data_4D0N # _model_server_result.job_id viBtVSNiBjmRuVE-Ldyahw _model_server_result.datetime_utc '2024-11-25 17:45:22' _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 4d0n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1182}' # _entry.id 4D0N # _exptl.entry_id 4D0N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 4D0N _cell.length_a 82.32 _cell.length_b 86.61 _cell.length_c 116.82 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D0N _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 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,F,G,H,I,J,K _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 92 n n PB O2B GDP sing 93 n n PB O3B GDP sing 94 n n PB O3A GDP sing 95 n n O2B HOB2 GDP sing 96 n n O3B HOB3 GDP sing 97 n n O3A PA GDP sing 98 n n PA O1A GDP doub 99 n n PA O2A GDP sing 100 n n PA O5' GDP sing 101 n n O2A HOA2 GDP sing 102 n n O5' C5' GDP sing 103 n n C5' C4' GDP sing 104 n n C5' H5' GDP sing 105 n n C5' "H5''" GDP sing 106 n n C4' O4' GDP sing 107 n n C4' C3' GDP sing 108 n n C4' H4' GDP sing 109 n n O4' C1' GDP sing 110 n n C3' O3' GDP sing 111 n n C3' C2' GDP sing 112 n n C3' H3' GDP sing 113 n n O3' HO3' GDP sing 114 n n C2' O2' GDP sing 115 n n C2' C1' GDP sing 116 n n C2' H2' GDP sing 117 n n O2' HO2' GDP sing 118 n n C1' N9 GDP sing 119 n n C1' H1' GDP sing 120 n n N9 C8 GDP sing 121 n y N9 C4 GDP sing 122 n y C8 N7 GDP doub 123 n y C8 H8 GDP sing 124 n n N7 C5 GDP sing 125 n y C5 C6 GDP sing 126 n n C5 C4 GDP doub 127 n y C6 O6 GDP doub 128 n n C6 N1 GDP sing 129 n n N1 C2 GDP sing 130 n n N1 HN1 GDP sing 131 n n C2 N2 GDP sing 132 n n C2 N3 GDP doub 133 n n N2 HN21 GDP sing 134 n n N2 HN22 GDP sing 135 n n N3 C4 GDP sing 136 n n # _atom_sites.entry_id 4D0N _atom_sites.fract_transf_matrix[1][1] 0.012148 _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] 0.011546 _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] 0.00856 _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 GDP A 1 1182 1182 GDP GDP . D 4 SO4 A 1 1183 1183 SO4 SO4 . E 5 EDO A 1 1184 1184 EDO EDO . F 4 SO4 B 1 3341 3341 SO4 SO4 . G 4 SO4 B 1 3342 3342 SO4 SO4 . H 4 SO4 B 1 3343 3343 SO4 SO4 . I 4 SO4 B 1 3344 3344 SO4 SO4 . