data_5DK6
#
_model_server_result.job_id            YYZnnjPpXjXgq0OPXnQPAg 
_model_server_result.datetime_utc      '2024-11-29 15:47:10' 
_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          5dk6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    5DK6 
#
_exptl.entry_id    5DK6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              75.067 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCINE 
_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         120 
_cell.entry_id            5DK6 
_cell.length_a            145.427 
_cell.length_b            145.427 
_cell.length_c            70.341 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DK6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
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 
PISA dimeric 2 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,B,C,D 1 1 
A,B,C,D 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 10_666 -y+1,-x+1,-z+7/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 72.7135 125.943476 82.0645 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 A C SER 22 A SER -1 1_555 A N MSE 23 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 A C MSE 23 A MSE 1 1_555 A N LYS 24 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale3 A C ALA 30 A ALA 8 1_555 A N MSE 31 A MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale4 A C MSE 31 A MSE 9 1_555 A N GLU 32 A GLU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale5 A C PHE 141 A PHE 119 1_555 A N MSE 142 A MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale6 A C MSE 142 A MSE 120 1_555 A N PRO 143 A PRO 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale7 A C PHE 179 A PHE 157 1_555 A N MSE 180 A MSE 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale8 A C MSE 180 A MSE 158 1_555 A N THR 181 A THR 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale9 A C THR 195 A THR 173 1_555 A N MSE 196 A MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale10 A C MSE 196 A MSE 174 1_555 A N ALA 197 A ALA 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale11 A C GLU 200 A GLU 178 1_555 A N MSE 201 A MSE 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale12 A C MSE 201 A MSE 179 1_555 A N GLU 202 A GLU 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale13 A C ASN 252 A ASN 230 1_555 A N MSE 253 A MSE 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale14 A C MSE 253 A MSE 231 1_555 A N LEU 254 A LEU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_chem_comp.formula           'C2 H5 N O2' 
_chem_comp.formula_weight    75.067 
_chem_comp.id                GLY 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              GLYCINE 
_chem_comp.type              '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 GLY sing 136 n n 
N H GLY sing 137 n n 
N H2 GLY sing 138 n n 
CA C GLY sing 139 n n 
CA HA2 GLY sing 140 n n 
CA HA3 GLY sing 141 n n 
C O GLY doub 142 n n 
C OXT GLY sing 143 n n 
OXT HXT GLY sing 144 n n 
#
_atom_sites.entry_id                     5DK6 
_atom_sites.fract_transf_matrix[1][1]    0.006876 
_atom_sites.fract_transf_matrix[1][2]    0.00397 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00794 
_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]    0.014216 
_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
B 2 GLY A 1 301 301 GLY GLY . 
C 3 ADE A 1 302 302 ADE ADE . 
D 4 HOH A 1 401 401 HOH HOH . 
D 4 HOH A 2 402 402 HOH HOH . 
D 4 HOH A 3 403 403 HOH HOH . 
D 4 HOH A 4 404 404 HOH HOH . 
D 4 HOH A 5 405 405 HOH HOH . 
D 4 HOH A 6 406 406 HOH HOH . 
D 4 HOH A 7 407 407 HOH HOH . 
D 4 HOH A 8 408 408 HOH HOH . 
D 4 HOH A 9 409 409 HOH HOH . 
D 4 HOH A 10 410 410 HOH HOH . 
D 4 HOH A 11 411 411 HOH HOH . 
D 4 HOH A 12 412 412 HOH HOH . 
D 4 HOH A 13 413 413 HOH HOH . 
D 4 HOH A 14 414 414 HOH HOH . 
D 4 HOH A 15 415 415 HOH HOH . 
D 4 HOH A 16 416 416 HOH HOH . 
D 4 HOH A 17 417 417 HOH HOH . 
D 4 HOH A 18 418 418 HOH HOH . 
D 4 HOH A 19 419 419 HOH HOH . 
D 4 HOH A 20 420 420 HOH HOH . 
D 4 HOH A 21 421 421 HOH HOH . 
D 4 HOH A 22 422 422 HOH HOH . 
D 4 HOH A 23 423 423 HOH HOH . 
D 4 HOH A 24 424 424 HOH HOH . 
D 4 HOH A 25 425 425 HOH HOH . 
D 4 HOH A 26 426 426 HOH HOH . 
D 4 HOH A 27 427 427 HOH HOH . 
D 4 HOH A 28 428 428 HOH HOH . 
D 4 HOH A 29 429 429 HOH HOH . 
D 4 HOH A 30 430 430 HOH HOH . 
D 4 HOH A 31 431 431 HOH HOH . 
D 4 HOH A 32 432 432 HOH HOH . 
