data_7PM4
#
_model_server_result.job_id            xTAYaYAQ899VDD8Ot90zjQ 
_model_server_result.datetime_utc      '2025-08-14 06:55:25' 
_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          7pm4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":502}' 
#
_entry.id    7PM4 
#
_exptl.entry_id    7PM4 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              147.172 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL 
_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            7PM4 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7PM4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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 
_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    ? 
_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 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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 241 A CYS 266 1_555 A SG CYS 249 A CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 B SG CYS 241 B CYS 266 1_555 B SG CYS 249 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 C SG CYS 241 C CYS 266 1_555 C SG CYS 249 C CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 D SG CYS 241 D CYS 266 1_555 D SG CYS 249 D CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale1 A ND2 ASN 211 A ASN 236 1_555 E C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale2 B ND2 ASN 211 B ASN 236 1_555 G C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale3 C ND2 ASN 211 C ASN 236 1_555 I C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale4 D ND2 ASN 211 D ASN 236 1_555 K C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
#
_chem_comp.formula           'C6 H13 N O3' 
_chem_comp.formula_weight    147.172 
_chem_comp.id                DFU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DEOXYFUCONOJIRIMYCIN 
#
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
C1 C2 DFU sing 83 n n 
C1 N5 DFU sing 84 n n 
C1 H11 DFU sing 85 n n 
C1 H12 DFU sing 86 n n 
C2 C3 DFU sing 87 n n 
C2 O2 DFU sing 88 n n 
C2 H2 DFU sing 89 n n 
C3 C4 DFU sing 90 n n 
C3 O3 DFU sing 91 n n 
C3 H3 DFU sing 92 n n 
C4 C5 DFU sing 93 n n 
C4 O4 DFU sing 94 n n 
C4 H4 DFU sing 95 n n 
C5 C6 DFU sing 96 n n 
C5 N5 DFU sing 97 n n 
C5 H5 DFU sing 98 n n 
C6 H61 DFU sing 99 n n 
C6 H62 DFU sing 100 n n 
C6 H63 DFU sing 101 n n 
O4 HO4 DFU sing 102 n n 
O3 HO3 DFU sing 103 n n 
O2 HO2 DFU sing 104 n n 
N5 HN5 DFU sing 105 n n 
#
_atom_sites.entry_id                     7PM4 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 NAG A 1 501 501 NAG NAG . 
F 3 DFU A 1 502 502 DFU DFU . 
G 2 NAG B 1 501 501 NAG NAG . 
H 3 DFU B 1 502 502 DFU DFU . 
I 2 NAG C 1 501 501 NAG NAG . 
J 3 DFU C 1 502 502 DFU DFU . 
K 2 NAG D 1 501 501 NAG NAG . 
L 3 DFU D 1 502 502 DFU DFU . 
M 4 HOH A 1 601 490 HOH HOH . 
M 4 HOH A 2 602 488 HOH HOH . 
M 4 HOH A 3 603 487 HOH HOH . 
M 4 HOH A 4 604 482 HOH HOH . 
M 4 HOH A 5 605 495 HOH HOH . 
M 4 HOH A 6 606 486 HOH HOH . 
M 4 HOH A 7 607 485 HOH HOH . 
M 4 HOH A 8 608 484 HOH HOH . 
M 4 HOH A 9 609 494 HOH HOH . 
M 4 HOH A 10 610 481 HOH HOH . 
M 4 HOH A 11 611 496 HOH HOH . 
M 4 HOH A 12 612 483 HOH HOH . 
M 4 HOH A 13 613 491 HOH HOH . 
M 4 HOH A 14 614 489 HOH HOH . 
M 4 HOH A 15 615 492 HOH HOH . 
N 4 HOH B 1 601 490 HOH HOH . 
N 4 HOH B 2 602 488 HOH HOH . 
N 4 HOH B 3 603 487 HOH HOH . 