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . J 6 HOH A 13 2013 2013 HOH HOH . J 6 HOH A 14 2014 2014 HOH HOH . J 6 HOH A 15 2015 2015 HOH HOH . J 6 HOH A 16 2016 2016 HOH HOH . J 6 HOH A 17 2017 2017 HOH HOH . J 6 HOH A 18 2018 2018 HOH HOH . J 6 HOH A 19 2019 2019 HOH HOH . J 6 HOH A 20 2020 2020 HOH HOH . J 6 HOH A 21 2021 2021 HOH HOH . J 6 HOH A 22 2022 2022 HOH HOH . J 6 HOH A 23 2023 2023 HOH HOH . J 6 HOH A 24 2024 2024 HOH HOH . J 6 HOH A 25 2025 2025 HOH HOH . J 6 HOH A 26 2026 2026 HOH HOH . J 6 HOH A 27 2027 2027 HOH HOH . J 6 HOH A 28 2028 2028 HOH HOH . J 6 HOH A 29 2029 2029 HOH HOH . J 6 HOH A 30 2030 2030 HOH HOH . J 6 HOH A 31 2031 2031 HOH HOH . J 6 HOH A 32 2032 2032 HOH HOH . J 6 HOH A 33 2033 2033 HOH HOH . J 6 HOH A 34 2034 2034 HOH HOH . J 6 HOH A 35 2035 2035 HOH HOH . J 6 HOH A 36 2036 2036 HOH HOH . J 6 HOH A 37 2037 2037 HOH HOH . J 6 HOH A 38 2038 2038 HOH HOH . J 6 HOH A 39 2039 2039 HOH HOH . J 6 HOH A 40 2040 2040 HOH HOH . J 6 HOH A 41 2041 2041 HOH HOH . J 6 HOH A 42 2042 2042 HOH HOH . J 6 HOH A 43 2043 2043 HOH HOH . J 6 HOH A 44 2044 2044 HOH HOH . J 6 HOH A 45 2045 2045 HOH HOH . J 6 HOH A 46 2046 2046 HOH HOH . J 6 HOH A 47 2047 2047 HOH HOH . J 6 HOH A 48 2048 2048 HOH HOH . J 6 HOH A 49 2049 2049 HOH HOH . J 6 HOH A 50 2050 2050 HOH HOH . J 6 HOH A 51 2051 2051 HOH HOH . J 6 HOH A 52 2052 2052 HOH HOH . J 6 HOH A 53 2053 2053 HOH HOH . J 6 HOH A 54 2054 2054 HOH HOH . J 6 HOH A 55 2055 2055 HOH HOH . J 6 HOH A 56 2056 2056 HOH HOH . J 6 HOH A 57 2057 2057 HOH HOH . J 6 HOH A 58 2058 2058 HOH HOH . J 6 HOH A 59 2059 2059 HOH HOH . J 6 HOH A 60 2060 2060 HOH HOH . J 6 HOH A 61 2061 2061 HOH HOH . J 6 HOH A 62 2062 2062 HOH HOH . J 6 HOH A 63 2063 2063 HOH HOH . J 6 HOH A 64 2064 2064 HOH HOH . J 6 HOH A 65 2065 2065 HOH HOH . J 6 HOH A 66 2066 2066 HOH HOH . J 6 HOH A 67 2067 2067 HOH HOH . J 6 HOH A 68 2068 2068 HOH HOH . J 6 HOH A 69 2069 2069 HOH HOH . J 6 HOH A 70 2070 2070 HOH HOH . J 6 HOH A 71 2071 2071 HOH HOH . J 6 HOH A 72 2072 2072 HOH HOH . J 6 HOH A 73 2073 2073 HOH HOH . J 6 HOH A 74 2074 2074 HOH HOH . J 6 HOH A 75 2075 2075 HOH HOH . J 6 HOH A 76 2076 2076 HOH HOH . J 6 HOH A 77 3577 3577 HOH HOH . K 6 HOH B 1 3501 3501 HOH HOH . K 6 HOH B 2 3502 3502 HOH HOH . K 6 HOH B 3 3503 3503 HOH HOH . K 6 HOH B 4 3504 3504 HOH HOH . K 6 HOH B 5 3505 3505 HOH HOH . K 6 HOH B 6 3506 3506 HOH HOH . K 6 HOH B 7 3507 3507 HOH HOH . K 6 HOH B 8 3508 3508 HOH HOH . K 6 HOH B 9 3509 3509 HOH HOH . K 6 HOH B 10 3510 3510 HOH HOH . K 6 HOH B 11 3511 3511 HOH HOH . K 6 HOH B 12 3512 3512 HOH HOH . K 6 HOH B 13 3513 3513 HOH HOH . K 6 HOH B 14 3514 3514 HOH HOH . K 6 HOH B 15 3515 3515 HOH HOH . K 6 HOH B 16 3516 3516 HOH HOH . K 6 HOH B 17 3517 3517 HOH HOH . K 6 HOH B 18 3518 3518 HOH HOH . K 6 HOH B 19 3519 3519 HOH HOH . K 6 HOH B 20 3520 3520 HOH HOH . K 6 HOH B 21 3521 3521 HOH HOH . K 