data_2PT9
#
_model_server_result.job_id            UHt_45lQt4U03OaTXuTN5Q 
_model_server_result.datetime_utc      '2024-11-14 04:57:11' 
_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          2pt9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    2PT9 
#
_exptl.entry_id    2PT9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              356.444 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE" 
_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          94.53 
_cell.angle_gamma         90 
_cell.entry_id            2PT9 
_cell.length_a            196.24 
_cell.length_b            134.1 
_cell.length_c            48.35 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PT9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_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,D,E,F,G,P 1 1,2 
B,C,H,I,J,K,L,M,N,O,Q,R 2 1 
#
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' 2_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
? 2 D N N 
? 2 I N N 
? 2 L N N 
#
_chem_comp.formula           'C14 H24 N6 O3 S' 
_chem_comp.formula_weight    356.444 
_chem_comp.id                S4M 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE" 
_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
CA N S4M sing 353 n n 
CA CB S4M sing 354 n n 
CA HA1 S4M sing 355 n n 
CA HA2 S4M sing 356 n n 
N HN1 S4M sing 357 n n 
N HN2 S4M sing 358 n n 
CB CG S4M sing 359 n n 
CB HB1 S4M sing 360 n n 
CB HB2 S4M sing 361 n n 
CG SD S4M sing 362 n n 
CG HG1 S4M sing 363 n n 
CG HG2 S4M sing 364 n n 
SD CE S4M sing 365 n n 
SD C5' S4M sing 366 n n 
SD HSD S4M sing 367 n n 
CE HE1 S4M sing 368 n n 
CE HE2 S4M sing 369 n n 
CE HE3 S4M sing 370 n n 
C5' C4' S4M sing 371 n n 
C5' "H5'1" S4M sing 372 n n 
C5' "H5'2" S4M sing 373 n n 
C4' C3' S4M sing 374 n n 
C4' O4' S4M sing 375 n n 
C4' H4' S4M sing 376 n n 
O4' C1' S4M sing 377 n n 
C1' C2' S4M sing 378 n n 
C1' N9 S4M sing 379 n n 
C1' H1' S4M sing 380 n n 
C2' O2' S4M sing 381 n n 
C2' C3' S4M sing 382 n n 
C2' H2' S4M sing 383 n n 
O2' HO2' S4M sing 384 n n 
C3' O3' S4M sing 385 n n 
C3' H3' S4M sing 386 n n 
O3' HO3' S4M sing 387 n n 
N9 C4 S4M sing 388 n y 
N9 C8 S4M sing 389 n y 
C8 N7 S4M doub 390 n y 
C8 H8 S4M sing 391 n n 
N7 C5 S4M sing 392 n y 
C5 C4 S4M doub 393 n y 
C5 C6 S4M sing 394 n y 
C6 N1 S4M doub 395 n y 
C6 N6 S4M sing 396 n n 
N6 HN61 S4M sing 397 n n 
N6 HN62 S4M sing 398 n n 
C4 N3 S4M sing 399 n y 
N3 C2 S4M doub 400 n y 
C2 N1 S4M sing 401 n y 
C2 H2 S4M sing 402 n n 
#
_atom_sites.entry_id                     2PT9 
_atom_sites.fract_transf_matrix[1][1]    0.005096 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000404 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007457 
_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]    0.020747 
_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 S4M A 1 501 501 S4M S4M . 
E 3 2MH A 1 401 401 2MH M2H . 
F 4 1PG A 1 701 701 1PG 1PG . 
G 5 GOL A 1 603 603 GOL GOL . 
H 6 SO4 B 1 604 604 SO4 SO4 . 
I 2 S4M B 1 502 502 S4M S4M . 
J 3 2MH B 1 402 402 2MH M2H . 
K 5 GOL B 1 601 601 GOL GOL . 
L 2 S4M C 1 503 503 S4M S4M . 
M 3 2MH C 1 403 403 2MH M2H . 
N 4 1PG C 1 702 702 1PG 1PG . 
O 5 GOL C 1 602 602 GOL GOL . 
P 7 HOH A 1 702 1 HOH HOH . 
P 7 HOH A 2 703 6 HOH HOH . 
P 7 HOH A 3 704 28 HOH HOH . 
P 7 HOH A 4 705 30 HOH HOH . 
P 7 HOH A 5 706 32 HOH HOH . 
P 7 HOH A 6 707 33 HOH HOH . 
P 7 HOH A 7 708 37 HOH HOH . 
