data_4AP6
#
_model_server_result.job_id            jounyvxI-z7cM3QZEJwV3w 
_model_server_result.datetime_utc      '2024-11-23 18:55:35' 
_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          4ap6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1430}' 
#
_entry.id    4AP6 
#
_exptl.entry_id    4AP6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              589.342 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" 
_entity.pdbx_number_of_molecules    4 
_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            4AP6 
_cell.length_a            153.01 
_cell.length_b            153.01 
_cell.length_c            185.68 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4AP6 
_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 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,S 1 1 
B,H,I,J,K,L,T 2 1 
C,M,N,O,P 3 1 
D,Q,R 4 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
? 2 E N N 
? 2 H N N 
? 2 M N N 
? 2 Q 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
disulf ? disulf1 A SG CYS 154 A CYS 161 1_555 A SG CYS 185 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf2 A SG CYS 405 A CYS 412 1_555 A SG CYS 412 A CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf3 B SG CYS 154 B CYS 161 1_555 B SG CYS 185 B CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf4 B SG CYS 405 B CYS 412 1_555 B SG CYS 412 B CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf5 C SG CYS 154 C CYS 161 1_555 C SG CYS 185 C CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf6 C SG CYS 405 C CYS 412 1_555 C SG CYS 412 C CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf7 D SG CYS 154 D CYS 161 1_555 D SG CYS 185 D CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf8 D SG CYS 405 D CYS 412 1_555 D SG CYS 412 D CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
covale ? covale1 A ND2 ASN 202 A ASN 209 1_555 F C1 NAG . A NAG 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale2 B ND2 ASN 182 B ASN 189 1_555 I C1 NAG . B NAG 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? 
covale ? covale3 B ND2 ASN 202 B ASN 209 1_555 J C1 NAG . B NAG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? 
covale ? covale4 B ND2 ASN 252 B ASN 259 1_555 K C1 NAG . B NAG 1433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale5 C ND2 ASN 182 C ASN 189 1_555 N C1 NAG . C NAG 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale6 C ND2 ASN 202 C ASN 209 1_555 O C1 NAG . C NAG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? 
#
_chem_comp.formula           'C16 H25 N5 O15 P2' 
_chem_comp.formula_weight    589.342 
_chem_comp.id                GFB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" 
_chem_comp.type              non-polymer 
_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
P O1P GFB sing 83 n n 
O1P HO1P GFB sing 84 n n 
O3P P GFB doub 85 n n 
