data_7KEM
#
_model_server_result.job_id            E6JgNys3zwYrCweww5DGTg 
_model_server_result.datetime_utc      '2025-08-31 04:12:35' 
_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          7kem 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":501}' 
#
_entry.id    7KEM 
#
_exptl.entry_id    7KEM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              191.205 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-CARBOXYLYSINE 
_entity.pdbx_number_of_molecules    1 
_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            7KEM 
_cell.length_a            117.528 
_cell.length_b            121.051 
_cell.length_c            122.699 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KEM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        24 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G 1 1 
B,H,I,J,K,L,M 2 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             H 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 G CD DGL . A DGL 505 1_555 H N 6CL . B 6CL 501 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.336 ? 
covale ? covale2 G CD DGL . A DGL 505 1_555 H N 6CL . B 6CL 501 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.226 ? 
metalc ? metalc1 A SD MET 157 A MET 157 1_555 D PT1 0JC . A 0JC 502 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.736 ? 
metalc ? metalc2 A ND1 HIS 347 A HIS 347 1_555 C PT1 0JC . A 0JC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc3 B SD MET 153 B MET 153 1_555 M PT1 0JC . B 0JC 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? 
metalc ? metalc4 B ND1 HIS 347 B HIS 347 1_555 J PT1 0JC . B 0JC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
#
_chem_comp.formula           'C7 H15 N2 O4 1' 
_chem_comp.formula_weight    191.205 
_chem_comp.id                6CL 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              6-CARBOXYLYSINE 
_chem_comp.type              'l-peptide linking' 
_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
N CA 6CL sing 31 n n 
N H2 6CL sing 32 n n 
N H 6CL sing 33 n n 
CA CB 6CL sing 34 n n 
CA C 6CL sing 35 n n 
CA HA 6CL sing 36 n n 
CB CG 6CL sing 37 n n 
CB HB2 6CL sing 38 n n 
CB HB3 6CL sing 39 n n 
CG CD 6CL sing 40 n n 
CG HG2 6CL sing 41 n n 
CG HG3 6CL sing 42 n n 
CD CE 6CL sing 43 n n 
CD HD2 6CL sing 44 n n 
CD HD3 6CL sing 45 n n 
CE CZ 6CL sing 46 n n 
CE NZ 6CL sing 47 n n 
CE HE 6CL sing 48 n n 
CZ OH1 6CL doub 49 n n 
CZ OH2 6CL sing 50 n n 
OH2 HH2 6CL sing 51 n n 
NZ HZ1 6CL sing 52 n n 
NZ HZ2 6CL sing 53 n n 
NZ HZ3 6CL sing 54 n n 
C O 6CL doub 55 n n 
C OXT 6CL sing 56 n n 
OXT HXT 6CL sing 57 n n 
#
_atom_sites.entry_id                     7KEM 
_atom_sites.fract_transf_matrix[1][1]    0.008509 
_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]    0.008261 
_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]    0.00815 
_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 0JC A 1 501 501 0JC 0JC . 
D 2 0JC A 1 502 502 0JC 0JC . 
E 2 0JC A 1 503 503 0JC 0JC . 
F 2 0JC A 1 504 504 0JC 0JC . 
G 3 DGL A 1 505 505 DGL DGL . 
H 4 6CL B 1 501 506 6CL 6CL . 
I 5 PT B 1 502 501 PT PT . 
J 2 0JC B 1 503 502 0JC 0JC . 
K 2 0JC B 1 504 503 0JC 0JC . 
L 2 0JC B 1 505 504 0JC 0JC . 
M 2 0JC B 1 506 505 0JC 0JC . 
#
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 N 6CL . A . H 4 127.169 132.194 23.465 0 35 ? N 6CL 501 B 1 
HETATM 2 N N 6CL . B . H 4 137.093 127.606 19.598 0 36.74 ? N 6CL 501 B 1 
HETATM 3 C CA 6CL . A . H 4 126.029 131.352 22.991 0 32.49 ? CA 6CL 501 B 1 
HETATM 4 C CA 6CL . B . H 4 138.342 128.208 20.082 0 33.92 ? CA 6CL 501 B 1 
HETATM 5 C CB 6CL . A . H 4 124.698 131.481 23.678 0 24.77 ? CB 6CL 501 B 1 
HETATM 6 C CB 6CL . B . H 4 139.673 127.474 19.872 0 29.4 ? CB 6CL 501 B 1 
HETATM 7 C CG 6CL . A . H 4 124.588 132.41 24.872 0 30.13 ? CG 6CL 501 B 1 
HETATM 8 C CG 6CL . B . H 4 139.66 126.138 19.134 0 34.53 ? CG 6CL 501 B 1 
HETATM 9 C CD 6CL . A . H 4 124.437 131.732 26.141 0 22.32 ? CD 6CL 501 B 1 
HETATM 10 C CD 6CL . B . H 4 140.104 125.02 20.029 0 35.13 ? CD 6CL 501 B 1 
HETATM 11 C CE 6CL . A . H 4 123.187 132.119 26.902 0 26.48 ? CE 6CL 501 B 1 
HETATM 12 C CE 6CL . B . H 4 141.236 124.213 19.455 0 36.73 ? CE 6CL 501 B 1 
HETATM 13 C CZ 6CL . A . H 4 123.019 131.485 28.266 0 34.31 ? CZ 6CL 501 B 1 
HETATM 14 C CZ 6CL . B . H 4 141.542 122.913 20.19 0 41 ? CZ 6CL 501 B 1 
HETATM 15 O OH1 6CL . A . H 4 123.931 130.789 28.744 0 36.43 ? OH1 6CL 501 B 1 
HETATM 16 O OH1 6CL . B . H 4 140.687 122.328 20.844 0 41.65 ? OH1 6CL 501 B 1 
HETATM 17 O OH2 6CL . A . H 4 121.957 131.684 28.846 0 31.81 ? OH2 6CL 501 B 1 
HETATM 18 O OH2 6CL . B . H 4 142.69 122.501 20.104 0 40.55 ? OH2 6CL 501 B 1 
HETATM 19 N NZ 6CL . A . H 4 121.941 131.769 26.326 0 27.84 ? NZ 6CL 501 B 1 
HETATM 20 N NZ 6CL . B . H 4 142.537 124.813 19.621 0 29.7 ? NZ 6CL 501 B 1 
HETATM 21 C C 6CL . A . H 4 126.065 131.934 21.556 0 31.86 ? C 6CL 501 B 1 
HETATM 22 C C 6CL . B . H 4 138.271 129.533 19.323 0 32.84 ? C 6CL 501 B 1 
HETATM 23 O O 6CL . A . H 4 126.653 131.395 20.614 0 33.41 ? O 6CL 501 B 1 
HETATM 24 O O 6CL . B . H 4 137.841 130.573 19.791 0 34.32 ? O 6CL 501 B 1 
HETATM 25 O OXT 6CL . A . H 4 125.589 132.965 21.266 0 32.51 ? OXT 6CL 501 B 1 
HETATM 26 O OXT 6CL . B . H 4 138.594 129.642 18.212 0 30.96 ? OXT 6CL 501 B 1 
#
_model_server_stats.io_time_ms              99 
_model_server_stats.parse_time_ms           103 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           496 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#