data_6GFU
#
_model_server_result.job_id            xImIfoIp2QovHZQYAr4FhQ 
_model_server_result.datetime_utc      '2024-10-19 21:26:37' 
_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          6gfu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    6GFU 
#
_exptl.entry_id    6GFU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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            6GFU 
_cell.length_a            56.944 
_cell.length_b            73.691 
_cell.length_c            113.756 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GFU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                             B 
_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
metalc ? metalc1 A OG1 THR 26 A THR 26 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc2 B O3B GDP . A GDP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc3 C MG MG . A MG 502 1_555 D O HOH . A HOH 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc4 C MG MG . A MG 502 1_555 D O HOH . A HOH 652 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc5 C MG MG . A MG 502 1_555 D O HOH . A HOH 653 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc6 C MG MG . A MG 502 1_555 D O HOH . A HOH 692 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
PB O1B GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     6GFU 
_atom_sites.fract_transf_matrix[1][1]    0.017561 
_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]    0.01357 
_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]    0.008791 
_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
B 2 GDP A 1 501 395 GDP GDP . 
C 3 MG A 1 502 396 MG MG . 
D 4 HOH A 1 601 494 HOH HOH . 
D 4 HOH A 2 602 460 HOH HOH . 
D 4 HOH A 3 603 517 HOH HOH . 
D 4 HOH A 4 604 508 HOH HOH . 
D 4 HOH A 5 605 480 HOH HOH . 
D 4 HOH A 6 606 422 HOH HOH . 
D 4 HOH A 7 607 455 HOH HOH . 
D 4 HOH A 8 608 458 HOH HOH . 
D 4 HOH A 9 609 523 HOH HOH . 
D 4 HOH A 10 610 413 HOH HOH . 
D 4 HOH A 11 611 415 HOH HOH . 
D 4 HOH A 12 612 509 HOH HOH . 
D 4 HOH A 13 613 474 HOH HOH . 
D 4 HOH A 14 614 496 HOH HOH . 
D 4 HOH A 15 615 447 HOH HOH . 
D 4 HOH A 16 616 498 HOH HOH . 
D 4 HOH A 17 617 433 HOH HOH . 
D 4 HOH A 18 618 417 HOH HOH . 
D 4 HOH A 19 619 488 HOH HOH . 
D 4 HOH A 20 620 441 HOH HOH . 
D 4 HOH A 21 621 401 HOH HOH . 
D 4 HOH A 22 622 467 HOH HOH . 
D 4 HOH A 23 623 434 HOH HOH . 
D 4 HOH A 24 624 466 HOH HOH . 
D 4 HOH A 25 625 402 HOH HOH . 
D 4 HOH A 26 626 416 HOH HOH . 
D 4 HOH A 27 627 502 HOH HOH . 
D 4 HOH A 28 628 446 HOH HOH . 
D 4 HOH A 29 629 426 HOH HOH . 
D 4 HOH A 30 630 431 HOH HOH . 
D 4 HOH A 31 631 495 HOH HOH . 
D 4 HOH A 32 632 521 HOH HOH . 
D 4 HOH A 33 633 397 HOH HOH . 
D 4 HOH A 34 634 518 HOH HOH . 
D 4 HOH A 35 635 403 HOH HOH . 
D 4 HOH A 36 636 400 HOH HOH . 
D 4 HOH A 37 637 399 HOH HOH . 
D 4 HOH A 38 638 530 HOH HOH . 
D 4 HOH A 39 639 514 HOH HOH . 
D 4 HOH A 40 640 420 HOH HOH . 
D 4 HOH A 41 641 528 HOH HOH . 
D 4 HOH A 42 642 469 HOH HOH . 
D 4 HOH A 43 643 418 HOH HOH . 
D 4 HOH A 44 644 473 HOH HOH . 
D 4 HOH A 45 645 463 HOH HOH . 
D 4 HOH A 46 646 423 HOH HOH . 
D 4 HOH A 47 647 456 HOH HOH . 
D 4 HOH A 48 648 468 HOH HOH . 
D 4 HOH A 49 649 520 HOH HOH . 
D 4 HOH A 50 650 486 HOH HOH . 
D 4 HOH A 51 651 505 HOH HOH . 
D 4 HOH A 52 652 513 HOH HOH . 
D 4 HOH A 53 653 516 HOH HOH . 
D 4 HOH A 54 654 409 HOH HOH . 
D 4 HOH A 55 655 482 HOH HOH . 