D 4 HOH A 33 433 433 HOH HOH . 
D 4 HOH A 34 434 434 HOH HOH . 
D 4 HOH A 35 435 435 HOH HOH . 
D 4 HOH A 36 436 436 HOH HOH . 
D 4 HOH A 37 437 437 HOH HOH . 
D 4 HOH A 38 438 438 HOH HOH . 
D 4 HOH A 39 439 439 HOH HOH . 
D 4 HOH A 40 440 440 HOH HOH . 
D 4 HOH A 41 441 441 HOH HOH . 
D 4 HOH A 42 442 442 HOH HOH . 
D 4 HOH A 43 443 443 HOH HOH . 
D 4 HOH A 44 444 444 HOH HOH . 
D 4 HOH A 45 445 445 HOH HOH . 
D 4 HOH A 46 446 446 HOH HOH . 
D 4 HOH A 47 447 447 HOH HOH . 
D 4 HOH A 48 448 448 HOH HOH . 
D 4 HOH A 49 449 449 HOH HOH . 
D 4 HOH A 50 450 450 HOH HOH . 
D 4 HOH A 51 451 451 HOH HOH . 
D 4 HOH A 52 452 452 HOH HOH . 
D 4 HOH A 53 453 453 HOH HOH . 
D 4 HOH A 54 454 454 HOH HOH . 
D 4 HOH A 55 455 455 HOH HOH . 
D 4 HOH A 56 456 456 HOH HOH . 
D 4 HOH A 57 457 457 HOH HOH . 
D 4 HOH A 58 458 458 HOH HOH . 
D 4 HOH A 59 459 459 HOH HOH . 
D 4 HOH A 60 460 460 HOH HOH . 
D 4 HOH A 61 461 461 HOH HOH . 
D 4 HOH A 62 462 462 HOH HOH . 
D 4 HOH A 63 463 463 HOH HOH . 
D 4 HOH A 64 464 464 HOH HOH . 
D 4 HOH A 65 465 465 HOH HOH . 
D 4 HOH A 66 466 466 HOH HOH . 
D 4 HOH A 67 467 467 HOH HOH . 
D 4 HOH A 68 468 468 HOH HOH . 
D 4 HOH A 69 469 469 HOH HOH . 
D 4 HOH A 70 470 470 HOH HOH . 
D 4 HOH A 71 471 471 HOH HOH . 
D 4 HOH A 72 472 472 HOH HOH . 
D 4 HOH A 73 473 473 HOH HOH . 
D 4 HOH A 74 474 474 HOH HOH . 
D 4 HOH A 75 475 475 HOH HOH . 
D 4 HOH A 76 476 476 HOH HOH . 
D 4 HOH A 77 477 477 HOH HOH . 
D 4 HOH A 78 478 478 HOH HOH . 
D 4 HOH A 79 479 479 HOH HOH . 
D 4 HOH A 80 480 480 HOH HOH . 
D 4 HOH A 81 481 481 HOH HOH . 
D 4 HOH A 82 482 482 HOH HOH . 
D 4 HOH A 83 483 483 HOH HOH . 
D 4 HOH A 84 484 484 HOH HOH . 
D 4 HOH A 85 485 485 HOH HOH . 
D 4 HOH A 86 486 486 HOH HOH . 
D 4 HOH A 87 487 487 HOH HOH . 
D 4 HOH A 88 488 488 HOH HOH . 
D 4 HOH A 89 489 489 HOH HOH . 
D 4 HOH A 90 490 490 HOH HOH . 
D 4 HOH A 91 491 491 HOH HOH . 
D 4 HOH A 92 492 492 HOH HOH . 
D 4 HOH A 93 493 493 HOH HOH . 
D 4 HOH A 94 494 494 HOH HOH . 
D 4 HOH A 95 495 495 HOH HOH . 
D 4 HOH A 96 496 496 HOH HOH . 
D 4 HOH A 97 497 497 HOH HOH . 
D 4 HOH A 98 498 498 HOH HOH . 
D 4 HOH A 99 499 499 HOH HOH . 
D 4 HOH A 100 500 500 HOH HOH . 
D 4 HOH A 101 501 501 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 N GLY . . . B 2 32.699 53.395 54.521 1 63.6 ? N GLY 301 A 1 
HETATM 2 C CA GLY . . . B 2 31.427 53.464 53.826 1 62.61 ? CA GLY 301 A 1 
HETATM 3 C C GLY . . . B 2 31.534 54.232 52.524 1 63.53 ? C GLY 301 A 1 
HETATM 4 O O GLY . . . B 2 31.297 53.685 51.444 1 63.58 ? O GLY 301 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           4 
#