data_1ECB
#
_model_server_result.job_id            '_Dawuei9BVZ1GIWbbPGN_Q' 
_model_server_result.datetime_utc      '2024-10-11 06:23:08' 
_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          1ecb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":505}' 
#
_entry.id    1ECB 
#
_exptl.entry_id    1ECB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              363.221 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_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            1ECB 
_cell.length_a            95.8 
_cell.length_b            113.2 
_cell.length_c            199.6 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ECB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA tetrameric 4 software_defined_assembly 3 
PISA tetrameric 4 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,B,E,F,G,H,I,J,Q,R 1 1 
C,D,K,L,M,N,O,P,S,T 2 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 3 1 
A,B,E,F,G,H,I,J,Q,R 4 1 
C,D,K,L,M,N,O,P,S,T 4 2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_655 -x+1,y+1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 95.8 56.6 99.8 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 G N N 
? 3 I N N 
? 3 J N N 
? 3 L N N 
? 3 M N N 
? 3 O N N 
? 3 P 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 OD1 ASP 366 A ASP 366 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc2 A OD1 ASP 367 A ASP 367 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc3 F O3' 5GP . A 5GP 505 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? 
metalc ? metalc4 F O2' 5GP . A 5GP 505 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? 
metalc ? metalc5 E MG MG . A MG 507 1_555 Q O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc6 E MG MG . A MG 507 1_555 Q O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc7 B OD1 ASP 366 B ASP 366 1_555 H MG MG . B MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc8 B OD1 ASP 367 B ASP 367 1_555 H MG MG . B MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc9 I O3' 5GP . B 5GP 505 1_555 H MG MG . B MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc10 I O2' 5GP . B 5GP 505 1_555 H MG MG . B MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
metalc ? metalc11 H MG MG . B MG 507 1_555 R O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc12 H MG MG . B MG 507 1_555 R O HOH . B HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc13 C OD1 ASP 366 C ASP 366 1_555 K MG MG . C MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc14 C OD2 ASP 367 C ASP 367 1_555 K MG MG . C MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc15 L O3' 5GP . C 5GP 505 1_555 K MG MG . C MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? 
metalc ? metalc16 L O2' 5GP . C 5GP 505 1_555 K MG MG . C MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc17 K MG MG . C MG 507 1_555 S O HOH . C HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc18 K MG MG . C MG 507 1_555 S O HOH . C HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc19 D OD1 ASP 366 D ASP 366 1_555 N MG MG . D MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc20 D OD2 ASP 367 D ASP 367 1_555 N MG MG . D MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc21 D OD1 ASP 367 D ASP 367 1_555 N MG MG . D MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc22 O O3' 5GP . D 5GP 505 1_555 N MG MG . D MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? 
