data_1BDA
#
_model_server_result.job_id            6BMuPdKSoc_3kD9GKOrRUw 
_model_server_result.datetime_utc      '2024-11-24 18:11:31' 
_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          1bda 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":245}' 
#
_entry.id    1BDA 
#
_exptl.entry_id    1BDA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              627.133 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide' 
_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            1BDA 
_cell.length_a            43.99 
_cell.length_b            80.78 
_cell.length_c            159.16 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1BDA 
_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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_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,E 1 1 
B,D,F 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D 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 2 A CYS 1 1_555 A SG CYS 133 A CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf2 A SG CYS 45 A CYS 42 1_555 A SG CYS 61 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
disulf ? disulf3 A SG CYS 53 A CYS 50 1_555 A SG CYS 122 A CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 A SG CYS 147 A CYS 136 1_555 A SG CYS 222 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf5 A SG CYS 179 A CYS 168 1_555 A SG CYS 195 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf6 A SG CYS 212 A CYS 191 1_555 A SG CYS 240 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf7 B SG CYS 2 B CYS 1 1_555 B SG CYS 133 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf8 B SG CYS 45 B CYS 42 1_555 B SG CYS 61 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf9 B SG CYS 53 B CYS 50 1_555 B SG CYS 122 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf10 B SG CYS 147 B CYS 136 1_555 B SG CYS 222 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf11 B SG CYS 179 B CYS 168 1_555 B SG CYS 195 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf12 B SG CYS 212 B CYS 191 1_555 B SG CYS 240 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
covale ? covale1 A NE2 HIS 60 A HIS 57 1_555 C CE 2Z0 . A 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? 
covale ? covale2 A OG SER 216 A SER 195 1_555 C CC 2Z0 . A 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? 
covale ? covale3 B NE2 HIS 60 B HIS 57 1_555 D CE 2Z0 . B 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.527 ? 
covale ? covale4 B OG SER 216 B SER 195 1_555 D CC 2Z0 . B 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? 
#
_chem_comp.formula           'C26 H37 Cl N7 O7 S 1' 
_chem_comp.formula_weight    627.133 
_chem_comp.id                2Z0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide' 
_chem_comp.type              peptide-like 
_chem_comp.pdbx_synonyms     dansyl-Glu-Gly-Arg-chloromethyl-ketone 
#
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 2Z0 doub 1 n y 
C1 C8A 2Z0 sing 2 n y 
