data_4F48
#
_model_server_result.job_id            aZEbvaoXS4tT85GHrt73qA 
_model_server_result.datetime_utc      '2024-11-05 00:34:08' 
_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          4f48 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    4F48 
#
_exptl.entry_id    4F48 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_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         120 
_cell.entry_id            4F48 
_cell.length_a            158.222 
_cell.length_b            158.222 
_cell.length_c            64.808 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4F48 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA tetrameric 4 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 1 1 
A,B,C,D,E 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' 7_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 64.808 
#
_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 
#
_chem_comp.formula           'C20 H24 N10 O14 P2' 
_chem_comp.formula_weight    690.411 
_chem_comp.id                C2E 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'c-di-GMP;Cyclic diguanosine monophosphate' 
#
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
P1 O2P C2E sing 70 n n 
O1P P1 C2E doub 71 n n 
O5' P1 C2E sing 72 n n 
C5' O5' C2E sing 73 n n 
C4' O4' C2E sing 74 n n 
C4' C5' C2E sing 75 n n 
C3' C4' C2E sing 76 n n 
O3' P11 C2E sing 77 n n 
O3' C3' C2E sing 78 n n 
C2' C3' C2E sing 79 n n 
C2' C1' C2E sing 80 n n 
O2' C2' C2E sing 81 n n 
C1' O4' C2E sing 82 n n 
C1' N9 C2E sing 83 n n 
N9 C4 C2E sing 84 n y 
N9 C8 C2E sing 85 n y 
C8 N7 C2E doub 86 n y 
C5 N7 C2E sing 87 n y 
C5 C6 C2E sing 88 n n 
C6 O6 C2E doub 89 n n 
N1 C6 C2E sing 90 n n 
C2 N1 C2E sing 91 n n 
N2 C2 C2E sing 92 n n 
N3 C2 C2E doub 93 n n 
N3 C4 C2E sing 94 n n 
C4 C5 C2E doub 95 n y 
P11 O21 C2E sing 96 n n 
P11 O5A C2E sing 97 n n 
O11 P11 C2E doub 98 n n 
C5A O5A C2E sing 99 n n 
C5A C4A C2E sing 100 n n 
C4A O4A C2E sing 101 n n 
C4A C3A C2E sing 102 n n 
O4A C1A C2E sing 103 n n 
C3A C2A C2E sing 104 n n 
O3A C3A C2E sing 105 n n 
O3A P1 C2E sing 106 n n 
C2A O2A C2E sing 107 n n 
C1A C2A C2E sing 108 n n 
C1A N91 C2E sing 109 n n 
N91 C41 C2E sing 110 n y 
C81 N71 C2E doub 111 n y 
C81 N91 C2E sing 112 n y 
N71 C51 C2E sing 113 n y 
C51 C41 C2E doub 114 n y 
C51 C61 C2E sing 115 n n 
C61 O61 C2E doub 116 n n 
C61 N11 C2E sing 117 n n 
C21 N11 C2E sing 118 n n 
C21 N21 C2E sing 119 n n 
N31 C21 C2E doub 120 n n 
C41 N31 C2E sing 121 n n 
O2P HO2P C2E sing 122 n n 
C5' "H5'1" C2E sing 123 n n 
C5' "H5'2" C2E sing 124 n n 
C4' H4' C2E sing 125 n n 
C3' H3' C2E sing 126 n n 
C2' H2' C2E sing 127 n n 
O2' HO2' C2E sing 128 n n 
C1' H1' C2E sing 129 n n 
C8 H8 C2E sing 130 n n 
N1 HN1 C2E sing 131 n n 
N2 HN21 C2E sing 132 n n 
N2 HN22 C2E sing 133 n n 
O21 HO21 C2E sing 134 n n 
C5A H511 C2E sing 135 n n 
C5A H512 C2E sing 136 n n 
C4A H4A C2E sing 137 n n 
C3A H3A C2E sing 138 n n 
C2A H2A C2E sing 139 n n 
O2A HO2A C2E sing 140 n n 
C1A H1A C2E sing 141 n n 
C81 H81 C2E sing 142 n n 
N11 HN11 C2E sing 143 n n 
N21 HN24 C2E sing 144 n n 
N21 HN23 C2E sing 145 n n 
#
_atom_sites.entry_id                     4F48 
_atom_sites.fract_transf_matrix[1][1]    0.00632 
_atom_sites.fract_transf_matrix[1][2]    0.003649 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007298 
_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]    0.01543 
_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 C2E A 1 501 501 C2E C2E . 
