data_2DF3
#
_model_server_result.job_id            aUASHCwozPyIhwoSYYfqZQ 
_model_server_result.datetime_utc      '2025-02-05 11:47:14' 
_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          2df3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":310}' 
#
_entry.id    2DF3 
#
_exptl.entry_id    2DF3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              121.158 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            CYSTEINE 
_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            2DF3 
_cell.length_a            53.07 
_cell.length_b            53.07 
_cell.length_c            92.88 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2DF3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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    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                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 2 2 1 GAL NAG C1 O1 . O3 HO3 . sing 
2 ? 2 3 2 SIA GAL C2 O2 . O3 HO3 . sing 
3 ? 2 4 1 SIA NAG C2 O2 . O6 HO6 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n B NAG 1 B 1 NAG D 201 NAG 
2 n B GAL 2 B 2 GAL D 202 GAL 
2 n B SIA 3 B 3 SIA D 203 SIA 
2 n B SIA 4 B 4 SIA D 200 SIA 
#
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 29 A CYS 46 1_555 A SG CYS 89 A CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
covale ? covale1 A ND2 ASN 88 A ASN 105 1_555 C C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale2 B O3 NAG . B NAG 1 1_555 B C1 GAL . B GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? 
covale ? covale3 B O6 NAG . B NAG 1 1_555 B C2 SIA . B SIA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 sing 
covale ? covale4 B O3 GAL . B GAL 2 1_555 B C2 SIA . B SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 sing 
#
_chem_comp.formula           'C3 H7 N O2 S' 
_chem_comp.formula_weight    121.158 
_chem_comp.id                CYS 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              CYSTEINE 
_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 CYS sing 70 n n 
N H CYS sing 71 n n 
N H2 CYS sing 72 n n 
CA C CYS sing 73 n n 
CA CB CYS sing 74 n n 
CA HA CYS sing 75 n n 
C O CYS doub 76 n n 
C OXT CYS sing 77 n n 
CB SG CYS sing 78 n n 
CB HB2 CYS sing 79 n n 
CB HB3 CYS sing 80 n n 
SG HG CYS sing 81 n n 
OXT HXT CYS sing 82 n n 
#
_atom_sites.entry_id                     2DF3 
_atom_sites.fract_transf_matrix[1][1]    0.01884 
_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]    0.01884 
_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]    0.01077 
_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 3 NAG A 1 301 301 NAG NAG . 
D 4 CYS A 1 310 201 CYS CYS . 
E 5 HOH A 1 401 1 HOH HOH . 
E 5 HOH A 2 402 2 HOH HOH . 
E 5 HOH A 3 403 3 HOH HOH . 
E 5 HOH A 4 404 5 HOH HOH . 
E 5 HOH A 5 405 6 HOH HOH . 
E 5 HOH A 6 406 7 HOH HOH . 
E 5 HOH A 7 407 8 HOH HOH . 
E 5 HOH A 8 408 9 HOH HOH . 
E 5 HOH A 9 409 10 HOH HOH . 
E 5 HOH A 10 410 11 HOH HOH . 
E 5 HOH A 11 411 12 HOH HOH . 
E 5 HOH A 12 412 13 HOH HOH . 
E 5 HOH A 13 413 14 HOH HOH . 
E 5 HOH A 14 414 15 HOH HOH . 
E 5 HOH A 15 415 16 HOH HOH . 
E 5 HOH A 16 416 17 HOH HOH . 
E 5 HOH A 17 417 18 HOH HOH . 
E 5 HOH A 18 418 19 HOH HOH . 
E 5 HOH A 19 419 20 HOH HOH . 
E 5 HOH A 20 420 21 HOH HOH . 
E 5 HOH A 21 421 22 HOH HOH . 
E 5 HOH A 22 422 23 HOH HOH . 
E 5 HOH A 23 423 24 HOH HOH . 
E 5 HOH A 24 424 25 HOH HOH . 
E 5 HOH A 25 425 29 HOH HOH . 
E 5 HOH A 26 426 31 HOH HOH . 
E 5 HOH A 27 427 32 HOH HOH . 
E 5 HOH A 28 428 34 HOH HOH . 
E 5 HOH A 29 429 35 HOH HOH . 
E 5 HOH A 30 430 36 HOH HOH . 
E 5 HOH A 31 431 38 HOH HOH . 
E 5 HOH A 32 432 40 HOH HOH . 
E 5 HOH A 33 433 41 HOH HOH . 
E 5 HOH A 34 434 43 HOH HOH . 
