data_3VKG
#
_model_server_result.job_id            7HCrBwMuQOhysFXloblXNw 
_model_server_result.datetime_utc      '2025-03-06 23:28:30' 
_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          3vkg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":9022}' 
#
_entry.id    3VKG 
#
_exptl.entry_id    3VKG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              202.34 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPERMINE 
_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         90 
_cell.entry_id            3VKG 
_cell.length_a            204.256 
_cell.length_b            221.806 
_cell.length_c            192.898 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VKG 
_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
? dimeric 2 author_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
PISA monomeric 1 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 
A,C,D,E,F,G,H,I,R 2 1 
B,J,K,L,M,N,O,P,Q,S 3 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 G N N 
? 3 H N N 
? 3 N N N 
? 3 O 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 I MG MG . A MG 1 1_555 A OG1 THR 920 A THR 2283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc2 I MG MG . A MG 1 1_555 A OE2 GLU 1033 A GLU 2396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc3 I MG MG . A MG 1 1_555 D O1B ADP . A ADP 9002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? 
metalc ? metalc4 I MG MG . A MG 1 1_555 D O3B ADP . A ADP 9002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? 
metalc ? metalc5 P MG MG . B MG 2 1_555 J O3B ADP . B ADP 9007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? 
metalc ? metalc6 P MG MG . B MG 2 1_555 J O2B ADP . B ADP 9007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? 
metalc ? metalc7 Q MG MG . B MG 3 1_555 B OG1 THR 920 B THR 2283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc8 Q MG MG . B MG 3 1_555 B OE2 GLU 1033 B GLU 2396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
metalc ? metalc9 Q MG MG . B MG 3 1_555 K O3B ADP . B ADP 9008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? 
#
_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 334 n n 
N1 HN11 SPM sing 335 n n 
N1 HN12 SPM sing 336 n n 
C2 C3 SPM sing 337 n n 
C2 H21 SPM sing 338 n n 
C2 H22 SPM sing 339 n n 
C3 C4 SPM sing 340 n n 
C3 H31 SPM sing 341 n n 
C3 H32 SPM sing 342 n n 
C4 N5 SPM sing 343 n n 
C4 H41 SPM sing 344 n n 
C4 H42 SPM sing 345 n n 
N5 C6 SPM sing 346 n n 
N5 HN5 SPM sing 347 n n 
C6 C7 SPM sing 348 n n 
C6 H61 SPM sing 349 n n 
C6 H62 SPM sing 350 n n 
C7 C8 SPM sing 351 n n 
C7 H71 SPM sing 352 n n 
C7 H72 SPM sing 353 n n 
C8 C9 SPM sing 354 n n 
C8 H81 SPM sing 355 n n 
C8 H82 SPM sing 356 n n 
C9 N10 SPM sing 357 n n 
C9 H91 SPM sing 358 n n 
C9 H92 SPM sing 359 n n 
N10 C11 SPM sing 360 n n 
N10 HN0 SPM sing 361 n n 
C11 C12 SPM sing 362 n n 
C11 H111 SPM sing 363 n n 
C11 H112 SPM sing 364 n n 
C12 C13 SPM sing 365 n n 
C12 H121 SPM sing 366 n n 
C12 H122 SPM sing 367 n n 
C13 N14 SPM sing 368 n n 
C13 H131 SPM sing 369 n n 
C13 H132 SPM sing 370 n n 
N14 HN41 SPM sing 371 n n 
N14 HN42 SPM sing 372 n n 
#
_atom_sites.entry_id                     3VKG 
_atom_sites.fract_transf_matrix[1][1]    0.004896 
_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]    0.004508 
_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]    0.005184 
_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 ADP A 1 9001 9001 ADP ADP . 
D 2 ADP A 1 9002 9002 ADP ADP . 
E 2 ADP A 1 9003 9003 ADP ADP . 
F 2 ADP A 1 9004 9004 ADP ADP . 
G 3 SPM A 1 9012 9012 SPM SPM . 
H 3 SPM A 1 9016 9016 SPM SPM . 
I 4 MG A 1 1 1 MG MG . 
J 2 ADP B 1 9007 9007 ADP ADP . 
K 2 ADP B 1 9008 9008 ADP ADP . 
L 2 ADP B 1 9009 9009 ADP ADP . 
M 2 ADP B 1 9010 9010 ADP ADP . 
N 3 SPM B 1 9018 9018 SPM SPM . 
O 3 SPM B 1 9022 9022 SPM SPM . 
P 4 MG B 1 2 2 MG MG . 