metalc ? metalc23 O O2' 5GP . D 5GP 505 1_555 N MG MG . D MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc24 N MG MG . D MG 507 1_555 T O HOH . D HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc25 N MG MG . D MG 507 1_555 T O HOH . D HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
#
_chem_comp.formula           'C10 H14 N5 O8 P' 
_chem_comp.formula_weight    363.221 
_chem_comp.id                5GP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GUANOSINE-5'-MONOPHOSPHATE" 
_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 5GP doub 1 n n 
P O2P 5GP sing 2 n n 
P O3P 5GP sing 3 n n 
P O5' 5GP sing 4 n n 
O2P HOP2 5GP sing 5 n n 
O3P HOP3 5GP sing 6 n n 
O5' C5' 5GP sing 7 n n 
C5' C4' 5GP sing 8 n n 
C5' "H5'1" 5GP sing 9 n n 
C5' "H5'2" 5GP sing 10 n n 
C4' O4' 5GP sing 11 n n 
C4' C3' 5GP sing 12 n n 
C4' H4' 5GP sing 13 n n 
O4' C1' 5GP sing 14 n n 
C3' O3' 5GP sing 15 n n 
C3' C2' 5GP sing 16 n n 
C3' H3' 5GP sing 17 n n 
O3' HO3' 5GP sing 18 n n 
C2' O2' 5GP sing 19 n n 
C2' C1' 5GP sing 20 n n 
C2' H2' 5GP sing 21 n n 
O2' HO2' 5GP sing 22 n n 
C1' N9 5GP sing 23 n n 
C1' H1' 5GP sing 24 n n 
N9 C8 5GP sing 25 n y 
N9 C4 5GP sing 26 n y 
C8 N7 5GP doub 27 n y 
C8 H8 5GP sing 28 n n 
N7 C5 5GP sing 29 n y 
C5 C6 5GP sing 30 n n 
C5 C4 5GP doub 31 n y 
C6 O6 5GP doub 32 n n 
C6 N1 5GP sing 33 n n 
N1 C2 5GP sing 34 n n 
N1 HN1 5GP sing 35 n n 
C2 N2 5GP sing 36 n n 
C2 N3 5GP doub 37 n n 
N2 HN21 5GP sing 38 n n 
N2 HN22 5GP sing 39 n n 
N3 C4 5GP sing 40 n n 
#
_atom_sites.entry_id                     1ECB 
_atom_sites.fract_transf_matrix[1][1]    0.010438 
_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]    0.008834 
_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]    0.00501 
_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 MG A 1 507 507 MG MG . 
F 3 5GP A 1 505 505 5GP 5GP . 
G 3 5GP A 1 506 506 5GP 5GP . 
H 2 MG B 1 507 507 MG MG . 
I 3 5GP B 1 505 505 5GP 5GP . 
J 3 5GP B 1 506 506 5GP 5GP . 
K 2 MG C 1 507 507 MG MG . 
L 3 5GP C 1 505 505 5GP 5GP . 
M 3 5GP C 1 506 506 5GP 5GP . 
N 2 MG D 1 507 507 MG MG . 
O 3 5GP D 1 505 505 5GP 5GP . 
P 3 5GP D 1 506 506 5GP 5GP . 
Q 4 HOH A 1 508 508 HOH HOH . 
Q 4 HOH A 2 509 509 HOH HOH . 
Q 4 HOH A 3 510 2 HOH HOH . 
Q 4 HOH A 4 511 22 HOH HOH . 
Q 4 HOH A 5 512 27 HOH HOH . 
Q 4 HOH A 6 513 28 HOH HOH . 
Q 4 HOH A 7 514 29 HOH HOH . 
R 4 HOH B 1 508 508 HOH HOH . 
R 4 HOH B 2 509 509 HOH HOH . 
R 4 HOH B 3 510 4 HOH HOH . 
R 4 HOH B 4 511 9 HOH HOH . 
R 4 HOH B 5 512 12 HOH HOH . 
R 4 HOH B 6 513 13 HOH HOH . 
R 4 HOH B 7 514 21 HOH HOH . 
R 4 HOH B 8 515 31 HOH HOH . 
S 4 HOH C 1 508 508 HOH HOH . 
S 4 HOH C 2 509 509 HOH HOH . 
S 4 HOH C 3 510 1 HOH HOH . 
S 4 HOH C 4 511 7 HOH HOH . 
S 4 HOH C 5 512 10 HOH HOH . 
S 4 HOH C 6 513 15 HOH HOH . 
S 4 HOH C 7 514 16 HOH HOH . 
S 4 HOH C 8 515 18 HOH HOH . 
S 4 HOH C 9 516 20 HOH HOH . 
S 4 HOH C 10 517 24 HOH HOH . 
S 4 HOH C 11 518 25 HOH HOH . 
S 4 HOH C 12 519 26 HOH HOH . 
S 4 HOH C 13 520 30 HOH HOH . 
T 4 HOH D 1 508 508 HOH HOH . 
T 4 HOH D 2 509 509 HOH HOH . 