P O5' GFB sing 86 n n 
P O2P GFB sing 87 n n 
O2P P1 GFB sing 88 n n 
O5' C5' GFB sing 89 n n 
O1 P1 GFB sing 90 n n 
O1X P1 GFB doub 91 n n 
P1 O2X GFB sing 92 n n 
C4' C5' GFB sing 93 n n 
C5' "H5'A" GFB sing 94 n n 
C5' H5' GFB sing 95 n n 
H4' C4' GFB sing 96 n n 
C3' C4' GFB sing 97 n n 
C4' O4' GFB sing 98 n n 
O4' C1' GFB sing 99 n n 
O3' C3' GFB sing 100 n n 
C3' C2' GFB sing 101 n n 
C3' H3' GFB sing 102 n n 
C2' C1' GFB sing 103 n n 
H1' C1' GFB sing 104 n n 
C1' N9 GFB sing 105 n n 
HO3' O3' GFB sing 106 n n 
O2' C2' GFB sing 107 n n 
C2' H2' GFB sing 108 n n 
O2' HO2' GFB sing 109 n n 
N9 C4 GFB sing 110 n y 
N9 C8 GFB sing 111 n y 
H8 C8 GFB sing 112 n n 
C8 N7 GFB doub 113 n y 
N3 C4 GFB sing 114 n n 
C4 C5 GFB doub 115 n y 
C5 N7 GFB sing 116 n y 
C5 C6 GFB sing 117 n n 
N1 C6 GFB sing 118 n n 
C6 O6 GFB doub 119 n n 
C2 N1 GFB sing 120 n n 
N1 HN1 GFB sing 121 n n 
N3 C2 GFB doub 122 n n 
N2 C2 GFB sing 123 n n 
HN2 N2 GFB sing 124 n n 
N2 HN2A GFB sing 125 n n 
C2A C1 GFB sing 126 n n 
C1 O5 GFB sing 127 n n 
C1 H1 GFB sing 128 n n 
C1 O1 GFB sing 129 n n 
C3 C2A GFB sing 130 n n 
O2 C2A GFB sing 131 n n 
H2A C2A GFB sing 132 n n 
C5A O5 GFB sing 133 n n 
O3 C3 GFB sing 134 n n 
C3 H3 GFB sing 135 n n 
C3 C4A GFB sing 136 n n 
HO2 O2 GFB sing 137 n n 
H4A C4A GFB sing 138 n n 
O4 C4A GFB sing 139 n n 
C4A C5A GFB sing 140 n n 
HO3 O3 GFB sing 141 n n 
C5A H5A GFB sing 142 n n 
C5A C6A GFB sing 143 n n 
O4 HO4 GFB sing 144 n n 
H6A C6A GFB sing 145 n n 
H6AA C6A GFB sing 146 n n 
C6A H6AB GFB sing 147 n n 
O2X HO2X GFB sing 148 n n 
#
_atom_sites.entry_id                     4AP6 
_atom_sites.fract_transf_matrix[1][1]    0.006536 
_atom_sites.fract_transf_matrix[1][2]    0.003773 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007547 
_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]    0.005386 
_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
E 2 GFB A 1 1430 1430 GFB GFB . 
F 3 NAG A 1 1431 1431 NAG NAG . 
G 4 CL A 1 1432 1432 CL CL . 
H 2 GFB B 1 1430 1430 GFB GFB . 
I 3 NAG B 1 1431 1431 NAG NAG . 
J 3 NAG B 1 1432 1432 NAG NAG . 
K 3 NAG B 1 1433 1433 NAG NAG . 
L 4 CL B 1 1434 1434 CL CL . 
M 2 GFB C 1 1430 1430 GFB GFB . 
N 3 NAG C 1 1431 1431 NAG NAG . 
O 3 NAG C 1 1432 1432 NAG NAG . 
P 4 CL C 1 1433 1433 CL CL . 
Q 2 GFB D 1 1430 1430 GFB GFB . 
R 4 CL D 1 1431 1431 CL CL . 
S 5 HOH A 1 2001 2001 HOH HOH . 
S 5 HOH A 2 2002 2002 HOH HOH . 
S 5 HOH A 3 2003 2003 HOH HOH . 
S 5 HOH A 4 2004 2004 HOH HOH . 
S 5 HOH A 5 2005 2005 HOH HOH . 
S 5 HOH A 6 2006 2006 HOH HOH . 
T 5 HOH B 1 2001 2001 HOH HOH . 
T 5 HOH B 2 2002 2002 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 O O1P GFB . . . H 2 -5.752 -49.614 5.06 1 62.97 ? O1P GFB 1430 B 1 
HETATM 2 P P GFB . . . H 2 -7.137 -49.442 4.502 1 52.92 ? P GFB 1430 B 1 
HETATM 3 O O3P GFB . . . H 2 -7.224 -48.985 3.069 1 68.37 ? O3P GFB 1430 B 1 
