data_6GDA
#
_model_server_result.job_id            v8c2JJogY2VOcE6ELllk9Q 
_model_server_result.datetime_utc      '2024-11-27 19:58:39' 
_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          6gda 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":214}' 
#
_entry.id    6GDA 
#
_exptl.entry_id    6GDA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              202.34 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPERMINE 
_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         90 
_cell.entry_id            6GDA 
_cell.length_a            101.252 
_cell.length_b            101.252 
_cell.length_c            85.31 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GDA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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,E,F,G,H,I,J,K,L,M,N,O,P,Q 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 O N N 
? 5 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
covale ? covale1 A SG CYS 19 A CYS 14 1_555 B CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.712 ? 
covale ? covale2 A SG CYS 19 A CYS 14 1_555 B CBB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
covale ? covale3 A SG CYS 22 A CYS 17 1_555 B CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.731 ? 
metalc ? metalc1 A NE2 HIS 23 A HIS 18 1_555 B FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc2 A SD MET 85 A MET 80 1_555 B FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
#
_chem_comp.formula           'C10 H26 N4' 
_chem_comp.formula_weight    202.34 
_chem_comp.id                SPM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SPERMINE 
_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
N1 C2 SPM sing 530 n n 
N1 HN11 SPM sing 531 n n 
N1 HN12 SPM sing 532 n n 
C2 C3 SPM sing 533 n n 
C2 H21 SPM sing 534 n n 
C2 H22 SPM sing 535 n n 
C3 C4 SPM sing 536 n n 
C3 H31 SPM sing 537 n n 
C3 H32 SPM sing 538 n n 
C4 N5 SPM sing 539 n n 
C4 H41 SPM sing 540 n n 
C4 H42 SPM sing 541 n n 
N5 C6 SPM sing 542 n n 
N5 HN5 SPM sing 543 n n 
C6 C7 SPM sing 544 n n 
C6 H61 SPM sing 545 n n 
C6 H62 SPM sing 546 n n 
C7 C8 SPM sing 547 n n 
C7 H71 SPM sing 548 n n 
C7 H72 SPM sing 549 n n 
C8 C9 SPM sing 550 n n 
C8 H81 SPM sing 551 n n 
C8 H82 SPM sing 552 n n 
C9 N10 SPM sing 553 n n 
C9 H91 SPM sing 554 n n 
C9 H92 SPM sing 555 n n 
N10 C11 SPM sing 556 n n 
N10 HN0 SPM sing 557 n n 
C11 C12 SPM sing 558 n n 
C11 H111 SPM sing 559 n n 
C11 H112 SPM sing 560 n n 
C12 C13 SPM sing 561 n n 
C12 H121 SPM sing 562 n n 
C12 H122 SPM sing 563 n n 
C13 N14 SPM sing 564 n n 
C13 H131 SPM sing 565 n n 
C13 H132 SPM sing 566 n n 
N14 HN41 SPM sing 567 n n 
N14 HN42 SPM sing 568 n n 
#
_atom_sites.entry_id                     6GDA 
_atom_sites.fract_transf_matrix[1][1]    0.009876 
_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]    0.009876 
_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]    0.011722 
_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 HEC A 1 201 118 HEC HEM . 
C 3 EVB A 1 202 1 EVB SC8 . 
D 3 EVB A 1 203 2 EVB SC8 . 
E 3 EVB A 1 204 3 EVB SC8 . 
F 4 SO4 A 1 205 1 SO4 SO4 . 
G 4 SO4 A 1 206 2 SO4 SO4 . 
H 4 SO4 A 1 207 3 SO4 SO4 . 
I 4 SO4 A 1 208 4 SO4 SO4 . 
J 4 SO4 A 1 209 5 SO4 SO4 . 
K 4 SO4 A 1 210 6 SO4 SO4 . 
L 4 SO4 A 1 211 7 SO4 SO4 . 
M 4 SO4 A 1 212 8 SO4 SO4 . 
N 4 SO4 A 1 213 9 SO4 SO4 . 
O 5 SPM A 1 214 1 SPM SPM . 
P 5 SPM A 1 215 2 SPM SPM . 
Q 6 HOH A 1 301 3 HOH HOH . 
Q 6 HOH A 2 302 8 HOH HOH . 
Q 6 HOH A 3 303 4 HOH HOH . 
Q 6 HOH A 4 304 9 HOH HOH . 
Q 6 HOH A 5 305 5 HOH HOH . 
Q 6 HOH A 6 306 1 HOH HOH . 
Q 6 HOH A 7 307 2 HOH HOH . 
Q 6 HOH A 8 308 6 HOH HOH . 
Q 6 HOH A 9 309 7 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 N N1 SPM . . . O 5 -24.55 -26.457 -13.917 1 100.87 ? N1 SPM 214 A 1 
HETATM 2 C C2 SPM . . . O 5 -23.86 -26.789 -12.663 1 100.55 ? C2 SPM 214 A 1 
HETATM 3 C C3 SPM . . . O 5 -22.723 -25.797 -12.397 1 100.05 ? C3 SPM 214 A 1 
HETATM 4 C C4 SPM . . . O 5 -23.227 -24.653 -11.51 1 98.51 ? C4 SPM 214 A 1 
HETATM 5 N N5 SPM . . . O 5 -22.26 -23.546 -11.537 1 97.75 ? N5 SPM 214 A 1 
HETATM 6 C C6 SPM . . . O 5 -22.663 -22.509 -10.574 1 96.38 ? C6 SPM 214 A 1 
HETATM 7 C C7 SPM . . . O 5 -22.815 -21.163 -11.289 1 97.39 ? C7 SPM 214 A 1 
HETATM 8 C C8 SPM . . . O 5 -21.461 -20.651 -11.795 1 98.79 ? C8 SPM 214 A 1 
HETATM 9 C C9 SPM . . . O 5 -21.628 -19.881 -13.113 1 100.24 ? C9 SPM 214 A 1 
HETATM 10 N N10 SPM . . . O 5 -20.705 -18.737 -13.207 1 101.71 ? N10 SPM 214 A 1 
HETATM 11 C C11 SPM . . . O 5 -19.333 -19.231 -13.419 1 103.35 ? C11 SPM 214 A 1 
HETATM 12 C C12 SPM . . . O 5 -18.457 -18.084 -13.93 1 104.6 ? C12 SPM 214 A 1 
HETATM 13 C C13 SPM . . . O 5 -18.729 -17.85 -15.418 1 104.83 ? C13 SPM 214 A 1 
HETATM 14 N N14 SPM . . . O 5 -18.155 -16.562 -15.835 1 104.74 ? N14 SPM 214 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#