 24 621 621 HOH HOH . Q 5 HOH C 25 624 624 HOH HOH . Q 5 HOH C 26 626 626 HOH HOH . Q 5 HOH C 27 627 627 HOH HOH . Q 5 HOH C 28 637 637 HOH HOH . Q 5 HOH C 29 638 638 HOH HOH . Q 5 HOH C 30 640 640 HOH HOH . Q 5 HOH C 31 643 643 HOH HOH . Q 5 HOH C 32 644 644 HOH HOH . Q 5 HOH C 33 645 645 HOH HOH . Q 5 HOH C 34 646 646 HOH HOH . Q 5 HOH C 35 652 652 HOH HOH . Q 5 HOH C 36 654 654 HOH HOH . Q 5 HOH C 37 660 660 HOH HOH . Q 5 HOH C 38 665 665 HOH HOH . Q 5 HOH C 39 668 668 HOH HOH . Q 5 HOH C 40 684 684 HOH HOH . Q 5 HOH C 41 690 690 HOH HOH . Q 5 HOH C 42 691 691 HOH HOH . Q 5 HOH C 43 695 695 HOH HOH . Q 5 HOH C 44 698 698 HOH HOH . Q 5 HOH C 45 703 703 HOH HOH . R 5 HOH D 1 508 508 HOH HOH . R 5 HOH D 2 515 515 HOH HOH . R 5 HOH D 3 522 522 HOH HOH . R 5 HOH D 4 523 523 HOH HOH . R 5 HOH D 5 526 526 HOH HOH . R 5 HOH D 6 528 528 HOH HOH . R 5 HOH D 7 529 529 HOH HOH . R 5 HOH D 8 530 530 HOH HOH . R 5 HOH D 9 533 533 HOH HOH . R 5 HOH D 10 540 540 HOH HOH . R 5 HOH D 11 542 542 HOH HOH . R 5 HOH D 12 545 545 HOH HOH . R 5 HOH D 13 555 555 HOH HOH . R 5 HOH D 14 561 561 HOH HOH . R 5 HOH D 15 574 574 HOH HOH . R 5 HOH D 16 577 577 HOH HOH . R 5 HOH D 17 578 578 HOH HOH . R 5 HOH D 18 585 585 HOH HOH . R 5 HOH D 19 587 587 HOH HOH . R 5 HOH D 20 590 590 HOH HOH . R 5 HOH D 21 598 598 HOH HOH . R 5 HOH D 22 600 600 HOH HOH . R 5 HOH D 23 603 603 HOH HOH . R 5 HOH D 24 608 608 HOH HOH . R 5 HOH D 25 609 609 HOH HOH . R 5 HOH D 26 619 619 HOH HOH . R 5 HOH D 27 622 622 HOH HOH . R 5 HOH D 28 625 625 HOH HOH . R 5 HOH D 29 629 629 HOH HOH . R 5 HOH D 30 635 635 HOH HOH . R 5 HOH D 31 639 639 HOH HOH . R 5 HOH D 32 641 641 HOH HOH . R 5 HOH D 33 661 661 HOH HOH . R 5 HOH D 34 662 662 HOH HOH . R 5 HOH D 35 664 664 HOH HOH . R 5 HOH D 36 669 669 HOH HOH . R 5 HOH D 37 670 670 HOH HOH . R 5 HOH D 38 677 677 HOH HOH . R 5 HOH D 39 681 681 HOH HOH . R 5 HOH D 40 682 682 HOH HOH . R 5 HOH D 41 683 683 HOH HOH . R 5 HOH D 42 685 685 HOH HOH . R 5 HOH D 43 686 686 HOH HOH . S 5 HOH J 1 509 509 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 KDO . . . I 4 31.299 -20.391 -20.301 1 76.99 ? C1 KDO 900 B 1 HETATM 2 O O1A KDO . . . I 4 30.854 -20.482 -19.092 1 77.25 ? O1A KDO 900 B 1 HETATM 3 O O1B KDO . . . I 4 32.377 -19.789 -20.579 1 77.09 ? O1B KDO 900 B 1 HETATM 4 C C2 KDO . . . I 4 30.535 -21.054 -21.433 1 76.68 ? C2 KDO 900 B 1 HETATM 5 O O2 KDO . . . I 4 30.971 -20.563 -22.72 1 76.79 ? O2 KDO 900 B 1 HETATM 6 C C3 KDO . . . I 4 30.789 -22.554 -21.367 1 76.55 ? C3 KDO 900 B 1 HETATM 7 C C4 KDO . . . I 4 30.026 -23.265 -22.475 1 77.1 ? C4 KDO 900 B 1 HETATM 8 O O4 KDO . . . I 4 30.071 -24.678 -22.235 1 77.3 ? O4 KDO 900 B 1 HETATM 9 C C5 KDO . . . I 4 28.564 -22.842 -22.545 1 77.51 ? C5 KDO 900 B 1 HETATM 10 O O5 KDO . . . I 4 27.913 -23.547 -21.494 1 77.85 ? O5 KDO 900 B 1 HETATM 11 C C6 KDO . . . I 4 28.338 -21.332 -22.373 1 77.39 ? C6 KDO 900 B 1 HETATM 12 O O6 KDO . . . I 4 29.13 -20.816 -21.27 1 77.06 ? O6 KDO 900 B 1 HETATM 13 C C7 KDO . . . I 4 26.831 -20.96 -22.295 1 77.28 ? C7 KDO 900 B 1 HETATM 14 O O7 KDO . . . I 4 26.422 -20.348 -23.559 1 77.32 ? O7 KDO 900 B 1 HETATM 15 C C8 KDO . . . I 4 26.479 -20.001 -21.157 1 77.3 ? C8 KDO 900 B 1 HETATM 16 O O8 KDO . . . I 4 25.585 -20.701 -20.197 1 77.32 ? O8 KDO 900 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 16 #