data_2Y4L
#
_model_server_result.job_id            U1oy1rE9Uddenau28_Af4w 
_model_server_result.datetime_utc      '2024-11-28 10:11:35' 
_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          2y4l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":401}' 
#
_entry.id    2Y4L 
#
_exptl.entry_id    2Y4L 
_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    2 
_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            2Y4L 
_cell.length_a            149.756 
_cell.length_b            149.756 
_cell.length_c            154.71 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Y4L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_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,C,D,E,F,G,H,R 1 1 
B,I,J,K,L,M,N,O,P,Q,S 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 J N 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 OD2 ASP 102 A ASP 102 1_555 C MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc2 A ND1 HIS 217 A HIS 217 1_555 C MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc3 C MN MN . A MN 400 1_555 D O3B GDP . A GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc4 C MN MN . A MN 400 1_555 D O2A GDP . A GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc5 C MN MN . A MN 400 1_555 R O HOH . A HOH 2056 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? 
metalc ? metalc6 C MN MN . A MN 400 1_555 R O HOH . A HOH 2057 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc7 B OD2 ASP 102 B ASP 102 1_555 I MN MN . B MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc8 I MN MN . B MN 400 1_555 J O2A GDP . B GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc9 I MN MN . B MN 400 1_555 J O3B GDP . B GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
#
_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                     2Y4L 
_atom_sites.fract_transf_matrix[1][1]    0.006678 
_atom_sites.fract_transf_matrix[1][2]    0.003855 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007711 
_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]    0.006464 
_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 MN A 1 400 400 MN MN . 
D 3 GDP A 1 401 401 GDP GDP . 
E 4 MLI A 1 402 402 MLI MLI . 
F 5 EDO A 1 502 502 EDO EDO . 
G 5 EDO A 1 503 503 EDO EDO . 
H 5 EDO A 1 506 506 EDO EDO . 
I 2 MN B 1 400 400 MN MN . 
J 3 GDP B 1 401 401 GDP GDP . 
K 4 MLI B 1 402 402 MLI MLI . 
L 5 EDO B 1 502 502 EDO EDO . 
M 5 EDO B 1 503 503 EDO EDO . 
N 5 EDO B 1 504 504 EDO EDO . 
O 5 EDO B 1 505 505 EDO EDO . 
P 5 EDO B 1 506 506 EDO EDO . 
Q 5 EDO B 1 507 507 EDO EDO . 
R 6 HOH A 1 2001 2001 HOH HOH . 
R 6 HOH A 2 2002 2002 HOH HOH . 
R 6 HOH A 3 2003 2003 HOH HOH . 
R 6 HOH A 4 2004 2004 HOH HOH . 
R 6 HOH A 5 2005 2005 HOH HOH . 
R 6 HOH A 6 2006 2006 HOH HOH . 
R 6 HOH A 7 2007 2007 HOH HOH . 
R 6 HOH A 8 2008 2008 HOH HOH . 
R 6 HOH A 9 2009 2009 HOH HOH . 
R 6 HOH A 10 2010 2010 HOH HOH . 
R 6 HOH A 11 2011 2011 HOH HOH . 
R 6 HOH A 12 2012 2012 HOH HOH . 
R 6 HOH A 13 2013 2013 HOH HOH . 
R 6 HOH A 14 2014 2014 HOH HOH . 
R 6 HOH A 15 2015 2015 HOH HOH . 
R 6 HOH A 16 2016 2016 HOH HOH . 
R 6 HOH A 17 2017 2017 HOH HOH . 
R 6 HOH A 18 2018 2018 HOH HOH . 
R 6 HOH A 19 2019 2019 HOH HOH . 
R 6 HOH A 20 2020 2020 HOH HOH . 
R 6 HOH A 21 2021 2021 HOH HOH . 
R 6 HOH A 22 2022 2022 HOH HOH . 
R 6 HOH A 23 2023 2023 HOH HOH . 
R 6 HOH A 24 2024 2024 HOH HOH . 
R 6 HOH A 25 2025 2025 HOH HOH . 
R 6 HOH A 26 2026 2026 HOH HOH . 
R 6 HOH A 27 2027 2027 HOH HOH . 
R 6 HOH A 28 2028 2028 HOH HOH . 
R 6 HOH A 29 2029 2029 HOH HOH . 