N 4 HOH B 4 604 482 HOH HOH . 
N 4 HOH B 5 605 495 HOH HOH . 
N 4 HOH B 6 606 486 HOH HOH . 
N 4 HOH B 7 607 485 HOH HOH . 
N 4 HOH B 8 608 484 HOH HOH . 
N 4 HOH B 9 609 494 HOH HOH . 
N 4 HOH B 10 610 481 HOH HOH . 
N 4 HOH B 11 611 496 HOH HOH . 
N 4 HOH B 12 612 483 HOH HOH . 
N 4 HOH B 13 613 491 HOH HOH . 
N 4 HOH B 14 614 489 HOH HOH . 
N 4 HOH B 15 615 492 HOH HOH . 
O 4 HOH C 1 601 490 HOH HOH . 
O 4 HOH C 2 602 488 HOH HOH . 
O 4 HOH C 3 603 487 HOH HOH . 
O 4 HOH C 4 604 482 HOH HOH . 
O 4 HOH C 5 605 495 HOH HOH . 
O 4 HOH C 6 606 486 HOH HOH . 
O 4 HOH C 7 607 485 HOH HOH . 
O 4 HOH C 8 608 484 HOH HOH . 
O 4 HOH C 9 609 494 HOH HOH . 
O 4 HOH C 10 610 481 HOH HOH . 
O 4 HOH C 11 611 496 HOH HOH . 
O 4 HOH C 12 612 483 HOH HOH . 
O 4 HOH C 13 613 491 HOH HOH . 
O 4 HOH C 14 614 489 HOH HOH . 
O 4 HOH C 15 615 492 HOH HOH . 
P 4 HOH D 1 601 490 HOH HOH . 
P 4 HOH D 2 602 488 HOH HOH . 
P 4 HOH D 3 603 487 HOH HOH . 
P 4 HOH D 4 604 482 HOH HOH . 
P 4 HOH D 5 605 495 HOH HOH . 
P 4 HOH D 6 606 486 HOH HOH . 
P 4 HOH D 7 607 485 HOH HOH . 
P 4 HOH D 8 608 484 HOH HOH . 
P 4 HOH D 9 609 494 HOH HOH . 
P 4 HOH D 10 610 481 HOH HOH . 
P 4 HOH D 11 611 496 HOH HOH . 
P 4 HOH D 12 612 483 HOH HOH . 
P 4 HOH D 13 613 491 HOH HOH . 
P 4 HOH D 14 614 489 HOH HOH . 
P 4 HOH D 15 615 492 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 C C1 DFU . . . J 3 168.92 169.248 138.132 1 24.93 ? C1 DFU 502 C 1 
HETATM 2 C C2 DFU . . . J 3 167.696 168.349 138.332 1 24.93 ? C2 DFU 502 C 1 
HETATM 3 C C3 DFU . . . J 3 168.113 166.952 138.686 1 24.93 ? C3 DFU 502 C 1 
HETATM 4 C C4 DFU . . . J 3 168.973 166.934 139.92 1 24.93 ? C4 DFU 502 C 1 
HETATM 5 C C5 DFU . . . J 3 170.183 167.871 139.794 1 24.93 ? C5 DFU 502 C 1 
HETATM 6 C C6 DFU . . . J 3 170.874 167.967 141.132 1 24.93 ? C6 DFU 502 C 1 
HETATM 7 O O4 DFU . . . J 3 168.185 167.335 141.032 1 24.93 ? O4 DFU 502 C 1 
HETATM 8 O O3 DFU . . . J 3 166.942 166.15 138.915 1 24.93 ? O3 DFU 502 C 1 
HETATM 9 O O2 DFU . . . J 3 166.935 168.323 137.13 1 24.93 ? O2 DFU 502 C 1 
HETATM 10 N N5 DFU . . . J 3 169.804 169.252 139.347 1 24.93 ? N5 DFU 502 C 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           343 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           10 
#