T 4 HOH D 3 510 3 HOH HOH . 
T 4 HOH D 4 511 5 HOH HOH . 
T 4 HOH D 5 512 6 HOH HOH . 
T 4 HOH D 6 513 8 HOH HOH . 
T 4 HOH D 7 514 11 HOH HOH . 
T 4 HOH D 8 515 14 HOH HOH . 
T 4 HOH D 9 516 17 HOH HOH . 
T 4 HOH D 10 517 19 HOH HOH . 
T 4 HOH D 11 518 23 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 P 5GP . . . L 3 20.708 3.474 23.956 1 46.29 ? P 5GP 505 C 1 
HETATM 2 O O1P 5GP . . . L 3 19.513 3.177 24.824 1 45.81 ? O1P 5GP 505 C 1 
HETATM 3 O O2P 5GP . . . L 3 21.893 3.473 24.844 1 42.98 ? O2P 5GP 505 C 1 
HETATM 4 O O3P 5GP . . . L 3 20.806 2.709 22.619 1 39.45 ? O3P 5GP 505 C 1 
HETATM 5 O O5' 5GP . . . L 3 20.553 5.038 23.445 1 44.84 ? O5' 5GP 505 C 1 
HETATM 6 C C5' 5GP . . . L 3 21.433 5.794 22.554 1 46.3 ? C5' 5GP 505 C 1 
HETATM 7 C C4' 5GP . . . L 3 20.712 7.052 22.046 1 48.44 ? C4' 5GP 505 C 1 
HETATM 8 O O4' 5GP . . . L 3 20.243 7.753 23.196 1 57.18 ? O4' 5GP 505 C 1 
HETATM 9 C C3' 5GP . . . L 3 21.51 8.074 21.229 1 47.16 ? C3' 5GP 505 C 1 
HETATM 10 O O3' 5GP . . . L 3 21.069 8.087 19.867 1 42.73 ? O3' 5GP 505 C 1 
HETATM 11 C C2' 5GP . . . L 3 21.224 9.482 21.783 1 50.12 ? C2' 5GP 505 C 1 
HETATM 12 O O2' 5GP . . . L 3 20.362 10.277 20.955 1 39.93 ? O2' 5GP 505 C 1 
HETATM 13 C C1' 5GP . . . L 3 20.483 9.199 23.096 1 59.69 ? C1' 5GP 505 C 1 
HETATM 14 N N9 5GP . . . L 3 21.297 9.562 24.253 1 72.03 ? N9 5GP 505 C 1 
HETATM 15 C C8 5GP . . . L 3 20.881 10.212 25.403 1 76.16 ? C8 5GP 505 C 1 
HETATM 16 N N7 5GP . . . L 3 21.848 10.352 26.27 1 82.73 ? N7 5GP 505 C 1 
HETATM 17 C C5 5GP . . . L 3 22.978 9.753 25.647 1 82.51 ? C5 5GP 505 C 1 
HETATM 18 C C6 5GP . . . L 3 24.308 9.601 26.104 1 84.99 ? C6 5GP 505 C 1 
HETATM 19 O O6 5GP . . . L 3 24.679 10.025 27.182 1 88.19 ? O6 5GP 505 C 1 
HETATM 20 N N1 5GP . . . L 3 25.189 8.928 25.192 1 83.64 ? N1 5GP 505 C 1 
HETATM 21 C C2 5GP . . . L 3 24.809 8.459 23.951 1 80.6 ? C2 5GP 505 C 1 
HETATM 22 N N2 5GP . . . L 3 25.683 7.861 23.136 1 78.94 ? N2 5GP 505 C 1 
HETATM 23 N N3 5GP . . . L 3 23.554 8.613 23.536 1 80.81 ? N3 5GP 505 C 1 
HETATM 24 C C4 5GP . . . L 3 22.678 9.261 24.415 1 78.82 ? C4 5GP 505 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           24 
#