R 6 HOH A 30 2030 2030 HOH HOH . 
R 6 HOH A 31 2031 2031 HOH HOH . 
R 6 HOH A 32 2032 2032 HOH HOH . 
R 6 HOH A 33 2033 2033 HOH HOH . 
R 6 HOH A 34 2034 2034 HOH HOH . 
R 6 HOH A 35 2035 2035 HOH HOH . 
R 6 HOH A 36 2036 2036 HOH HOH . 
R 6 HOH A 37 2037 2037 HOH HOH . 
R 6 HOH A 38 2038 2038 HOH HOH . 
R 6 HOH A 39 2039 2039 HOH HOH . 
R 6 HOH A 40 2040 2040 HOH HOH . 
R 6 HOH A 41 2041 2041 HOH HOH . 
R 6 HOH A 42 2042 2042 HOH HOH . 
R 6 HOH A 43 2043 2043 HOH HOH . 
R 6 HOH A 44 2044 2044 HOH HOH . 
R 6 HOH A 45 2045 2045 HOH HOH . 
R 6 HOH A 46 2046 2046 HOH HOH . 
R 6 HOH A 47 2047 2047 HOH HOH . 
R 6 HOH A 48 2048 2048 HOH HOH . 
R 6 HOH A 49 2049 2049 HOH HOH . 
R 6 HOH A 50 2050 2050 HOH HOH . 
R 6 HOH A 51 2051 2051 HOH HOH . 
R 6 HOH A 52 2052 2052 HOH HOH . 
R 6 HOH A 53 2053 2053 HOH HOH . 
R 6 HOH A 54 2054 2054 HOH HOH . 
R 6 HOH A 55 2055 2055 HOH HOH . 
R 6 HOH A 56 2056 2056 HOH HOH . 
R 6 HOH A 57 2057 2057 HOH HOH . 
S 6 HOH B 1 2001 2001 HOH HOH . 
S 6 HOH B 2 2002 2002 HOH HOH . 
S 6 HOH B 3 2003 2003 HOH HOH . 
S 6 HOH B 4 2004 2004 HOH HOH . 
S 6 HOH B 5 2005 2005 HOH HOH . 
S 6 HOH B 6 2006 2006 HOH HOH . 
S 6 HOH B 7 2007 2007 HOH HOH . 
S 6 HOH B 8 2008 2008 HOH HOH . 
S 6 HOH B 9 2009 2009 HOH HOH . 
S 6 HOH B 10 2010 2010 HOH HOH . 
S 6 HOH B 11 2011 2011 HOH HOH . 
S 6 HOH B 12 2012 2012 HOH HOH . 
S 6 HOH B 13 2013 2013 HOH HOH . 
S 6 HOH B 14 2014 2014 HOH HOH . 
S 6 HOH B 15 2015 2015 HOH HOH . 
S 6 HOH B 16 2016 2016 HOH HOH . 
S 6 HOH B 17 2017 2017 HOH HOH . 
S 6 HOH B 18 2018 2018 HOH HOH . 
S 6 HOH B 19 2019 2019 HOH HOH . 
S 6 HOH B 20 2020 2020 HOH HOH . 
S 6 HOH B 21 2021 2021 HOH HOH . 
S 6 HOH B 22 2022 2022 HOH HOH . 
S 6 HOH B 23 2023 2023 HOH HOH . 
S 6 HOH B 24 2024 2024 HOH HOH . 
S 6 HOH B 25 2025 2025 HOH HOH . 
S 6 HOH B 26 2026 2026 HOH HOH . 
S 6 HOH B 27 2027 2027 HOH HOH . 
S 6 HOH B 28 2028 2028 HOH HOH . 
S 6 HOH B 29 2029 2029 HOH HOH . 
S 6 HOH B 30 2030 2030 HOH HOH . 
S 6 HOH B 31 2031 2031 HOH HOH . 
S 6 HOH B 32 2032 2032 HOH HOH . 
S 6 HOH B 33 2033 2033 HOH HOH . 
S 6 HOH B 34 2034 2034 HOH HOH . 
S 6 HOH B 35 2035 2035 HOH HOH . 
S 6 HOH B 36 2036 2036 HOH HOH . 
S 6 HOH B 37 2037 2037 HOH HOH . 
S 6 HOH B 38 2038 2038 HOH HOH . 