D 4 HOH A 1 601 503 HOH HOH . 
D 4 HOH A 2 602 504 HOH HOH . 
D 4 HOH A 3 603 505 HOH HOH . 
D 4 HOH A 4 604 506 HOH HOH . 
D 4 HOH A 5 605 507 HOH HOH . 
D 4 HOH A 6 606 508 HOH HOH . 
D 4 HOH A 7 607 509 HOH HOH . 
D 4 HOH A 8 608 510 HOH HOH . 
D 4 HOH A 9 609 511 HOH HOH . 
D 4 HOH A 10 610 512 HOH HOH . 
D 4 HOH A 11 611 514 HOH HOH . 
D 4 HOH A 12 612 515 HOH HOH . 
D 4 HOH A 13 613 517 HOH HOH . 
D 4 HOH A 14 614 518 HOH HOH . 
D 4 HOH A 15 615 520 HOH HOH . 
D 4 HOH A 16 616 521 HOH HOH . 
D 4 HOH A 17 617 522 HOH HOH . 
D 4 HOH A 18 618 523 HOH HOH . 
D 4 HOH A 19 619 524 HOH HOH . 
D 4 HOH A 20 620 526 HOH HOH . 
D 4 HOH A 21 621 527 HOH HOH . 
D 4 HOH A 22 622 528 HOH HOH . 
D 4 HOH A 23 623 529 HOH HOH . 
D 4 HOH A 24 624 530 HOH HOH . 
D 4 HOH A 25 625 531 HOH HOH . 
D 4 HOH A 26 626 532 HOH HOH . 
D 4 HOH A 27 627 533 HOH HOH . 
D 4 HOH A 28 628 534 HOH HOH . 
D 4 HOH A 29 629 535 HOH HOH . 
D 4 HOH A 30 630 536 HOH HOH . 
D 4 HOH A 31 631 537 HOH HOH . 
D 4 HOH A 32 632 538 HOH HOH . 
D 4 HOH A 33 633 539 HOH HOH . 
D 4 HOH A 34 634 540 HOH HOH . 
D 4 HOH A 35 635 541 HOH HOH . 
D 4 HOH A 36 636 543 HOH HOH . 
D 4 HOH A 37 637 544 HOH HOH . 
D 4 HOH A 38 638 545 HOH HOH . 
D 4 HOH A 39 639 546 HOH HOH . 
D 4 HOH A 40 640 547 HOH HOH . 
D 4 HOH A 41 641 548 HOH HOH . 
D 4 HOH A 42 642 549 HOH HOH . 
D 4 HOH A 43 643 550 HOH HOH . 
D 4 HOH A 44 644 557 HOH HOH . 
D 4 HOH A 45 645 560 HOH HOH . 
D 4 HOH A 46 646 561 HOH HOH . 
D 4 HOH A 47 647 562 HOH HOH . 
D 4 HOH A 48 648 563 HOH HOH . 
D 4 HOH A 49 649 564 HOH HOH . 
D 4 HOH A 50 650 565 HOH HOH . 
D 4 HOH A 51 651 566 HOH HOH . 
D 4 HOH A 52 652 567 HOH HOH . 
D 4 HOH A 53 653 568 HOH HOH . 
D 4 HOH A 54 654 569 HOH HOH . 
D 4 HOH A 55 655 570 HOH HOH . 
D 4 HOH A 56 656 571 HOH HOH . 
D 4 HOH A 57 657 572 HOH HOH . 
