data_3KOZ
#
_model_server_result.job_id            8OScQ56guHqv9qLwKNFC3A 
_model_server_result.datetime_utc      '2024-10-19 16:43:22' 
_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          3koz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":767}' 
#
_entry.id    3KOZ 
#
_exptl.entry_id    3KOZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              361.288 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (E)-N~5~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-ornithine 
_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          103.43 
_cell.angle_gamma         90 
_cell.entry_id            3KOZ 
_cell.length_a            66.52 
_cell.length_b            233.22 
_cell.length_c            124.14 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KOZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
PISA tetrameric 4 software_defined_assembly 5 
PISA tetrameric 4 software_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
E,F,O,P,Q 1 1 
A,B,I,J,K 2 1 
G,H,R,S,T 3 1 
C,D,L,M,N 4 1 
A,B,E,F,I,J,K,O,P,Q 5 1 
C,D,G,H,L,M,N,R,S,T 6 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 K N N 
? 5 M N N 
? 5 P N N 
? 5 S 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 NE2 HIS 615 A HIS 618 1_555 I CO B12 . A B12 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc2 J C5' 5AD . A 5AD 1500 1_555 Q CO B12 . C B12 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc3 I CO B12 . A B12 1801 1_555 O C5' 5AD . C 5AD 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc4 C NE2 HIS 615 B HIS 618 1_555 N CO B12 . B B12 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc5 L C5' 5AD . B 5AD 1500 1_555 R CO B12 . D B12 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc6 N CO B12 . B B12 1801 1_555 T C5' 5AD . D 5AD 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc7 E NE2 HIS 615 C HIS 618 1_555 Q CO B12 . C B12 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc8 G NE2 HIS 615 D HIS 618 1_555 R CO B12 . D B12 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
#
_chem_comp.formula           'C13 H20 N3 O7 P' 
_chem_comp.formula_weight    361.288 
_chem_comp.id                Z97 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (E)-N~5~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-ornithine 
_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
O C Z97 doub 597 n n 
C CA Z97 sing 598 n n 
C OXT Z97 sing 599 n n 
CA N Z97 sing 600 n n 
N HN Z97 sing 601 n n 
N HNA Z97 sing 602 n n 
OP1 P Z97 doub 603 n n 
P OP2 Z97 sing 604 n n 
P OP3 Z97 sing 605 n n 
P OP4 Z97 sing 606 n n 
N1 C6 Z97 doub 607 n y 
N1 C2 Z97 sing 608 n y 
C2A C2 Z97 sing 609 n n 
C2 C3 Z97 doub 610 n y 
C3 C4 Z97 sing 611 n y 
C3 O3 Z97 sing 612 n n 
O3 HO3 Z97 sing 613 n n 
C5 C4 Z97 doub 614 n y 
C4 C4A Z97 sing 615 n n 
C6 C5 Z97 sing 616 n y 
C5A C5 Z97 sing 617 n n 
C6 H6 Z97 sing 618 n n 
CB CA Z97 sing 619 n n 
CA HA Z97 sing 620 n n 
CG CB Z97 sing 621 n n 
CB HB Z97 sing 622 n n 
CB HBA Z97 sing 623 n n 
NE CD Z97 sing 624 n n 
CD CG Z97 sing 625 n n 
CD HD Z97 sing 626 n n 
CD HDA Z97 sing 627 n n 
C4A NE Z97 doub 628 n n 
CG HG Z97 sing 629 n n 
CG HGA Z97 sing 630 n n 
C2A H2A Z97 sing 631 n n 
C2A H2AA Z97 sing 632 n n 
C2A H2AB Z97 sing 633 n n 
C4A H4A Z97 sing 634 n n 
OP4 C5A Z97 sing 635 n n 
C5A H5A Z97 sing 636 n n 
C5A H5AA Z97 sing 637 n n 
OP2 HOP2 Z97 sing 638 n n 
OP3 HOP3 Z97 sing 639 n n 
OXT HOXT Z97 sing 640 n n 
#
_atom_sites.entry_id                     3KOZ 
_atom_sites.fract_transf_matrix[1][1]    0.015033 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00359 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004288 
_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]    0.008282 
_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
I 3 B12 A 1 1801 1801 B12 B12 . 
