data_9MGP
#
_model_server_result.job_id            MxOLw9F-BB62P2qn3zG3hA 
_model_server_result.datetime_utc      '2025-07-07 10:58:01' 
_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          9mgp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":701}' 
#
_entry.id    9MGP 
#
_exptl.entry_id    9MGP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              297.334 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_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            9MGP 
_cell.length_a            99.14 
_cell.length_b            137.69 
_cell.length_c            178.43 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9MGP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    'I 2 2' 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
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,S,T,U,V,W,X,Y,Z,AA,BA 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 1 2 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 1 3 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 1 4 
#
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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -137.69 0 
3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -137.69 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 B SG CYS 216 B CYS 208 1_555 B SG CYS 255 B CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
metalc ? metalc1 V NA NA . A NA 720 1_555 AA O HOH . A HOH 858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.139 ? 
#
_chem_comp.formula           'C11 H15 N5 O3 S' 
_chem_comp.formula_weight    297.334 
_chem_comp.id                MTA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-DEOXY-5'-METHYLTHIOADENOSINE" 
_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
CS S5' MTA sing 337 n n 
CS HCS1 MTA sing 338 n n 
CS HCS2 MTA sing 339 n n 
CS HCS3 MTA sing 340 n n 
S5' C5' MTA sing 341 n n 
C5' C4' MTA sing 342 n n 
C5' "H5'1" MTA sing 343 n n 
C5' "H5'2" MTA sing 344 n n 
C4' O4' MTA sing 345 n n 
C4' C3' MTA sing 346 n n 
C4' H4' MTA sing 347 n n 
O4' C1' MTA sing 348 n n 
C2' O2' MTA sing 349 n n 
C2' C3' MTA sing 350 n n 
C2' C1' MTA sing 351 n n 
C2' H2' MTA sing 352 n n 
O2' HO2' MTA sing 353 n n 
C3' O3' MTA sing 354 n n 
C3' H3' MTA sing 355 n n 
O3' H3T MTA sing 356 n n 
C1' N9 MTA sing 357 n n 
C1' H1' MTA sing 358 n n 
N9 C8 MTA sing 359 n y 
N9 C4 MTA sing 360 n y 
C8 N7 MTA doub 361 n y 
C8 H8 MTA sing 362 n n 
N7 C5 MTA sing 363 n y 
C5 C6 MTA sing 364 n y 
C5 C4 MTA doub 365 n y 
C6 N6 MTA sing 366 n n 
C6 N1 MTA doub 367 n y 
N6 H61 MTA sing 368 n n 
N6 H62 MTA sing 369 n n 
N1 C2 MTA sing 370 n y 
C2 N3 MTA doub 371 n y 
C2 H2 MTA sing 372 n n 
N3 C4 MTA sing 373 n y 
#
_atom_sites.entry_id                     9MGP 
_atom_sites.fract_transf_matrix[1][1]    0.010087 
_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]    0.007263 
_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]    0.005604 
_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
C 3 MTA A 1 701 1 MTA MTA . 
D 4 A1BLI A 1 702 1 A1BLI LIG . 
E 5 EDO A 1 703 1 EDO EDO . 
F 5 EDO A 1 704 2 EDO EDO . 
G 5 EDO A 1 705 3 EDO EDO . 
H 5 EDO A 1 706 4 EDO EDO . 
I 5 EDO A 1 707 5 EDO EDO . 
J 5 EDO A 1 708 6 EDO EDO . 
K 5 EDO A 1 709 7 EDO EDO . 
L 5 EDO A 1 710 8 EDO EDO . 
M 5 EDO A 1 711 9 EDO EDO . 
N 5 EDO A 1 712 11 EDO EDO . 
O 5 EDO A 1 713 12 EDO EDO . 
P 5 EDO A 1 714 14 EDO EDO . 
Q 5 EDO A 1 715 15 EDO EDO . 
R 5 EDO A 1 716 16 EDO EDO . 
S 6 NA A 1 717 2 NA NA . 
T 6 NA A 1 718 3 NA NA . 
U 6 NA A 1 719 4 NA NA . 
V 6 NA A 1 720 5 NA NA . 
W 7 GOL A 1 721 1 GOL GOL . 
X 8 CL A 1 722 1 CL CL . 
Y 5 EDO B 1 401 10 EDO EDO . 
Z 5 EDO B 1 402 13 EDO EDO . 
AA 9 HOH A 1 801 34 HOH HOH . 
AA 9 HOH A 2 802 36 HOH HOH . 
AA 9 HOH A 3 803 11 HOH HOH . 
AA 9 HOH A 4 804 43 HOH HOH . 
AA 9 HOH A 5 805 9 HOH HOH . 
AA 9 HOH A 6 806 2 HOH HOH . 