D 4 HOH A 58 658 573 HOH HOH . 
D 4 HOH A 59 659 574 HOH HOH . 
D 4 HOH A 60 660 578 HOH HOH . 
D 4 HOH A 61 661 579 HOH HOH . 
D 4 HOH A 62 662 580 HOH HOH . 
D 4 HOH A 63 663 581 HOH HOH . 
D 4 HOH A 64 664 582 HOH HOH . 
E 4 HOH B 1 201 542 HOH HOH . 
E 4 HOH B 2 202 502 HOH HOH . 
E 4 HOH B 3 203 513 HOH HOH . 
E 4 HOH B 4 204 516 HOH HOH . 
E 4 HOH B 5 205 519 HOH HOH . 
E 4 HOH B 6 206 551 HOH HOH . 
E 4 HOH B 7 207 552 HOH HOH . 
E 4 HOH B 8 208 553 HOH HOH . 
E 4 HOH B 9 209 554 HOH HOH . 
E 4 HOH B 10 210 555 HOH HOH . 
E 4 HOH B 11 211 556 HOH HOH . 
E 4 HOH B 12 212 558 HOH HOH . 
E 4 HOH B 13 213 559 HOH HOH . 
E 4 HOH B 14 214 575 HOH HOH . 
E 4 HOH B 15 215 576 HOH HOH . 
E 4 HOH B 16 216 577 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 P P1 C2E . . . C 3 18.646 62.18 23.945 0.5 46.56 ? P1 C2E 501 A 1 
HETATM 2 O O2P C2E . . . C 3 19.386 62.981 24.98 0.5 46.07 ? O2P C2E 501 A 1 
HETATM 3 O O1P C2E . . . C 3 19.111 60.748 23.953 0.5 45.79 ? O1P C2E 501 A 1 
HETATM 4 O O5' C2E . . . C 3 17.04 62.186 24.195 0.5 46.5 ? O5' C2E 501 A 1 
HETATM 5 C C5' C2E . . . C 3 16.191 61.47 23.264 0.5 46.46 ? C5' C2E 501 A 1 
HETATM 6 C C4' C2E . . . C 3 14.653 61.516 23.567 0.5 46.37 ? C4' C2E 501 A 1 
HETATM 7 O O4' C2E . . . C 3 14.294 60.32 24.245 0.5 46.53 ? O4' C2E 501 A 1 
HETATM 8 C C3' C2E . . . C 3 14.089 62.673 24.416 0.5 47.17 ? C3' C2E 501 A 1 
HETATM 9 O O3' C2E . . . C 3 13.635 63.831 23.584 0.5 47.08 ? O3' C2E 501 A 1 
HETATM 10 C C2' C2E . . . C 3 12.965 61.951 25.213 0.5 46.57 ? C2' C2E 501 A 1 
HETATM 11 O O2' C2E . . . C 3 11.678 62.224 24.627 0.5 45.9 ? O2' C2E 501 A 1 
HETATM 12 C C1' C2E . . . C 3 13.248 60.428 25.22 0.5 46 ? C1' C2E 501 A 1 
HETATM 13 N N9 C2E . . . C 3 13.691 59.935 26.584 0.5 47.26 ? N9 C2E 501 A 1 
HETATM 14 C C8 C2E . . . C 3 14.929 59.5 26.937 0.5 46.36 ? C8 C2E 501 A 1 
HETATM 15 N N7 C2E . . . C 3 14.994 59.106 28.238 0.5 45.55 ? N7 C2E 501 A 1 
HETATM 16 C C5 C2E . . . C 3 13.779 59.273 28.75 0.5 45.79 ? C5 C2E 501 A 1 
HETATM 17 C C6 C2E . . . C 3 13.146 59.037 30.071 0.5 44.14 ? C6 C2E 501 A 1 
HETATM 18 O O6 C2E . . . C 3 13.829 58.571 31.016 0.5 44.53 ? O6 C2E 501 A 1 
HETATM 19 N N1 C2E . . . C 3 11.815 59.334 30.226 0.5 44.83 ? N1 C2E 501 A 1 