C1 H1 2Z0 sing 3 n n 
C2 C3 2Z0 sing 4 n y 
C2 S 2Z0 sing 5 n n 
C3 C4 2Z0 doub 6 n y 
C3 H3 2Z0 sing 7 n n 
C4 C4A 2Z0 sing 8 n y 
C4 H4 2Z0 sing 9 n n 
C4A C5 2Z0 doub 10 n y 
C4A C8A 2Z0 sing 11 n y 
C5 C6 2Z0 sing 12 n y 
C5 N 2Z0 sing 13 n n 
C6 C7 2Z0 doub 14 n y 
C6 H6 2Z0 sing 15 n n 
C7 C8 2Z0 sing 16 n y 
C7 H7 2Z0 sing 17 n n 
C8 C8A 2Z0 doub 18 n y 
C8 H8 2Z0 sing 19 n n 
N CM1 2Z0 sing 20 n n 
N CM2 2Z0 sing 21 n n 
CM1 HM11 2Z0 sing 22 n n 
CM1 HM12 2Z0 sing 23 n n 
CM1 HM13 2Z0 sing 24 n n 
CM2 HM21 2Z0 sing 25 n n 
CM2 HM22 2Z0 sing 26 n n 
CM2 HM23 2Z0 sing 27 n n 
S O1S 2Z0 doub 28 n n 
S N1 2Z0 sing 29 n n 
S O2S 2Z0 doub 30 n n 
N1 CA 2Z0 sing 31 n n 
N1 H 2Z0 sing 32 n n 
CA C 2Z0 sing 33 n n 
CA CB 2Z0 sing 34 n n 
CA HA 2Z0 sing 35 n n 
C O 2Z0 doub 36 n n 
C N2 2Z0 sing 37 n n 
CB CG 2Z0 sing 38 n n 
CB HB2 2Z0 sing 39 n n 
CB HB3 2Z0 sing 40 n n 
CG CD 2Z0 sing 41 n n 
CG HG2 2Z0 sing 42 n n 
CG HG3 2Z0 sing 43 n n 
CD OE1 2Z0 doub 44 n n 
CD OE2 2Z0 sing 45 n n 
OE2 HE2 2Z0 sing 46 n n 
N2 CA1 2Z0 sing 47 n n 
N2 H2 2Z0 sing 48 n n 
CA1 C9 2Z0 sing 49 n n 
CA1 HA2 2Z0 sing 50 n n 
CA1 HA3 2Z0 sing 51 n n 
C9 O1 2Z0 doub 52 n n 
C9 N3 2Z0 sing 53 n n 
N3 CA2 2Z0 sing 54 n n 
N3 H5 2Z0 sing 55 n n 
CA2 CC 2Z0 sing 56 n n 
CA2 CB1 2Z0 sing 57 n n 
CA2 HA1 2Z0 sing 58 n n 
CC O2 2Z0 doub 59 n n 
CC CE 2Z0 sing 60 n n 
CB1 CG1 2Z0 sing 61 n n 
CB1 HB21 2Z0 sing 62 n n 
CB1 HB31 2Z0 sing 63 n n 
CG1 CD1 2Z0 sing 64 n n 
CG1 HG21 2Z0 sing 65 n n 
CG1 HG31 2Z0 sing 66 n n 
CD1 NE 2Z0 sing 67 n n 
CD1 HD2 2Z0 sing 68 n n 
CD1 HD3 2Z0 sing 69 n n 
NE CZ 2Z0 sing 70 n n 
NE HE 2Z0 sing 71 n n 
CZ NH1 2Z0 sing 72 n n 
CZ NH2 2Z0 doub 73 n n 
NH1 HH11 2Z0 sing 74 n n 
NH1 HH12 2Z0 sing 75 n n 
NH2 HH21 2Z0 sing 76 n n 
NH2 HH22 2Z0 sing 77 n n 
CE H11 2Z0 sing 78 n n 
CE H21 2Z0 sing 79 n n 
CL1 CE 2Z0 sing 80 n n 
#
_atom_sites.entry_id                     1BDA 
_atom_sites.fract_transf_matrix[1][1]    0.022732 
_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]    0.012379 
_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]    0.006283 
_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 2Z0 A 1 245 1 2Z0 DSY . 
D 2 2Z0 B 1 245 1 2Z0 DSY . 
E 3 HOH A 1 246 3 HOH HOH . 
E 3 HOH A 2 247 4 HOH HOH . 
E 3 HOH A 3 248 5 HOH HOH . 
E 3 HOH A 4 249 6 HOH HOH . 
E 3 HOH A 5 250 7 HOH HOH . 
E 3 HOH A 6 251 11 HOH HOH . 
E 3 HOH A 7 252 12 HOH HOH . 
E 3 HOH A 8 253 14 HOH HOH . 
E 3 HOH A 9 254 16 HOH HOH . 
E 3 HOH A 10 255 17 HOH HOH . 
E 3 HOH A 11 256 2 HOH HOH . 
F 3 HOH B 1 246 11 HOH HOH . 
F 3 HOH B 2 247 15 HOH HOH . 
F 3 HOH B 3 248 20 HOH HOH . 
F 3 HOH B 4 249 21 HOH HOH . 
F 3 HOH B 5 250 22 HOH HOH . 
F 3 HOH B 6 251 23 HOH HOH . 
F 3 HOH B 7 252 24 HOH HOH . 
F 3 HOH B 8 253 15 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 2Z0 . . . D 2 13.395 53.086 36.425 1 23.42 ? C1 2Z0 245 B 1 
HETATM 2 C C2 2Z0 . . . D 2 13.977 53.659 35.365 1 21.99 ? C2 2Z0 245 B 1 
