data_4KBY
#
_model_server_result.job_id            6-sh3480hhhwZwmOuZh-Ng 
_model_server_result.datetime_utc      '2025-07-31 17:35:32' 
_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          4kby 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    4KBY 
#
_exptl.entry_id    4KBY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          2 
_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            4KBY 
_cell.length_a            79.058 
_cell.length_b            79.058 
_cell.length_c            49.693 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KBY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_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                      2 
_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                     4KBY 
_atom_sites.fract_transf_matrix[1][1]    0.012649 
_atom_sites.fract_transf_matrix[1][2]    0.007303 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014606 
_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]    0.020124 
_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 2 C2E A 1 401 401 C2E C2E . 
D 3 HOH A 1 501 501 HOH HOH . 
D 3 HOH A 2 502 502 HOH HOH . 
D 3 HOH A 3 503 503 HOH HOH . 
D 3 HOH A 4 504 504 HOH HOH . 
D 3 HOH A 5 505 505 HOH HOH . 
D 3 HOH A 6 506 506 HOH HOH . 
D 3 HOH A 7 507 507 HOH HOH . 
D 3 HOH A 8 508 508 HOH HOH . 
D 3 HOH A 9 509 509 HOH HOH . 
D 3 HOH A 10 510 510 HOH HOH . 
D 3 HOH A 11 511 511 HOH HOH . 
D 3 HOH A 12 512 512 HOH HOH . 
D 3 HOH A 13 513 513 HOH HOH . 
D 3 HOH A 14 514 514 HOH HOH . 
D 3 HOH A 15 515 515 HOH HOH . 
D 3 HOH A 16 516 516 HOH HOH . 
D 3 HOH A 17 517 517 HOH HOH . 
D 3 HOH A 18 518 518 HOH HOH . 
D 3 HOH A 19 519 519 HOH HOH . 
D 3 HOH A 20 520 520 HOH HOH . 
D 3 HOH A 21 521 521 HOH HOH . 
D 3 HOH A 22 522 522 HOH HOH . 
D 3 HOH A 23 523 523 HOH HOH . 
D 3 HOH A 24 524 524 HOH HOH . 
D 3 HOH A 25 525 525 HOH HOH . 
D 3 HOH A 26 526 526 HOH HOH . 
D 3 HOH A 27 527 527 HOH HOH . 
D 3 HOH A 28 528 528 HOH HOH . 
D 3 HOH A 29 529 529 HOH HOH . 
D 3 HOH A 30 530 530 HOH HOH . 
D 3 HOH A 31 531 531 HOH HOH . 
D 3 HOH A 32 532 532 HOH HOH . 
D 3 HOH A 33 533 533 HOH HOH . 
D 3 HOH A 34 534 534 HOH HOH . 
D 3 HOH A 35 535 535 HOH HOH . 
D 3 HOH A 36 536 536 HOH HOH . 
D 3 HOH A 37 537 537 HOH HOH . 
D 3 HOH A 38 538 538 HOH HOH . 
D 3 HOH A 39 539 539 HOH HOH . 
D 3 HOH A 40 540 540 HOH HOH . 
D 3 HOH A 41 541 541 HOH HOH . 
D 3 HOH A 42 542 542 HOH HOH . 
D 3 HOH A 43 543 543 HOH HOH . 
D 3 HOH A 44 544 544 HOH HOH . 
D 3 HOH A 45 545 545 HOH HOH . 
D 3 HOH A 46 546 546 HOH HOH . 
D 3 HOH A 47 547 547 HOH HOH . 
D 3 HOH A 48 548 548 HOH HOH . 
D 3 HOH A 49 549 549 HOH HOH . 
D 3 HOH A 50 550 550 HOH HOH . 
D 3 HOH A 51 551 551 HOH HOH . 
D 3 HOH A 52 552 552 HOH HOH . 
E 3 HOH B 1 401 401 HOH HOH . 
E 3 HOH B 2 402 402 HOH HOH . 
E 3 HOH B 3 403 403 HOH HOH . 
E 3 HOH B 4 404 404 HOH HOH . 
E 3 HOH B 5 405 405 HOH HOH . 
E 3 HOH B 6 406 406 HOH HOH . 
E 3 HOH B 7 407 407 HOH HOH . 
E 3 HOH B 8 408 408 HOH HOH . 
E 3 HOH B 9 409 409 HOH HOH . 
E 3 HOH B 10 410 410 HOH HOH . 