P 7 HOH A 8 709 39 HOH HOH . 
P 7 HOH A 9 710 44 HOH HOH . 
P 7 HOH A 10 711 49 HOH HOH . 
P 7 HOH A 11 712 50 HOH HOH . 
P 7 HOH A 12 713 56 HOH HOH . 
P 7 HOH A 13 714 60 HOH HOH . 
P 7 HOH A 14 715 76 HOH HOH . 
P 7 HOH A 15 716 77 HOH HOH . 
P 7 HOH A 16 717 79 HOH HOH . 
P 7 HOH A 17 718 84 HOH HOH . 
P 7 HOH A 18 719 87 HOH HOH . 
P 7 HOH A 19 720 97 HOH HOH . 
P 7 HOH A 20 721 100 HOH HOH . 
P 7 HOH A 21 722 101 HOH HOH . 
P 7 HOH A 22 723 108 HOH HOH . 
P 7 HOH A 23 724 121 HOH HOH . 
P 7 HOH A 24 725 123 HOH HOH . 
P 7 HOH A 25 726 126 HOH HOH . 
P 7 HOH A 26 727 127 HOH HOH . 
P 7 HOH A 27 728 131 HOH HOH . 
P 7 HOH A 28 729 136 HOH HOH . 
P 7 HOH A 29 730 140 HOH HOH . 
P 7 HOH A 30 731 142 HOH HOH . 
P 7 HOH A 31 732 144 HOH HOH . 
P 7 HOH A 32 733 145 HOH HOH . 
P 7 HOH A 33 734 149 HOH HOH . 
P 7 HOH A 34 735 150 HOH HOH . 
P 7 HOH A 35 736 155 HOH HOH . 
P 7 HOH A 36 737 157 HOH HOH . 
P 7 HOH A 37 738 158 HOH HOH . 
P 7 HOH A 38 739 166 HOH HOH . 
P 7 HOH A 39 740 167 HOH HOH . 
P 7 HOH A 40 741 169 HOH HOH . 
P 7 HOH A 41 742 170 HOH HOH . 
Q 7 HOH B 1 605 4 HOH HOH . 
Q 7 HOH B 2 606 5 HOH HOH . 
Q 7 HOH B 3 607 9 HOH HOH . 
Q 7 HOH B 4 608 10 HOH HOH . 
Q 7 HOH B 5 609 12 HOH HOH . 
Q 7 HOH B 6 610 17 HOH HOH . 
Q 7 HOH B 7 611 18 HOH HOH . 
Q 7 HOH B 8 612 21 HOH HOH . 
Q 7 HOH B 9 613 27 HOH HOH . 
Q 7 HOH B 10 614 29 HOH HOH . 
Q 7 HOH B 11 615 34 HOH HOH . 
Q 7 HOH B 12 616 35 HOH HOH . 
Q 7 HOH B 13 617 38 HOH HOH . 
Q 7 HOH B 14 618 41 HOH HOH . 
Q 7 HOH B 15 619 42 HOH HOH . 
Q 7 HOH B 16 620 46 HOH HOH . 
Q 7 HOH B 17 621 47 HOH HOH . 
Q 7 HOH B 18 622 48 HOH HOH . 
Q 7 HOH B 19 623 55 HOH HOH . 
Q 7 HOH B 20 624 58 HOH HOH . 
Q 7 HOH B 21 625 61 HOH HOH . 
Q 7 HOH B 22 626 64 HOH HOH . 
Q 7 HOH B 23 627 67 HOH HOH . 
Q 7 HOH B 24 628 68 HOH HOH . 
Q 7 HOH B 25 629 70 HOH HOH . 
Q 7 HOH B 26 630 78 HOH HOH . 
Q 7 HOH B 27 631 83 HOH HOH . 
Q 7 HOH B 28 632 89 HOH HOH . 
Q 7 HOH B 29 633 90 HOH HOH . 
Q 7 HOH B 30 634 92 HOH HOH . 
Q 7 HOH B 31 635 95 HOH HOH . 
Q 7 HOH B 32 636 96 HOH HOH . 
Q 7 HOH B 33 637 98 HOH HOH . 
Q 7 HOH B 34 638 104 HOH HOH . 
Q 7 HOH B 35 639 106 HOH HOH . 
Q 7 HOH B 36 640 109 HOH HOH . 
Q 7 HOH B 37 641 110 HOH HOH . 
Q 7 HOH B 38 642 111 HOH HOH . 
Q 7 HOH B 39 643 112 HOH HOH . 