D 4 HOH A 56 656 481 HOH HOH . 
D 4 HOH A 57 657 507 HOH HOH . 
D 4 HOH A 58 658 497 HOH HOH . 
D 4 HOH A 59 659 419 HOH HOH . 
D 4 HOH A 60 660 452 HOH HOH . 
D 4 HOH A 61 661 491 HOH HOH . 
D 4 HOH A 62 662 464 HOH HOH . 
D 4 HOH A 63 663 408 HOH HOH . 
D 4 HOH A 64 664 479 HOH HOH . 
D 4 HOH A 65 665 532 HOH HOH . 
D 4 HOH A 66 666 437 HOH HOH . 
D 4 HOH A 67 667 453 HOH HOH . 
D 4 HOH A 68 668 404 HOH HOH . 
D 4 HOH A 69 669 398 HOH HOH . 
D 4 HOH A 70 670 484 HOH HOH . 
D 4 HOH A 71 671 485 HOH HOH . 
D 4 HOH A 72 672 483 HOH HOH . 
D 4 HOH A 73 673 522 HOH HOH . 
D 4 HOH A 74 674 448 HOH HOH . 
D 4 HOH A 75 675 510 HOH HOH . 
D 4 HOH A 76 676 429 HOH HOH . 
D 4 HOH A 77 677 432 HOH HOH . 
D 4 HOH A 78 678 504 HOH HOH . 
D 4 HOH A 79 679 527 HOH HOH . 
D 4 HOH A 80 680 439 HOH HOH . 
D 4 HOH A 81 681 472 HOH HOH . 
D 4 HOH A 82 682 411 HOH HOH . 
D 4 HOH A 83 683 524 HOH HOH . 
D 4 HOH A 84 684 454 HOH HOH . 
D 4 HOH A 85 685 529 HOH HOH . 
D 4 HOH A 86 686 512 HOH HOH . 
D 4 HOH A 87 687 421 HOH HOH . 
D 4 HOH A 88 688 428 HOH HOH . 
D 4 HOH A 89 689 533 HOH HOH . 
D 4 HOH A 90 690 407 HOH HOH . 
D 4 HOH A 91 691 506 HOH HOH . 
D 4 HOH A 92 692 515 HOH HOH . 
D 4 HOH A 93 693 477 HOH HOH . 
D 4 HOH A 94 694 436 HOH HOH . 
D 4 HOH A 95 695 445 HOH HOH . 
D 4 HOH A 96 696 414 HOH HOH . 
D 4 HOH A 97 697 459 HOH HOH . 
D 4 HOH A 98 698 500 HOH HOH . 
D 4 HOH A 99 699 424 HOH HOH . 
D 4 HOH A 100 700 412 HOH HOH . 
D 4 HOH A 101 701 503 HOH HOH . 
D 4 HOH A 102 702 450 HOH HOH . 
D 4 HOH A 103 703 462 HOH HOH . 
D 4 HOH A 104 704 511 HOH HOH . 
D 4 HOH A 105 705 489 HOH HOH . 
D 4 HOH A 106 706 427 HOH HOH . 
D 4 HOH A 107 707 405 HOH HOH . 
D 4 HOH A 108 708 457 HOH HOH . 
D 4 HOH A 109 709 449 HOH HOH . 
D 4 HOH A 110 710 461 HOH HOH . 
D 4 HOH A 111 711 438 HOH HOH . 
D 4 HOH A 112 712 451 HOH HOH . 
D 4 HOH A 113 713 406 HOH HOH . 
D 4 HOH A 114 714 526 HOH HOH . 
D 4 HOH A 115 715 435 HOH HOH . 
D 4 HOH A 116 716 487 HOH HOH . 
D 4 HOH A 117 717 410 HOH HOH . 
D 4 HOH A 118 718 531 HOH HOH . 
D 4 HOH A 119 719 470 HOH HOH . 
D 4 HOH A 120 720 476 HOH HOH . 
D 4 HOH A 121 721 519 HOH HOH . 
D 4 HOH A 122 722 465 HOH HOH . 
D 4 HOH A 123 723 471 HOH HOH . 
D 4 HOH A 124 724 534 HOH HOH . 
D 4 HOH A 125 725 525 HOH HOH . 
D 4 HOH A 126 726 442 HOH HOH . 
D 4 HOH A 127 727 444 HOH HOH . 
D 4 HOH A 128 728 478 HOH HOH . 
D 4 HOH A 129 729 475 HOH HOH . 