E 3 HOH B 11 411 411 HOH HOH . 
E 3 HOH B 12 412 412 HOH HOH . 
E 3 HOH B 13 413 413 HOH HOH . 
E 3 HOH B 14 414 414 HOH HOH . 
E 3 HOH B 15 415 415 HOH HOH . 
E 3 HOH B 16 416 416 HOH HOH . 
E 3 HOH B 17 417 417 HOH HOH . 
E 3 HOH B 18 418 418 HOH HOH . 
E 3 HOH B 19 419 419 HOH HOH . 
E 3 HOH B 20 420 420 HOH HOH . 
E 3 HOH B 21 421 421 HOH HOH . 
E 3 HOH B 22 422 422 HOH HOH . 
E 3 HOH B 23 423 423 HOH HOH . 
E 3 HOH B 24 424 424 HOH HOH . 
E 3 HOH B 25 425 425 HOH HOH . 
E 3 HOH B 26 426 426 HOH HOH . 
E 3 HOH B 27 427 427 HOH HOH . 
E 3 HOH B 28 428 428 HOH HOH . 
E 3 HOH B 29 429 429 HOH HOH . 
E 3 HOH B 30 430 430 HOH HOH . 
E 3 HOH B 31 431 431 HOH HOH . 
E 3 HOH B 32 432 432 HOH HOH . 
E 3 HOH B 33 433 433 HOH HOH . 
E 3 HOH B 34 434 434 HOH HOH . 
E 3 HOH B 35 435 435 HOH HOH . 
E 3 HOH B 36 436 436 HOH HOH . 
E 3 HOH B 37 437 437 HOH HOH . 
E 3 HOH B 38 438 438 HOH HOH . 
E 3 HOH B 39 439 439 HOH HOH . 
E 3 HOH B 40 440 440 HOH HOH . 
E 3 HOH B 41 441 441 HOH HOH . 
E 3 HOH B 42 442 442 HOH HOH . 
E 3 HOH B 43 443 443 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 2 -17.51 -14.421 -6.271 0.77 83.68 ? P1 C2E 401 A 1 
HETATM 2 O O2P C2E . . . C 2 -16.554 -13.54 -5.531 0.77 88.29 -1 O2P C2E 401 A 1 
HETATM 3 O O1P C2E . . . C 2 -18.523 -13.474 -6.909 0.77 74.3 ? O1P C2E 401 A 1 
HETATM 4 O O5' C2E . . . C 2 -16.838 -15.179 -7.464 0.77 84.17 ? O5' C2E 401 A 1 
HETATM 5 C C5' C2E . . . C 2 -17.465 -15.31 -8.69 0.77 80.41 ? C5' C2E 401 A 1 
HETATM 6 C C4' C2E . . . C 2 -17.677 -16.629 -9.293 0.77 84.57 ? C4' C2E 401 A 1 
HETATM 7 O O4' C2E . . . C 2 -16.691 -17.612 -9.041 0.77 80.1 ? O4' C2E 401 A 1 
HETATM 8 C C3' C2E . . . C 2 -18.821 -17.293 -8.708 0.77 84.76 ? C3' C2E 401 A 1 
HETATM 9 O O3' C2E . . . C 2 -20.085 -16.693 -8.941 0.77 78.82 ? O3' C2E 401 A 1 
HETATM 10 C C2' C2E . . . C 2 -18.75 -18.582 -9.298 0.77 89.72 ? C2' C2E 401 A 1 
HETATM 11 O O2' C2E . . . C 2 -19.526 -18.607 -10.48 0.77 89.48 ? O2' C2E 401 A 1 
HETATM 12 C C1' C2E . . . C 2 -17.318 -18.744 -9.589 0.77 102.08 ? C1' C2E 401 A 1 
HETATM 13 N N9 C2E . . . C 2 -16.83 -20.129 -9.303 0.77 82.02 ? N9 C2E 401 A 1 
HETATM 14 C C8 C2E . . . C 2 -17.555 -21.149 -8.83 0.77 78.35 ? C8 C2E 401 A 1 
HETATM 15 N N7 C2E . . . C 2 -16.799 -22.255 -8.75 0.77 86.9 ? N7 C2E 401 A 1 
HETATM 16 C C5 C2E . . . C 2 -15.56 -21.954 -9.194 0.77 79.62 ? C5 C2E 401 A 1 
HETATM 17 C C6 C2E . . . C 2 -14.368 -22.68 -9.341 0.77 79.31 ? C6 C2E 401 A 1 