AA 9 HOH A 7 807 79 HOH HOH . 
AA 9 HOH A 8 808 16 HOH HOH . 
AA 9 HOH A 9 809 68 HOH HOH . 
AA 9 HOH A 10 810 38 HOH HOH . 
AA 9 HOH A 11 811 4 HOH HOH . 
AA 9 HOH A 12 812 44 HOH HOH . 
AA 9 HOH A 13 813 78 HOH HOH . 
AA 9 HOH A 14 814 55 HOH HOH . 
AA 9 HOH A 15 815 15 HOH HOH . 
AA 9 HOH A 16 816 13 HOH HOH . 
AA 9 HOH A 17 817 90 HOH HOH . 
AA 9 HOH A 18 818 14 HOH HOH . 
AA 9 HOH A 19 819 39 HOH HOH . 
AA 9 HOH A 20 820 8 HOH HOH . 
AA 9 HOH A 21 821 1 HOH HOH . 
AA 9 HOH A 22 822 98 HOH HOH . 
AA 9 HOH A 23 823 73 HOH HOH . 
AA 9 HOH A 24 824 3 HOH HOH . 
AA 9 HOH A 25 825 66 HOH HOH . 
AA 9 HOH A 26 826 28 HOH HOH . 
AA 9 HOH A 27 827 70 HOH HOH . 
AA 9 HOH A 28 828 92 HOH HOH . 
AA 9 HOH A 29 829 100 HOH HOH . 
AA 9 HOH A 30 830 106 HOH HOH . 
AA 9 HOH A 31 831 76 HOH HOH . 
AA 9 HOH A 32 832 87 HOH HOH . 
AA 9 HOH A 33 833 5 HOH HOH . 
AA 9 HOH A 34 834 27 HOH HOH . 
AA 9 HOH A 35 835 77 HOH HOH . 
AA 9 HOH A 36 836 40 HOH HOH . 
AA 9 HOH A 37 837 74 HOH HOH . 
AA 9 HOH A 38 838 18 HOH HOH . 
AA 9 HOH A 39 839 65 HOH HOH . 
AA 9 HOH A 40 840 12 HOH HOH . 
AA 9 HOH A 41 841 111 HOH HOH . 
AA 9 HOH A 42 842 17 HOH HOH . 
AA 9 HOH A 43 843 56 HOH HOH . 
AA 9 HOH A 44 844 105 HOH HOH . 
AA 9 HOH A 45 845 110 HOH HOH . 
AA 9 HOH A 46 846 6 HOH HOH . 
AA 9 HOH A 47 847 31 HOH HOH . 
AA 9 HOH A 48 848 99 HOH HOH . 
AA 9 HOH A 49 849 35 HOH HOH . 
AA 9 HOH A 50 850 85 HOH HOH . 
AA 9 HOH A 51 851 95 HOH HOH . 
AA 9 HOH A 52 852 7 HOH HOH . 
AA 9 HOH A 53 853 69 HOH HOH . 
AA 9 HOH A 54 854 67 HOH HOH . 
AA 9 HOH A 55 855 21 HOH HOH . 
AA 9 HOH A 56 856 49 HOH HOH . 
AA 9 HOH A 57 857 29 HOH HOH . 
AA 9 HOH A 58 858 33 HOH HOH . 
AA 9 HOH A 59 859 41 HOH HOH . 
AA 9 HOH A 60 860 83 HOH HOH . 
AA 9 HOH A 61 861 109 HOH HOH . 
AA 9 HOH A 62 862 108 HOH HOH . 
AA 9 HOH A 63 863 26 HOH HOH . 
AA 9 HOH A 64 864 54 HOH HOH . 
AA 9 HOH A 65 865 71 HOH HOH . 
AA 9 HOH A 66 866 89 HOH HOH . 
AA 9 HOH A 67 867 88 HOH HOH . 
AA 9 HOH A 68 868 32 HOH HOH . 
AA 9 HOH A 69 869 24 HOH HOH . 
AA 9 HOH A 70 870 107 HOH HOH . 
AA 9 HOH A 71 871 50 HOH HOH . 
AA 9 HOH A 72 872 72 HOH HOH . 
AA 9 HOH A 73 873 93 HOH HOH . 
AA 9 HOH A 74 874 113 HOH HOH . 
AA 9 HOH A 75 875 48 HOH HOH . 
AA 9 HOH A 76 876 81 HOH HOH . 
AA 9 HOH A 77 877 101 HOH HOH . 
AA 9 HOH A 78 878 112 HOH HOH . 
BA 9 HOH B 1 501 46 HOH HOH . 
BA 9 HOH B 2 502 10 HOH HOH . 
BA 9 HOH B 3 503 103 HOH HOH . 
BA 9 HOH B 4 504 61 HOH HOH . 