D 4 HOH A 130 730 440 HOH HOH . 
D 4 HOH A 131 731 443 HOH HOH . 
D 4 HOH A 132 732 499 HOH HOH . 
D 4 HOH A 133 733 425 HOH HOH . 
D 4 HOH A 134 734 501 HOH HOH . 
D 4 HOH A 135 735 493 HOH HOH . 
D 4 HOH A 136 736 490 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 PB GDP . . . B 2 -19.39 -0.422 -19.865 1 26.47 ? PB GDP 501 A 1 
HETATM 2 O O1B GDP . . . B 2 -20.354 -0.012 -20.95 1 27.35 ? O1B GDP 501 A 1 
HETATM 3 O O2B GDP . . . B 2 -18.895 -1.873 -20.036 1 23.81 ? O2B GDP 501 A 1 
HETATM 4 O O3B GDP . . . B 2 -18.272 0.467 -19.515 1 23.92 ? O3B GDP 501 A 1 
HETATM 5 O O3A GDP . . . B 2 -20.412 -0.647 -18.627 1 25.91 ? O3A GDP 501 A 1 
HETATM 6 P PA GDP . . . B 2 -20.505 0.259 -17.318 1 28.38 ? PA GDP 501 A 1 
HETATM 7 O O1A GDP . . . B 2 -20.798 1.66 -17.76 1 29.13 ? O1A GDP 501 A 1 
HETATM 8 O O2A GDP . . . B 2 -19.301 0.148 -16.383 1 27.6 ? O2A GDP 501 A 1 
HETATM 9 O O5' GDP . . . B 2 -21.747 -0.316 -16.621 1 26.79 ? O5' GDP 501 A 1 
HETATM 10 C C5' GDP . . . B 2 -23.023 -0.425 -17.301 1 27.43 ? C5' GDP 501 A 1 
HETATM 11 C C4' GDP . . . B 2 -24.163 -0.498 -16.32 1 29.95 ? C4' GDP 501 A 1 
HETATM 12 O O4' GDP . . . B 2 -24.124 -1.744 -15.567 1 29.77 ? O4' GDP 501 A 1 
HETATM 13 C C3' GDP . . . B 2 -24.143 0.626 -15.286 1 31.34 ? C3' GDP 501 A 1 
HETATM 14 O O3' GDP . . . B 2 -25.498 0.998 -14.923 1 32.66 ? O3' GDP 501 A 1 
HETATM 15 C C2' GDP . . . B 2 -23.481 -0.032 -14.092 1 31.28 ? C2' GDP 501 A 1 
HETATM 16 O O2' GDP . . . B 2 -23.673 0.631 -12.811 1 30.78 ? O2' GDP 501 A 1 
HETATM 17 C C1' GDP . . . B 2 -24.028 -1.449 -14.181 1 27.31 ? C1' GDP 501 A 1 
HETATM 18 N N9 GDP . . . B 2 -23.079 -2.355 -13.494 1 27.41 ? N9 GDP 501 A 1 
HETATM 19 C C8 GDP . . . B 2 -21.74 -2.378 -13.604 1 27.34 ? C8 GDP 501 A 1 
HETATM 20 N N7 GDP . . . B 2 -21.209 -3.312 -12.798 1 26.98 ? N7 GDP 501 A 1 
HETATM 21 C C5 GDP . . . B 2 -22.231 -3.929 -12.197 1 27.96 ? C5 GDP 501 A 1 
HETATM 22 C C6 GDP . . . B 2 -22.389 -5.006 -11.229 1 29.2 ? C6 GDP 501 A 1 
HETATM 23 O O6 GDP . . . B 2 -21.38 -5.606 -10.755 1 28.74 ? O6 GDP 501 A 1 
HETATM 24 N N1 GDP . . . B 2 -23.645 -5.315 -10.849 1 26.8 ? N1 GDP 501 A 1 
HETATM 25 C C2 GDP . . . B 2 -24.721 -4.676 -11.315 1 32.41 ? C2 GDP 501 A 1 
HETATM 26 N N2 GDP . . . B 2 -25.948 -5.052 -10.878 1 29.23 ? N2 GDP 501 A 1 
HETATM 27 N N3 GDP . . . B 2 -24.653 -3.669 -12.214 1 29.61 ? N3 GDP 501 A 1 
HETATM 28 C C4 GDP . . . B 2 -23.456 -3.289 -12.669 1 27.71 ? C4 GDP 501 A 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#