J 4 5AD A 1 1500 1500 5AD 5AD . 
K 5 Z97 A 1 767 767 Z97 Z97 . 
L 4 5AD B 1 1500 1500 5AD 5AD . 
M 5 Z97 B 1 767 767 Z97 Z97 . 
N 3 B12 B 1 1801 1801 B12 B12 . 
O 4 5AD C 1 1500 1500 5AD 5AD . 
P 5 Z97 C 1 767 767 Z97 Z97 . 
Q 3 B12 C 1 1801 1801 B12 B12 . 
R 3 B12 D 1 1801 1801 B12 B12 . 
S 5 Z97 D 1 767 767 Z97 Z97 . 
T 4 5AD D 1 1500 1500 5AD 5AD . 
#
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 C C Z97 . . . M 5 22.753 46.91 32.339 1 23.3 ? C Z97 767 B 1 
HETATM 2 N N Z97 . . . M 5 21.258 45.018 32.004 1 30.77 ? N Z97 767 B 1 
HETATM 3 O O Z97 . . . M 5 23.098 47.932 32.883 1 24.84 ? O Z97 767 B 1 
HETATM 4 P P Z97 . . . M 5 22.775 42.126 42.052 1 48.34 ? P Z97 767 B 1 
HETATM 5 N N1 Z97 . . . M 5 23.989 47.407 40.618 1 29.57 ? N1 Z97 767 B 1 
HETATM 6 C C2 Z97 . . . M 5 23.351 48.036 39.557 1 26.99 ? C2 Z97 767 B 1 
HETATM 7 C C3 Z97 . . . M 5 22.559 47.257 38.672 1 26.37 ? C3 Z97 767 B 1 
HETATM 8 O O3 Z97 . . . M 5 21.917 47.837 37.588 1 29.84 ? O3 Z97 767 B 1 
HETATM 9 C C4 Z97 . . . M 5 22.437 45.917 38.871 1 29.14 ? C4 Z97 767 B 1 
HETATM 10 C C5 Z97 . . . M 5 23.136 45.293 40.017 1 30.32 ? C5 Z97 767 B 1 
HETATM 11 C C6 Z97 . . . M 5 23.9 46.055 40.867 1 26.8 ? C6 Z97 767 B 1 
HETATM 12 C CA Z97 . . . M 5 21.589 46.133 32.857 1 25.3 ? CA Z97 767 B 1 
HETATM 13 C CB Z97 . . . M 5 21.674 45.779 34.317 1 27.15 ? CB Z97 767 B 1 
HETATM 14 C CD Z97 . . . M 5 20.17 44.652 36.054 1 36.77 ? CD Z97 767 B 1 
HETATM 15 N NE Z97 . . . M 5 20.7 45.655 36.996 1 34.97 ? NE Z97 767 B 1 
HETATM 16 C CG Z97 . . . M 5 20.953 44.524 34.739 1 32.57 ? CG Z97 767 B 1 
HETATM 17 C C2A Z97 . . . M 5 23.51 49.509 39.342 1 25.27 ? C2A Z97 767 B 1 
HETATM 18 C C4A Z97 . . . M 5 21.596 45.034 37.929 1 32.53 ? C4A Z97 767 B 1 
HETATM 19 C C5A Z97 . . . M 5 22.983 43.791 40.214 1 38.38 ? C5A Z97 767 B 1 
HETATM 20 O OP1 Z97 . . . M 5 21.656 41.591 41.115 1 48.29 ? OP1 Z97 767 B 1 
HETATM 21 O OP2 Z97 . . . M 5 22.096 42.931 43.219 1 38.49 ? OP2 Z97 767 B 1 
HETATM 22 O OP3 Z97 . . . M 5 23.617 40.962 42.543 1 47.52 ? OP3 Z97 767 B 1 
HETATM 23 O OP4 Z97 . . . M 5 23.659 43.151 41.248 1 39.54 ? OP4 Z97 767 B 1 
HETATM 24 O OXT Z97 . . . M 5 22.961 46.844 30.981 1 33.47 ? OXT Z97 767 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    46 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           24 
#