S 6 HOH B 39 2039 2039 HOH HOH . 
S 6 HOH B 40 2040 2040 HOH HOH . 
S 6 HOH B 41 2041 2041 HOH HOH . 
S 6 HOH B 42 2042 2042 HOH HOH . 
S 6 HOH B 43 2043 2043 HOH HOH . 
S 6 HOH B 44 2044 2044 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 . . . J 3 110.807 -45.796 133.372 1 80.86 ? PB GDP 401 B 1 
HETATM 2 O O1B GDP . . . J 3 109.616 -46.673 133.759 1 79.65 ? O1B GDP 401 B 1 
HETATM 3 O O2B GDP . . . J 3 111.548 -46.461 132.191 1 80.36 ? O2B GDP 401 B 1 
HETATM 4 O O3B GDP . . . J 3 111.66 -45.673 134.631 1 80.41 ? O3B GDP 401 B 1 
HETATM 5 O O3A GDP . . . J 3 110.405 -44.262 132.928 1 75.2 ? O3A GDP 401 B 1 
HETATM 6 P PA GDP . . . J 3 111.481 -43.044 132.769 1 68.55 ? PA GDP 401 B 1 
HETATM 7 O O1A GDP . . . J 3 110.774 -41.715 132.541 1 68.57 ? O1A GDP 401 B 1 
HETATM 8 O O2A GDP . . . J 3 112.361 -43.013 133.987 1 66.67 ? O2A GDP 401 B 1 
HETATM 9 O O5' GDP . . . J 3 112.29 -43.404 131.403 1 65.79 ? O5' GDP 401 B 1 
HETATM 10 C C5' GDP . . . J 3 113.429 -44.243 131.237 1 59.2 ? C5' GDP 401 B 1 
HETATM 11 C C4' GDP . . . J 3 114.604 -43.398 130.742 1 56.66 ? C4' GDP 401 B 1 
HETATM 12 O O4' GDP . . . J 3 114.367 -42.86 129.443 1 55.41 ? O4' GDP 401 B 1 
HETATM 13 C C3' GDP . . . J 3 114.94 -42.197 131.603 1 55.09 ? C3' GDP 401 B 1 
HETATM 14 O O3' GDP . . . J 3 116.362 -42.098 131.533 1 53.68 ? O3' GDP 401 B 1 
HETATM 15 C C2' GDP . . . J 3 114.311 -41.013 130.883 1 54.41 ? C2' GDP 401 B 1 
HETATM 16 O O2' GDP . . . J 3 115.08 -39.836 131.006 1 55.88 ? O2' GDP 401 B 1 
HETATM 17 C C1' GDP . . . J 3 114.492 -41.418 129.461 1 54.16 ? C1' GDP 401 B 1 
HETATM 18 N N9 GDP . . . J 3 113.53 -40.912 128.469 1 52.98 ? N9 GDP 401 B 1 
HETATM 19 C C8 GDP . . . J 3 112.194 -41.095 128.463 1 52.98 ? C8 GDP 401 B 1 
HETATM 20 N N7 GDP . . . J 3 111.629 -40.573 127.348 1 52.04 ? N7 GDP 401 B 1 
HETATM 21 C C5 GDP . . . J 3 112.629 -40.058 126.624 1 51.22 ? C5 GDP 401 B 1 
HETATM 22 C C6 GDP . . . J 3 112.738 -39.362 125.34 1 49.57 ? C6 GDP 401 B 1 
HETATM 23 O O6 GDP . . . J 3 111.701 -39.168 124.697 1 48.01 ? O6 GDP 401 B 1 
HETATM 24 N N1 GDP . . . J 3 113.961 -38.998 124.904 1 49.89 ? N1 GDP 401 B 1 
HETATM 25 C C2 GDP . . . J 3 115.086 -39.239 125.622 1 49.44 ? C2 GDP 401 B 1 
HETATM 26 N N2 GDP . . . J 3 116.293 -38.834 125.152 1 49.07 ? N2 GDP 401 B 1 
HETATM 27 N N3 GDP . . . J 3 115.055 -39.872 126.816 1 49.92 ? N3 GDP 401 B 1 
HETATM 28 C C4 GDP . . . J 3 113.883 -40.3 127.348 1 51.93 ? C4 GDP 401 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           337 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#