Q 7 HOH B 40 644 113 HOH HOH . 
Q 7 HOH B 41 645 115 HOH HOH . 
Q 7 HOH B 42 646 116 HOH HOH . 
Q 7 HOH B 43 647 118 HOH HOH . 
Q 7 HOH B 44 648 120 HOH HOH . 
Q 7 HOH B 45 649 122 HOH HOH . 
Q 7 HOH B 46 650 129 HOH HOH . 
Q 7 HOH B 47 651 133 HOH HOH . 
Q 7 HOH B 48 652 134 HOH HOH . 
Q 7 HOH B 49 653 135 HOH HOH . 
Q 7 HOH B 50 654 138 HOH HOH . 
Q 7 HOH B 51 655 151 HOH HOH . 
Q 7 HOH B 52 656 153 HOH HOH . 
Q 7 HOH B 53 657 154 HOH HOH . 
Q 7 HOH B 54 658 156 HOH HOH . 
Q 7 HOH B 55 659 160 HOH HOH . 
Q 7 HOH B 56 660 161 HOH HOH . 
Q 7 HOH B 57 661 168 HOH HOH . 
Q 7 HOH B 58 662 172 HOH HOH . 
Q 7 HOH B 59 663 173 HOH HOH . 
R 7 HOH C 1 703 2 HOH HOH . 
R 7 HOH C 2 704 3 HOH HOH . 
R 7 HOH C 3 705 7 HOH HOH . 
R 7 HOH C 4 706 8 HOH HOH . 
R 7 HOH C 5 707 11 HOH HOH . 
R 7 HOH C 6 708 13 HOH HOH . 
R 7 HOH C 7 709 14 HOH HOH . 
R 7 HOH C 8 710 15 HOH HOH . 
R 7 HOH C 9 711 16 HOH HOH . 
R 7 HOH C 10 712 19 HOH HOH . 
R 7 HOH C 11 713 20 HOH HOH . 
R 7 HOH C 12 714 22 HOH HOH . 
R 7 HOH C 13 715 23 HOH HOH . 
R 7 HOH C 14 716 24 HOH HOH . 
R 7 HOH C 15 717 25 HOH HOH . 
R 7 HOH C 16 718 26 HOH HOH . 
R 7 HOH C 17 719 31 HOH HOH . 
R 7 HOH C 18 720 36 HOH HOH . 
R 7 HOH C 19 721 40 HOH HOH . 
R 7 HOH C 20 722 43 HOH HOH . 
R 7 HOH C 21 723 45 HOH HOH . 
R 7 HOH C 22 724 51 HOH HOH . 
R 7 HOH C 23 725 52 HOH HOH . 
R 7 HOH C 24 726 53 HOH HOH . 
R 7 HOH C 25 727 54 HOH HOH . 
R 7 HOH C 26 728 57 HOH HOH . 
R 7 HOH C 27 729 59 HOH HOH . 
R 7 HOH C 28 730 62 HOH HOH . 
R 7 HOH C 29 731 63 HOH HOH . 
R 7 HOH C 30 732 65 HOH HOH . 
R 7 HOH C 31 733 66 HOH HOH . 
R 7 HOH C 32 734 69 HOH HOH . 
R 7 HOH C 33 735 71 HOH HOH . 
R 7 HOH C 34 736 72 HOH HOH . 
R 7 HOH C 35 737 73 HOH HOH . 
R 7 HOH C 36 738 74 HOH HOH . 
R 7 HOH C 37 739 75 HOH HOH . 
R 7 HOH C 38 740 80 HOH HOH . 
R 7 HOH C 39 741 81 HOH HOH . 
R 7 HOH C 40 742 82 HOH HOH . 
R 7 HOH C 41 743 85 HOH HOH . 
R 7 HOH C 42 744 86 HOH HOH . 
R 7 HOH C 43 745 88 HOH HOH . 
R 7 HOH C 44 746 91 HOH HOH . 
R 7 HOH C 45 747 93 HOH HOH . 
R 7 HOH C 46 748 94 HOH HOH . 
R 7 HOH C 47 749 99 HOH HOH . 
R 7 HOH C 48 750 102 HOH HOH . 
R 7 HOH C 49 751 103 HOH HOH . 
R 7 HOH C 50 752 105 HOH HOH . 
R 7 HOH C 51 753 107 HOH HOH . 
R 7 HOH C 52 754 114 HOH HOH . 
R 7 HOH C 53 755 117 HOH HOH . 
R 7 HOH C 54 756 119 HOH HOH . 