HETATM 3 C C3 2Z0 . . . D 2 15.277 54.14 35.416 1 20.01 ? C3 2Z0 245 B 1 
HETATM 4 C C4 2Z0 . . . D 2 16.007 54.035 36.599 1 21.57 ? C4 2Z0 245 B 1 
HETATM 5 C C4A 2Z0 . . . D 2 15.407 53.439 37.723 1 25.13 ? C4A 2Z0 245 B 1 
HETATM 6 C C5 2Z0 . . . D 2 16.066 53.294 38.946 1 28.22 ? C5 2Z0 245 B 1 
HETATM 7 C C6 2Z0 . . . D 2 15.46 52.716 40.006 1 27.01 ? C6 2Z0 245 B 1 
HETATM 8 C C7 2Z0 . . . D 2 14.174 52.25 39.894 1 27.9 ? C7 2Z0 245 B 1 
HETATM 9 C C8 2Z0 . . . D 2 13.472 52.36 38.728 1 24.72 ? C8 2Z0 245 B 1 
HETATM 10 C C8A 2Z0 . . . D 2 14.079 52.957 37.623 1 24.42 ? C8A 2Z0 245 B 1 
HETATM 11 N N 2Z0 . . . D 2 17.418 53.729 39.236 1 32.96 ? N 2Z0 245 B 1 
HETATM 12 C CM1 2Z0 . . . D 2 18.551 52.93 38.682 1 35.79 ? CM1 2Z0 245 B 1 
HETATM 13 C CM2 2Z0 . . . D 2 17.58 54.929 40.105 1 35.1 ? CM2 2Z0 245 B 1 
HETATM 14 S S 2Z0 . . . D 2 12.898 53.659 34.097 1 25.97 ? S 2Z0 245 B 1 
HETATM 15 O O1S 2Z0 . . . D 2 11.408 53.753 34.708 1 27.01 ? O1S 2Z0 245 B 1 
HETATM 16 O O2S 2Z0 . . . D 2 13.195 54.875 33.118 1 25.8 ? O2S 2Z0 245 B 1 
HETATM 17 N N1 2Z0 . . . D 2 12.595 52.026 33.968 1 20.33 ? N1 2Z0 245 B 1 
HETATM 18 C CA 2Z0 . . . D 2 13.411 51.532 32.882 1 19.17 ? CA 2Z0 245 B 1 
HETATM 19 C C 2Z0 . . . D 2 12.772 51.916 31.569 1 19.35 ? C 2Z0 245 B 1 
HETATM 20 O O 2Z0 . . . D 2 11.543 52.02 31.468 1 20.68 ? O 2Z0 245 B 1 
HETATM 21 C CB 2Z0 . . . D 2 13.548 50.011 32.937 1 18.59 ? CB 2Z0 245 B 1 
HETATM 22 C CG 2Z0 . . . D 2 14.398 49.509 34.067 1 20.55 ? CG 2Z0 245 B 1 
HETATM 23 C CD 2Z0 . . . D 2 13.609 48.726 35.073 1 21.66 ? CD 2Z0 245 B 1 
HETATM 24 O OE1 2Z0 . . . D 2 12.925 49.375 35.895 1 21.35 ? OE1 2Z0 245 B 1 
HETATM 25 O OE2 2Z0 . . . D 2 13.68 47.47 35.041 1 20.51 ? OE2 2Z0 245 B 1 
HETATM 26 N N2 2Z0 . . . D 2 13.615 52.191 30.583 1 18.7 ? N2 2Z0 245 B 1 
HETATM 27 C CA1 2Z0 . . . D 2 13.12 52.519 29.258 1 17.04 ? CA1 2Z0 245 B 1 
HETATM 28 C C9 2Z0 . . . D 2 12.592 51.242 28.624 1 14.15 ? C9 2Z0 245 B 1 
HETATM 29 O O1 2Z0 . . . D 2 12.784 50.128 29.155 1 10.36 ? O1 2Z0 245 B 1 
HETATM 30 O O2 2Z0 . . . D 2 11.56 48.994 24.783 1 11.71 ? O2 2Z0 245 B 1 
HETATM 31 N N3 2Z0 . . . D 2 11.924 51.397 27.491 1 10.17 ? N3 2Z0 245 B 1 
HETATM 32 C CA2 2Z0 . . . D 2 11.366 50.252 26.809 1 12.03 ? CA2 2Z0 245 B 1 
HETATM 33 C CC 2Z0 . . . D 2 11.563 50.358 25.31 1 14.52 ? CC 2Z0 245 B 1 
HETATM 34 C CB1 2Z0 . . . D 2 9.893 50.08 27.211 1 10.83 ? CB1 2Z0 245 B 1 
HETATM 35 C CG1 2Z0 . . . D 2 9.635 49.809 28.701 1 9.82 ? CG1 2Z0 245 B 1 
HETATM 36 C CD1 2Z0 . . . D 2 8.148 49.622 28.929 1 10.28 ? CD1 2Z0 245 B 1 
HETATM 37 N NE 2Z0 . . . D 2 7.801 49.281 30.308 1 12.22 ? NE 2Z0 245 B 1 
HETATM 38 C CZ 2Z0 . . . D 2 6.549 49.191 30.762 1 12.53 ? CZ 2Z0 245 B 1 
HETATM 39 N NH2 2Z0 . . . D 2 6.326 48.851 32.02 1 14.15 ? NH2 2Z0 245 B 1 
HETATM 40 N NH1 2Z0 . . . D 2 5.516 49.414 29.956 1 5.26 ? NH1 2Z0 245 B 1 
HETATM 41 C CE 2Z0 . . . D 2 12.825 51.26 24.963 1 18.22 ? CE 2Z0 245 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           41 
#