Q 4 MG B 1 3 3 MG MG . 
R 5 HOH A 1 13 13 HOH HOH . 
R 5 HOH A 2 14 14 HOH HOH . 
R 5 HOH A 3 15 15 HOH HOH . 
R 5 HOH A 4 16 16 HOH HOH . 
R 5 HOH A 5 17 17 HOH HOH . 
R 5 HOH A 6 18 18 HOH HOH . 
R 5 HOH A 7 19 19 HOH HOH . 
R 5 HOH A 8 20 20 HOH HOH . 
R 5 HOH A 9 21 21 HOH HOH . 
R 5 HOH A 10 22 22 HOH HOH . 
R 5 HOH A 11 23 23 HOH HOH . 
R 5 HOH A 12 25 25 HOH HOH . 
R 5 HOH A 13 27 27 HOH HOH . 
R 5 HOH A 14 28 28 HOH HOH . 
R 5 HOH A 15 30 30 HOH HOH . 
R 5 HOH A 16 32 32 HOH HOH . 
R 5 HOH A 17 33 33 HOH HOH . 
R 5 HOH A 18 35 35 HOH HOH . 
R 5 HOH A 19 36 36 HOH HOH . 
R 5 HOH A 20 37 37 HOH HOH . 
R 5 HOH A 21 38 38 HOH HOH . 
R 5 HOH A 22 41 41 HOH HOH . 
R 5 HOH A 23 42 42 HOH HOH . 
S 5 HOH B 1 1 1 HOH HOH . 
S 5 HOH B 2 4 4 HOH HOH . 
S 5 HOH B 3 5 5 HOH HOH . 
S 5 HOH B 4 6 6 HOH HOH . 
S 5 HOH B 5 7 7 HOH HOH . 
S 5 HOH B 6 8 8 HOH HOH . 
S 5 HOH B 7 9 9 HOH HOH . 
S 5 HOH B 8 10 10 HOH HOH . 
S 5 HOH B 9 11 11 HOH HOH . 
S 5 HOH B 10 12 12 HOH HOH . 
S 5 HOH B 11 24 24 HOH HOH . 
S 5 HOH B 12 26 26 HOH HOH . 
S 5 HOH B 13 29 29 HOH HOH . 
S 5 HOH B 14 31 31 HOH HOH . 
S 5 HOH B 15 34 34 HOH HOH . 
S 5 HOH B 16 39 39 HOH HOH . 
S 5 HOH B 17 40 40 HOH HOH . 
S 5 HOH B 18 4731 2 HOH HOH . 
S 5 HOH B 19 4732 3 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 3 97.548 76.756 156.515 1 49.05 ? N1 SPM 9022 B 1 
HETATM 2 C C2 SPM . . . O 3 96.126 76.787 156.904 1 49.46 ? C2 SPM 9022 B 1 
HETATM 3 C C3 SPM . . . O 3 95.992 76.593 158.419 1 48.34 ? C3 SPM 9022 B 1 
HETATM 4 C C4 SPM . . . O 3 95.622 75.131 158.725 1 48.1 ? C4 SPM 9022 B 1 
HETATM 5 N N5 SPM . . . O 3 96.362 74.679 159.921 1 46.8 ? N5 SPM 9022 B 1 
HETATM 6 C C6 SPM . . . O 3 95.463 73.829 160.72 1 44.87 ? C6 SPM 9022 B 1 
HETATM 7 C C7 SPM . . . O 3 95.597 72.364 160.282 1 44.51 ? C7 SPM 9022 B 1 
HETATM 8 C C8 SPM . . . O 3 94.503 71.497 160.914 1 42.31 ? C8 SPM 9022 B 1 
HETATM 9 C C9 SPM . . . O 3 93.123 71.843 160.336 1 43.77 ? C9 SPM 9022 B 1 
HETATM 10 N N10 SPM . . . O 3 93.074 71.543 158.906 1 42.15 ? N10 SPM 9022 B 1 
HETATM 11 C C11 SPM . . . O 3 91.679 71.721 158.503 1 39.69 ? C11 SPM 9022 B 1 
HETATM 12 C C12 SPM . . . O 3 91.631 72.13 157.035 1 39.3 ? C12 SPM 9022 B 1 
HETATM 13 C C13 SPM . . . O 3 91.429 70.895 156.164 1 37.26 ? C13 SPM 9022 B 1 
HETATM 14 N N14 SPM . . . O 3 91.928 71.16 154.818 1 38.43 ? N14 SPM 9022 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    67 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#