R 7 HOH C 55 757 124 HOH HOH . 
R 7 HOH C 56 758 125 HOH HOH . 
R 7 HOH C 57 759 128 HOH HOH . 
R 7 HOH C 58 760 130 HOH HOH . 
R 7 HOH C 59 761 132 HOH HOH . 
R 7 HOH C 60 762 137 HOH HOH . 
R 7 HOH C 61 763 139 HOH HOH . 
R 7 HOH C 62 764 141 HOH HOH . 
R 7 HOH C 63 765 143 HOH HOH . 
R 7 HOH C 64 766 146 HOH HOH . 
R 7 HOH C 65 767 147 HOH HOH . 
R 7 HOH C 66 768 148 HOH HOH . 
R 7 HOH C 67 769 152 HOH HOH . 
R 7 HOH C 68 770 159 HOH HOH . 
R 7 HOH C 69 771 162 HOH HOH . 
R 7 HOH C 70 772 163 HOH HOH . 
R 7 HOH C 71 773 164 HOH HOH . 
R 7 HOH C 72 774 165 HOH HOH . 
R 7 HOH C 73 775 171 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 CA S4M . . . D 2 14.565 -20.566 7.664 1 51.68 ? CA S4M 501 A 1 
HETATM 2 N N S4M . . . D 2 15.511 -21.53 8.254 1 51.66 ? N S4M 501 A 1 
HETATM 3 C CB S4M . . . D 2 15.139 -20.024 6.356 1 51.56 ? CB S4M 501 A 1 
HETATM 4 C CG S4M . . . D 2 15.915 -18.736 6.616 1 50.99 ? CG S4M 501 A 1 
HETATM 5 S SD S4M . . . D 2 17.713 -18.958 6.869 0.5 49.13 ? SD S4M 501 A 1 
HETATM 6 C CE S4M . . . D 2 17.899 -17.591 7.995 1 48.2 ? CE S4M 501 A 1 
HETATM 7 C C5' S4M . . . D 2 18.59 -18.398 5.325 1 44.56 ? C5' S4M 501 A 1 
HETATM 8 C C4' S4M . . . D 2 20.151 -18.32 5.382 1 40.27 ? C4' S4M 501 A 1 
HETATM 9 O O4' S4M . . . D 2 20.934 -18.573 4.156 1 37.5 ? O4' S4M 501 A 1 
HETATM 10 C C1' S4M . . . D 2 22.181 -17.94 4.437 1 34.68 ? C1' S4M 501 A 1 
HETATM 11 C C2' S4M . . . D 2 21.655 -16.551 4.732 1 38.78 ? C2' S4M 501 A 1 
HETATM 12 O O2' S4M . . . D 2 22.683 -15.774 5.358 1 41.14 ? O2' S4M 501 A 1 
HETATM 13 C C3' S4M . . . D 2 20.511 -16.872 5.696 1 39.33 ? C3' S4M 501 A 1 
HETATM 14 O O3' S4M . . . D 2 20.99 -16.847 7.017 1 39.26 ? O3' S4M 501 A 1 
HETATM 15 N N9 S4M . . . D 2 23.052 -17.924 3.246 1 33.43 ? N9 S4M 501 A 1 
HETATM 16 C C8 S4M . . . D 2 22.77 -17.292 2.112 1 33.37 ? C8 S4M 501 A 1 
HETATM 17 N N7 S4M . . . D 2 23.768 -17.496 1.242 1 33.93 ? N7 S4M 501 A 1 
HETATM 18 C C5 S4M . . . D 2 24.696 -18.272 1.815 1 33.32 ? C5 S4M 501 A 1 
HETATM 19 C C6 S4M . . . D 2 25.925 -18.801 1.393 1 32.2 ? C6 S4M 501 A 1 
HETATM 20 N N6 S4M . . . D 2 26.398 -18.569 0.158 1 33.36 ? N6 S4M 501 A 1 
HETATM 21 C C4 S4M . . . D 2 24.242 -18.536 3.11 1 32.47 ? C4 S4M 501 A 1 
HETATM 22 N N3 S4M . . . D 2 25.004 -19.321 3.911 1 32.06 ? N3 S4M 501 A 1 
HETATM 23 C C2 S4M . . . D 2 26.174 -19.813 3.479 1 33.51 ? C2 S4M 501 A 1 
HETATM 24 N N1 S4M . . . D 2 26.637 -19.564 2.246 1 32.47 ? N1 S4M 501 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           24 
#