6 HOH B 22 3522 3522 HOH HOH . K 6 HOH B 23 3523 3523 HOH HOH . K 6 HOH B 24 3524 3524 HOH HOH . K 6 HOH B 25 3525 3525 HOH HOH . K 6 HOH B 26 3526 3526 HOH HOH . K 6 HOH B 27 3527 3527 HOH HOH . K 6 HOH B 28 3528 3528 HOH HOH . K 6 HOH B 29 3529 3529 HOH HOH . K 6 HOH B 30 3530 3530 HOH HOH . K 6 HOH B 31 3531 3531 HOH HOH . K 6 HOH B 32 3532 3532 HOH HOH . K 6 HOH B 33 3533 3533 HOH HOH . K 6 HOH B 34 3534 3534 HOH HOH . K 6 HOH B 35 3535 3535 HOH HOH . K 6 HOH B 36 3536 3536 HOH HOH . K 6 HOH B 37 3537 3537 HOH HOH . K 6 HOH B 38 3538 3538 HOH HOH . K 6 HOH B 39 3539 3539 HOH HOH . K 6 HOH B 40 3540 3540 HOH HOH . K 6 HOH B 41 3541 3541 HOH HOH . K 6 HOH B 42 3542 3542 HOH HOH . K 6 HOH B 43 3543 3543 HOH HOH . K 6 HOH B 44 3544 3544 HOH HOH . K 6 HOH B 45 3545 3545 HOH HOH . K 6 HOH B 46 3546 3546 HOH HOH . K 6 HOH B 47 3547 3547 HOH HOH . K 6 HOH B 48 3548 3548 HOH HOH . K 6 HOH B 49 3549 3549 HOH HOH . K 6 HOH B 50 3550 3550 HOH HOH . K 6 HOH B 51 3551 3551 HOH HOH . K 6 HOH B 52 3552 3552 HOH HOH . K 6 HOH B 53 3553 3553 HOH HOH . K 6 HOH B 54 3554 3554 HOH HOH . K 6 HOH B 55 3555 3555 HOH HOH . K 6 HOH B 56 3556 3556 HOH HOH . K 6 HOH B 57 3557 3557 HOH HOH . K 6 HOH B 58 3558 3558 HOH HOH . K 6 HOH B 59 3559 3559 HOH HOH . K 6 HOH B 60 3560 3560 HOH HOH . K 6 HOH B 61 3561 3561 HOH HOH . K 6 HOH B 62 3562 3562 HOH HOH . K 6 HOH B 63 3563 3563 HOH HOH . K 6 HOH B 64 3564 3564 HOH HOH . K 6 HOH B 65 3565 3565 HOH HOH . K 6 HOH B 66 3566 3566 HOH HOH . K 6 HOH B 67 3567 3567 HOH HOH . K 6 HOH B 68 3568 3568 HOH HOH . K 6 HOH B 69 3569 3569 HOH HOH . K 6 HOH B 70 3570 3570 HOH HOH . K 6 HOH B 71 3571 3571 HOH HOH . K 6 HOH B 72 3572 3572 HOH HOH . K 6 HOH B 73 3573 3573 HOH HOH . K 6 HOH B 74 3574 3574 HOH HOH . K 6 HOH B 75 3575 3575 HOH HOH . K 6 HOH B 76 3576 3576 HOH HOH . K 6 HOH B 77 3577 3577 HOH HOH . K 6 HOH B 78 3578 3578 HOH HOH . K 6 HOH B 79 3579 3579 HOH HOH . K 6 HOH B 80 3580 3580 HOH HOH . K 6 HOH B 81 3581 3581 HOH HOH . K 6 HOH B 82 3582 3582 HOH HOH . K 6 HOH B 83 3583 3583 HOH HOH . K 6 HOH B 84 3584 3584 HOH HOH . K 6 HOH B 85 3585 3585 HOH HOH . K 6 HOH B 86 3586 3586 HOH HOH . K 6 HOH B 87 3587 3587 HOH HOH . K 6 HOH B 88 3588 3588 HOH HOH . K 6 HOH B 89 3589 3589 HOH HOH . K 6 HOH B 90 3590 3590 HOH HOH . K 6 HOH B 91 3591 3591 HOH HOH . K 6 HOH B 92 3592 3592 HOH HOH . K 6 HOH B 93 3593 3593 HOH HOH . K 6 HOH B 94 3594 3594 HOH HOH . K 6 HOH B 95 3595 3595 HOH HOH . K 6 HOH B 96 3596 3596 HOH HOH . K 6 HOH B 97 3597 3597 HOH HOH . K 6 HOH B 98 3598 3598 HOH