HETATM 4 O O2P GFB . . . H 2 -7.885 -50.862 4.709 1 42.63 ? O2P GFB 1430 B 1 
HETATM 5 O O5' GFB . . . H 2 -7.97 -48.487 5.449 1 61.3 ? O5' GFB 1430 B 1 
HETATM 6 P P1 GFB . . . H 2 -9.43 -51.23 4.973 1 68.38 ? P1 GFB 1430 B 1 
HETATM 7 C C5' GFB . . . H 2 -7.238 -47.668 6.351 1 62.86 ? C5' GFB 1430 B 1 
HETATM 8 C C4' GFB . . . H 2 -6.988 -46.361 5.612 1 61.07 ? C4' GFB 1430 B 1 
HETATM 9 O O4' GFB . . . H 2 -6.681 -45.349 6.561 1 59.16 ? O4' GFB 1430 B 1 
HETATM 10 C C3' GFB . . . H 2 -5.81 -46.441 4.649 1 65.56 ? C3' GFB 1430 B 1 
HETATM 11 C C1' GFB . . . H 2 -5.327 -44.96 6.445 1 58.37 ? C1' GFB 1430 B 1 
HETATM 12 O O3' GFB . . . H 2 -6.213 -46.496 3.268 1 73.95 ? O3' GFB 1430 B 1 
HETATM 13 C C2' GFB . . . H 2 -4.983 -45.205 4.994 1 58.63 ? C2' GFB 1430 B 1 
HETATM 14 O O2' GFB . . . H 2 -5.374 -44.071 4.205 1 53.93 ? O2' GFB 1430 B 1 
HETATM 15 N N9 GFB . . . H 2 -4.433 -45.864 7.216 1 63.86 ? N9 GFB 1430 B 1 
HETATM 16 C C8 GFB . . . H 2 -4.686 -47.072 7.76 1 56.83 ? C8 GFB 1430 B 1 
HETATM 17 C C4 GFB . . . H 2 -3.201 -45.507 7.569 1 61.1 ? C4 GFB 1430 B 1 
HETATM 18 N N7 GFB . . . H 2 -3.579 -47.5 8.416 1 52.32 ? N7 GFB 1430 B 1 
HETATM 19 C C5 GFB . . . H 2 -2.649 -46.529 8.311 1 55.62 ? C5 GFB 1430 B 1 
HETATM 20 C C6 GFB . . . H 2 -1.344 -46.377 8.767 1 56.3 ? C6 GFB 1430 B 1 
HETATM 21 O O6 GFB . . . H 2 -0.829 -47.289 9.44 1 56.54 ? O6 GFB 1430 B 1 
HETATM 22 N N1 GFB . . . H 2 -0.678 -45.237 8.46 1 56.98 ? N1 GFB 1430 B 1 
HETATM 23 C C2 GFB . . . H 2 -1.253 -44.261 7.728 1 59.71 ? C2 GFB 1430 B 1 
HETATM 24 N N2 GFB . . . H 2 -0.632 -43.117 7.392 1 61.31 ? N2 GFB 1430 B 1 
HETATM 25 N N3 GFB . . . H 2 -2.505 -44.387 7.286 1 61.89 ? N3 GFB 1430 B 1 
HETATM 26 C C1 GFB . . . H 2 -11.65 -50.188 3.977 1 154.88 ? C1 GFB 1430 B 1 
HETATM 27 C C2A GFB . . . H 2 -11.903 -48.671 3.963 1 154.93 ? C2A GFB 1430 B 1 
HETATM 28 O O1 GFB . . . H 2 -10.25 -50.364 3.913 1 153.41 ? O1 GFB 1430 B 1 
HETATM 29 O O5 GFB . . . H 2 -12.003 -50.779 5.232 1 155.93 ? O5 GFB 1430 B 1 
HETATM 30 C C3 GFB . . . H 2 -13.32 -48.297 4.38 1 154.43 ? C3 GFB 1430 B 1 
HETATM 31 O O2 GFB . . . H 2 -11.675 -48.171 2.647 1 155.4 ? O2 GFB 1430 B 1 
HETATM 32 C C4A GFB . . . H 2 -13.68 -49.017 5.683 1 155.43 ? C4A GFB 1430 B 1 
HETATM 33 O O3 GFB . . . H 2 -13.422 -46.853 4.526 1 153.05 ? O3 GFB 1430 B 1 
HETATM 34 C C5A GFB . . . H 2 -13.348 -50.516 5.668 1 155.8 ? C5A GFB 1430 B 1 
HETATM 35 O O4 GFB . . . H 2 -12.949 -48.407 6.756 1 155.37 ? O4 GFB 1430 B 1 
HETATM 36 C C6A GFB . . . H 2 -13.5 -51.103 7.067 1 155.18 ? C6A GFB 1430 B 1 
HETATM 37 O O1X GFB . . . H 2 -9.559 -52.724 4.746 1 73.53 ? O1X GFB 1430 B 1 
HETATM 38 O O2X GFB . . . H 2 -9.821 -50.719 6.332 1 71.38 ? O2X GFB 1430 B 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    47 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           38 
#