HETATM 20 C C2 C2E . . . C 3 11.053 59.843 29.2 0.5 44.26 ? C2 C2E 501 A 1 
HETATM 21 N N2 C2E . . . C 3 9.739 60.115 29.406 0.5 43.04 ? N2 C2E 501 A 1 
HETATM 22 N N3 C2E . . . C 3 11.583 60.088 27.946 0.5 45.29 ? N3 C2E 501 A 1 
HETATM 23 C C4 C2E . . . C 3 12.91 59.827 27.667 0.5 45.36 ? C4 C2E 501 A 1 
HETATM 24 P P11 C2E . . . C 3 14.591 65.185 23.655 0.5 47.71 ? P11 C2E 501 A 1 
HETATM 25 O O21 C2E . . . C 3 14.72 65.599 25.111 0.5 48.4 ? O21 C2E 501 A 1 
HETATM 26 O O11 C2E . . . C 3 13.933 66.25 22.812 0.5 48.08 ? O11 C2E 501 A 1 
HETATM 27 O O5A C2E . . . C 3 16.031 64.896 23 0.5 48.49 ? O5A C2E 501 A 1 
HETATM 28 C C5A C2E . . . C 3 16.106 64.532 21.597 0.5 47.67 ? C5A C2E 501 A 1 
HETATM 29 C C4A C2E . . . C 3 17.539 64.259 21.133 0.5 47.51 ? C4A C2E 501 A 1 
HETATM 30 O O4A C2E . . . C 3 18.049 65.187 20.135 0.5 47.93 ? O4A C2E 501 A 1 
HETATM 31 C C3A C2E . . . C 3 18.573 64.18 22.287 0.5 47.38 ? C3A C2E 501 A 1 
HETATM 32 O O3A C2E . . . C 3 18.997 62.793 22.457 0.5 46.36 ? O3A C2E 501 A 1 
HETATM 33 C C2A C2E . . . C 3 19.667 65.171 21.897 0.5 47.23 ? C2A C2E 501 A 1 
HETATM 34 O O2A C2E . . . C 3 20.958 64.514 21.9 0.5 47.34 ? O2A C2E 501 A 1 
HETATM 35 C C1A C2E . . . C 3 19.322 65.743 20.507 0.5 46.88 ? C1A C2E 501 A 1 
HETATM 36 N N91 C2E . . . C 3 19.296 67.252 20.487 0.5 46.25 ? N91 C2E 501 A 1 
HETATM 37 C C81 C2E . . . C 3 18.316 68.057 20.961 0.5 45.81 ? C81 C2E 501 A 1 
HETATM 38 N N71 C2E . . . C 3 18.615 69.372 20.778 0.5 45.8 ? N71 C2E 501 A 1 
HETATM 39 C C51 C2E . . . C 3 19.819 69.439 20.167 0.5 47.06 ? C51 C2E 501 A 1 
HETATM 40 C C61 C2E . . . C 3 20.75 70.521 19.669 0.5 44.98 ? C61 C2E 501 A 1 
HETATM 41 O O61 C2E . . . C 3 20.475 71.739 19.777 0.5 45.3 ? O61 C2E 501 A 1 
HETATM 42 N N11 C2E . . . C 3 21.921 70.149 19.085 0.5 45.19 ? N11 C2E 501 A 1 
HETATM 43 C C21 C2E . . . C 3 22.283 68.836 18.936 0.5 44.9 ? C21 C2E 501 A 1 
HETATM 44 N N21 C2E . . . C 3 23.471 68.547 18.34 0.5 44.78 ? N21 C2E 501 A 1 
HETATM 45 N N31 C2E . . . C 3 21.482 67.802 19.369 0.5 47.58 ? N31 C2E 501 A 1 
HETATM 46 C C41 C2E . . . C 3 20.262 68.037 19.979 0.5 45.64 ? C41 C2E 501 A 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           46 
#