E 5 HOH A 35 435 44 HOH HOH . 
E 5 HOH A 36 436 46 HOH HOH . 
E 5 HOH A 37 437 49 HOH HOH . 
E 5 HOH A 38 438 50 HOH HOH . 
E 5 HOH A 39 439 51 HOH HOH . 
E 5 HOH A 40 440 52 HOH HOH . 
E 5 HOH A 41 441 53 HOH HOH . 
E 5 HOH A 42 442 57 HOH HOH . 
E 5 HOH A 43 443 58 HOH HOH . 
E 5 HOH A 44 444 60 HOH HOH . 
E 5 HOH A 45 445 61 HOH HOH . 
E 5 HOH A 46 446 65 HOH HOH . 
E 5 HOH A 47 447 68 HOH HOH . 
E 5 HOH A 48 448 69 HOH HOH . 
E 5 HOH A 49 449 70 HOH HOH . 
E 5 HOH A 50 450 72 HOH HOH . 
E 5 HOH A 51 451 73 HOH HOH . 
E 5 HOH A 52 452 75 HOH HOH . 
E 5 HOH A 53 453 76 HOH HOH . 
E 5 HOH A 54 454 77 HOH HOH . 
E 5 HOH A 55 455 78 HOH HOH . 
E 5 HOH A 56 456 79 HOH HOH . 
E 5 HOH A 57 457 81 HOH HOH . 
E 5 HOH A 58 458 82 HOH HOH . 
E 5 HOH A 59 459 83 HOH HOH . 
E 5 HOH A 60 460 84 HOH HOH . 
E 5 HOH A 61 461 85 HOH HOH . 
E 5 HOH A 62 462 86 HOH HOH . 
E 5 HOH A 63 463 87 HOH HOH . 
E 5 HOH A 64 464 89 HOH HOH . 
E 5 HOH A 65 465 90 HOH HOH . 
E 5 HOH A 66 466 92 HOH HOH . 
E 5 HOH A 67 467 93 HOH HOH . 
E 5 HOH A 68 468 94 HOH HOH . 
E 5 HOH A 69 469 95 HOH HOH . 
E 5 HOH A 70 470 96 HOH HOH . 
E 5 HOH A 71 471 99 HOH HOH . 
E 5 HOH A 72 472 100 HOH HOH . 
E 5 HOH A 73 473 101 HOH HOH . 
E 5 HOH A 74 474 102 HOH HOH . 
E 5 HOH A 75 475 103 HOH HOH . 
E 5 HOH A 76 476 104 HOH HOH . 
E 5 HOH A 77 477 105 HOH HOH . 
E 5 HOH A 78 478 106 HOH HOH . 
E 5 HOH A 79 479 107 HOH HOH . 
E 5 HOH A 80 480 108 HOH HOH . 
E 5 HOH A 81 481 109 HOH HOH . 
E 5 HOH A 82 482 110 HOH HOH . 
E 5 HOH A 83 483 111 HOH HOH . 
E 5 HOH A 84 484 114 HOH HOH . 
E 5 HOH A 85 485 115 HOH HOH . 
E 5 HOH A 86 486 116 HOH HOH . 
E 5 HOH A 87 487 119 HOH HOH . 
E 5 HOH A 88 488 125 HOH HOH . 
E 5 HOH A 89 489 126 HOH HOH . 
E 5 HOH A 90 490 127 HOH HOH . 
E 5 HOH A 91 491 131 HOH HOH . 
E 5 HOH A 92 492 133 HOH HOH . 
E 5 HOH A 93 493 134 HOH HOH . 
E 5 HOH A 94 494 146 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 CYS . . . D 4 12.994 -0.382 33.283 1 38.82 ? N CYS 310 A 1 
HETATM 2 C CA CYS . . . D 4 13.636 0.547 32.305 1 37.82 ? CA CYS 310 A 1 
HETATM 3 C C CYS . . . D 4 14.879 -0.057 31.637 1 39.51 ? C CYS 310 A 1 
HETATM 4 O O CYS . . . D 4 15.571 0.592 30.831 1 39.79 ? O CYS 310 A 1 
HETATM 5 C CB CYS . . . D 4 13.99 1.892 32.953 1 35.08 ? CB CYS 310 A 1 
HETATM 6 S SG CYS . . . D 4 13.647 2.073 34.71 1 32.67 ? SG CYS 310 A 1 
HETATM 7 O OXT CYS . . . D 4 15.231 -1.214 31.872 1 40.38 ? OXT CYS 310 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           7 
#