HETATM 18 O O6 C2E . . . C 2 -14.309 -24.014 -8.989 0.77 82.93 ? O6 C2E 401 A 1 
HETATM 19 N N1 C2E . . . C 2 -13.281 -22.058 -9.827 0.77 83.99 ? N1 C2E 401 A 1 
HETATM 20 C C2 C2E . . . C 2 -13.355 -20.755 -10.162 0.77 78.43 ? C2 C2E 401 A 1 
HETATM 21 N N2 C2E . . . C 2 -12.189 -20.098 -10.683 0.77 81.42 ? N2 C2E 401 A 1 
HETATM 22 N N3 C2E . . . C 2 -14.471 -20.029 -10.041 0.77 86.79 ? N3 C2E 401 A 1 
HETATM 23 C C4 C2E . . . C 2 -15.582 -20.601 -9.559 0.77 83.33 ? C4 C2E 401 A 1 
HETATM 24 P P11 C2E . . . C 2 -21.267 -17.399 -8.169 0.77 97.75 ? P11 C2E 401 A 1 
HETATM 25 O O21 C2E . . . C 2 -22.136 -18.207 -9.057 0.77 96.06 -1 O21 C2E 401 A 1 
HETATM 26 O O11 C2E . . . C 2 -22.171 -16.267 -7.695 0.77 108.41 ? O11 C2E 401 A 1 
HETATM 27 O O5A C2E . . . C 2 -20.779 -18.167 -6.854 0.77 74.54 ? O5A C2E 401 A 1 
HETATM 28 C C5A C2E . . . C 2 -20.74 -17.544 -5.582 0.77 77.23 ? C5A C2E 401 A 1 
HETATM 29 C C4A C2E . . . C 2 -19.506 -17.455 -4.856 0.77 86.69 ? C4A C2E 401 A 1 
HETATM 30 O O4A C2E . . . C 2 -18.904 -18.781 -4.642 0.77 89.35 ? O4A C2E 401 A 1 
HETATM 31 C C3A C2E . . . C 2 -18.476 -16.722 -5.623 0.77 80.57 ? C3A C2E 401 A 1 
HETATM 32 O O3A C2E . . . C 2 -18.352 -15.377 -5.293 0.77 86.61 ? O3A C2E 401 A 1 
HETATM 33 C C2A C2E . . . C 2 -17.21 -17.467 -5.424 0.77 80.24 ? C2A C2E 401 A 1 
HETATM 34 O O2A C2E . . . C 2 -16.201 -16.674 -4.969 0.77 84.29 ? O2A C2E 401 A 1 
HETATM 35 C C1A C2E . . . C 2 -17.563 -18.452 -4.366 0.77 83.23 ? C1A C2E 401 A 1 
HETATM 36 N N91 C2E . . . C 2 -16.594 -19.566 -4.171 0.77 67.69 ? N91 C2E 401 A 1 
HETATM 37 C C81 C2E . . . C 2 -16.913 -20.708 -3.564 0.77 69.27 ? C81 C2E 401 A 1 
HETATM 38 N N71 C2E . . . C 2 -15.845 -21.518 -3.522 0.77 72.24 ? N71 C2E 401 A 1 
HETATM 39 C C51 C2E . . . C 2 -14.798 -20.883 -4.089 0.77 68.35 ? C51 C2E 401 A 1 
HETATM 40 C C61 C2E . . . C 2 -13.455 -21.221 -4.314 0.77 62.18 ? C61 C2E 401 A 1 
HETATM 41 O O61 C2E . . . C 2 -12.973 -22.435 -3.915 0.77 60.66 ? O61 C2E 401 A 1 
HETATM 42 N N11 C2E . . . C 2 -12.632 -20.343 -4.923 0.77 55.88 ? N11 C2E 401 A 1 
HETATM 43 C C21 C2E . . . C 2 -13.113 -19.154 -5.313 0.77 57.2 ? C21 C2E 401 A 1 
HETATM 44 N N21 C2E . . . C 2 -12.232 -18.214 -5.983 0.77 53.89 ? N21 C2E 401 A 1 
HETATM 45 N N31 C2E . . . C 2 -14.391 -18.805 -5.108 0.77 63.87 ? N31 C2E 401 A 1 
HETATM 46 C C41 C2E . . . C 2 -15.27 -19.637 -4.499 0.77 65.35 ? C41 C2E 401 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           46 
#