BA 9 HOH B 5 505 64 HOH HOH . 
BA 9 HOH B 6 506 19 HOH HOH . 
BA 9 HOH B 7 507 97 HOH HOH . 
BA 9 HOH B 8 508 25 HOH HOH . 
BA 9 HOH B 9 509 75 HOH HOH . 
BA 9 HOH B 10 510 42 HOH HOH . 
BA 9 HOH B 11 511 58 HOH HOH . 
BA 9 HOH B 12 512 51 HOH HOH . 
BA 9 HOH B 13 513 63 HOH HOH . 
BA 9 HOH B 14 514 86 HOH HOH . 
BA 9 HOH B 15 515 47 HOH HOH . 
BA 9 HOH B 16 516 60 HOH HOH . 
BA 9 HOH B 17 517 20 HOH HOH . 
BA 9 HOH B 18 518 57 HOH HOH . 
BA 9 HOH B 19 519 22 HOH HOH . 
BA 9 HOH B 20 520 91 HOH HOH . 
BA 9 HOH B 21 521 96 HOH HOH . 
BA 9 HOH B 22 522 104 HOH HOH . 
BA 9 HOH B 23 523 37 HOH HOH . 
BA 9 HOH B 24 524 30 HOH HOH . 
BA 9 HOH B 25 525 59 HOH HOH . 
BA 9 HOH B 26 526 80 HOH HOH . 
BA 9 HOH B 27 527 62 HOH HOH . 
BA 9 HOH B 28 528 45 HOH HOH . 
BA 9 HOH B 29 529 94 HOH HOH . 
BA 9 HOH B 30 530 52 HOH HOH . 
BA 9 HOH B 31 531 102 HOH HOH . 
BA 9 HOH B 32 532 84 HOH HOH . 
BA 9 HOH B 33 533 23 HOH HOH . 
BA 9 HOH B 34 534 53 HOH HOH . 
BA 9 HOH B 35 535 82 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 CS MTA . . . C 3 21.418 -38.851 -6.566 1 58.73 ? CS MTA 701 A 1 
HETATM 2 S S5' MTA . . . C 3 19.907 -39.739 -6.57 1 61.75 ? S5' MTA 701 A 1 
HETATM 3 C C5' MTA . . . C 3 18.927 -38.332 -6.2 1 60.35 ? C5' MTA 701 A 1 
HETATM 4 C C4' MTA . . . C 3 19.196 -37.773 -4.807 1 60.43 ? C4' MTA 701 A 1 
HETATM 5 O O4' MTA . . . C 3 18.195 -36.78 -4.629 1 58.51 ? O4' MTA 701 A 1 
HETATM 6 C C2' MTA . . . C 3 17.699 -38.478 -3.059 1 57.99 ? C2' MTA 701 A 1 
HETATM 7 O O2' MTA . . . C 3 17.664 -38.623 -1.636 1 60.62 ? O2' MTA 701 A 1 
HETATM 8 C C3' MTA . . . C 3 19.069 -38.747 -3.638 1 60.1 ? C3' MTA 701 A 1 
HETATM 9 O O3' MTA . . . C 3 20.067 -38.441 -2.66 1 51.89 ? O3' MTA 701 A 1 
HETATM 10 C C1' MTA . . . C 3 17.439 -37.034 -3.457 1 56.85 ? C1' MTA 701 A 1 
HETATM 11 N N9 MTA . . . C 3 16.008 -36.767 -3.708 1 54.74 ? N9 MTA 701 A 1 
HETATM 12 C C8 MTA . . . C 3 15.124 -37.559 -4.343 1 56.64 ? C8 MTA 701 A 1 
HETATM 13 N N7 MTA . . . C 3 13.899 -36.978 -4.37 1 50.24 ? N7 MTA 701 A 1 
HETATM 14 C C5 MTA . . . C 3 13.999 -35.797 -3.745 1 52.21 ? C5 MTA 701 A 1 
HETATM 15 C C6 MTA . . . C 3 13.089 -34.682 -3.415 1 53.91 ? C6 MTA 701 A 1 
HETATM 16 N N6 MTA . . . C 3 11.789 -34.72 -3.779 1 61.7 ? N6 MTA 701 A 1 
HETATM 17 N N1 MTA . . . C 3 13.6 -33.622 -2.749 1 53.32 ? N1 MTA 701 A 1 
HETATM 18 C C2 MTA . . . C 3 14.896 -33.562 -2.378 1 63.58 ? C2 MTA 701 A 1 
HETATM 19 N N3 MTA . . . C 3 15.775 -34.547 -2.644 1 61.73 ? N3 MTA 701 A 1 
HETATM 20 C C4 MTA . . . C 3 15.393 -35.661 -3.314 1 57.2 ? C4 MTA 701 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           254 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#