HOH . K 6 HOH B 99 3599 3599 HOH HOH . K 6 HOH B 100 3600 3600 HOH HOH . K 6 HOH B 101 3601 3601 HOH HOH . K 6 HOH B 102 3602 3602 HOH HOH . K 6 HOH B 103 3603 3603 HOH HOH . K 6 HOH B 104 3604 3604 HOH HOH . K 6 HOH B 105 3605 3605 HOH HOH . K 6 HOH B 106 3606 3606 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 . . . C 3 -22.994 -15.181 27.714 1 41.85 ? PB GDP 1182 A 1 HETATM 2 O O1B GDP . . . C 3 -22.982 -16.435 26.942 1 43.49 ? O1B GDP 1182 A 1 HETATM 3 O O2B GDP . . . C 3 -23.493 -15.283 29.086 1 36.58 ? O2B GDP 1182 A 1 HETATM 4 O O3B GDP . . . C 3 -21.722 -14.405 27.628 1 38.58 ? O3B GDP 1182 A 1 HETATM 5 O O3A GDP . . . C 3 -23.998 -14.305 26.866 1 42.13 ? O3A GDP 1182 A 1 HETATM 6 P PA GDP . . . C 3 -25.041 -14.9 25.737 1 49.43 ? PA GDP 1182 A 1 HETATM 7 O O1A GDP . . . C 3 -25.781 -15.979 26.438 1 47 ? O1A GDP 1182 A 1 HETATM 8 O O2A GDP . . . C 3 -24.355 -15.199 24.445 1 41.84 ? O2A GDP 1182 A 1 HETATM 9 O O5' GDP . . . C 3 -26.068 -13.598 25.578 1 48.46 ? O5' GDP 1182 A 1 HETATM 10 C C5' GDP . . . C 3 -26.666 -12.981 26.752 1 49.22 ? C5' GDP 1182 A 1 HETATM 11 C C4' GDP . . . C 3 -27.856 -12.13 26.296 1 51.14 ? C4' GDP 1182 A 1 HETATM 12 O O4' GDP . . . C 3 -27.439 -11.017 25.44 1 49.41 ? O4' GDP 1182 A 1 HETATM 13 C C3' GDP . . . C 3 -28.864 -12.942 25.466 1 51.92 ? C3' GDP 1182 A 1 HETATM 14 O O3' GDP . . . C 3 -30.183 -12.451 25.705 1 56.52 ? O3' GDP 1182 A 1 HETATM 15 C C2' GDP . . . C 3 -28.472 -12.632 24.051 1 52.66 ? C2' GDP 1182 A 1 HETATM 16 O O2' GDP . . . C 3 -29.584 -12.794 23.182 1 51.3 ? O2' GDP 1182 A 1 HETATM 17 C C1' GDP . . . C 3 -28.048 -11.16 24.134 1 50.91 ? C1' GDP 1182 A 1 HETATM 18 N N9 GDP . . . C 3 -27.076 -10.775 23.056 1 51.28 ? N9 GDP 1182 A 1 HETATM 19 C C8 GDP . . . C 3 -26.008 -11.47 22.648 1 53.27 ? C8 GDP 1182 A 1 HETATM 20 N N7 GDP . . . C 3 -25.405 -10.797 21.671 1 51.78 ? N7 GDP 1182 A 1 HETATM 21 C C5 GDP . . . C 3 -26.092 -9.672 21.466 1 53.63 ? C5 GDP 1182 A 1 HETATM 22 C C6 GDP . . . C 3 -25.897 -8.659 20.605 1 55.25 ? C6 GDP 1182 A 1 HETATM 23 O O6 GDP . . . C 3 -24.95 -8.643 19.81 1 52.68 ? O6 GDP 1182 A 1 HETATM 24 N N1 GDP . . . C 3 -26.798 -7.584 20.609 1 54.98 ? N1 GDP 1182 A 1 HETATM 25 C C2 GDP . . . C 3 -27.867 -7.589 21.517 1 52.77 ? C2 GDP 1182 A 1 HETATM 26 N N2 GDP . . . C 3 -28.719 -6.568 21.535 1 53.02 ? N2 GDP 1182 A 1 HETATM 27 N N3 GDP . . . C 3 -28.009 -8.627 22.36 1 50.57 ? N3 GDP 1182 A 1 HETATM 28 C C4 GDP . . . C 3 -27.132 -9.657 22.329 1 52.62 ? C4 GDP 1182 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #