data_4D9N
#
_model_server_result.job_id            jVlwjaSn5duBJ_FMHrnvBg 
_model_server_result.datetime_utc      '2025-07-08 02:30:04' 
_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          4d9n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    4D9N 
#
_exptl.entry_id    4D9N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              105.093 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            D-SERINE 
_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            4D9N 
_cell.length_a            85.611 
_cell.length_b            85.611 
_cell.length_c            207.652 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D9N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
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 265 A CYS 265 1_555 A SG CYS 291 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 B SG CYS 265 B CYS 265 1_555 B SG CYS 291 B CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 A C PHE 76 A PHE 76 1_555 A N LLP 77 A LLP 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 A C LLP 77 A LLP 77 1_555 A N MET 78 A MET 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale3 B C PHE 76 B PHE 76 1_555 B N LLP 77 B LLP 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale4 B C LLP 77 B LLP 77 1_555 B N MET 78 B MET 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
#
_chem_comp.formula           'C3 H7 N O3' 
_chem_comp.formula_weight    105.093 
_chem_comp.id                DSN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              D-SERINE 
_chem_comp.type              'd-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 DSN sing 83 n n 
N H DSN sing 84 n n 
N H2 DSN sing 85 n n 
CA C DSN sing 86 n n 
CA CB DSN sing 87 n n 
CA HA DSN sing 88 n n 
C O DSN doub 89 n n 
C OXT DSN sing 90 n n 
OXT HXT DSN sing 91 n n 
CB OG DSN sing 92 n n 
CB HB2 DSN sing 93 n n 
CB HB3 DSN sing 94 n n 
OG HG DSN sing 95 n n 
#
_atom_sites.entry_id                     4D9N 
_atom_sites.fract_transf_matrix[1][1]    0.011681 
_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]    0.011681 
_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]    0.004816 
_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 DSN A 1 401 1 DSN DSN . 
D 2 DSN B 1 401 1 DSN DSN . 
E 3 HOH A 1 501 2 HOH HOH . 
E 3 HOH A 2 502 12 HOH HOH . 
E 3 HOH A 3 503 15 HOH HOH . 
E 3 HOH A 4 504 18 HOH HOH . 
E 3 HOH A 5 505 34 HOH HOH . 
E 3 HOH A 6 506 38 HOH HOH . 
E 3 HOH A 7 507 101 HOH HOH . 
E 3 HOH A 8 508 104 HOH HOH . 
E 3 HOH A 9 509 105 HOH HOH . 
E 3 HOH A 10 510 106 HOH HOH . 
E 3 HOH A 11 511 107 HOH HOH . 
E 3 HOH A 12 512 108 HOH HOH . 
E 3 HOH A 13 513 116 HOH HOH . 
E 3 HOH A 14 514 121 HOH HOH . 
E 3 HOH A 15 515 125 HOH HOH . 
E 3 HOH A 16 516 128 HOH HOH . 
E 3 HOH A 17 517 133 HOH HOH . 
E 3 HOH A 18 518 134 HOH HOH . 
E 3 HOH A 19 519 135 HOH HOH . 
E 3 HOH A 20 520 137 HOH HOH . 
E 3 HOH A 21 521 138 HOH HOH . 
E 3 HOH A 22 522 139 HOH HOH . 
E 3 HOH A 23 523 141 HOH HOH . 
E 3 HOH A 24 524 9 HOH HOH . 
E 3 HOH A 25 525 14 HOH HOH . 
E 3 HOH A 26 526 17 HOH HOH . 
E 3 HOH A 27 527 27 HOH HOH . 
E 3 HOH A 28 528 28 HOH HOH . 
E 3 HOH A 29 529 29 HOH HOH . 
E 3 HOH A 30 530 32 HOH HOH . 
E 3 HOH A 31 531 35 HOH HOH . 
E 3 HOH A 32 532 43 HOH HOH . 
E 3 HOH A 33 533 53 HOH HOH . 
E 3 HOH A 34 534 54 HOH HOH . 
E 3 HOH A 35 535 57 HOH HOH . 
E 3 HOH A 36 536 63 HOH HOH . 
E 3 HOH A 37 537 66 HOH HOH . 
E 3 HOH A 38 538 73 HOH HOH . 
E 3 HOH A 39 539 80 HOH HOH . 
E 3 HOH A 40 540 95 HOH HOH . 
E 3 HOH A 41 541 139 HOH HOH . 
E 3 HOH A 42 542 148 HOH HOH . 
E 3 HOH A 43 543 150 HOH HOH . 
E 3 HOH A 44 544 155 HOH HOH . 
F 3 HOH B 1 501 1 HOH HOH . 
F 3 HOH B 2 502 3 HOH HOH . 
F 3 HOH B 3 503 7 HOH HOH . 
F 3 HOH B 4 504 9 HOH HOH . 
F 3 HOH B 5 505 14 HOH HOH . 
F 3 HOH B 6 506 21 HOH HOH . 
F 3 HOH B 7 507 33 HOH HOH . 
F 3 HOH B 8 508 109 HOH HOH . 
F 3 HOH B 9 509 110 HOH HOH . 
F 3 HOH B 10 510 111 HOH HOH . 
F 3 HOH B 11 511 112 HOH HOH . 
F 3 HOH B 12 512 113 HOH HOH . 
F 3 HOH B 13 513 114 HOH HOH . 
F 3 HOH B 14 514 115 HOH HOH . 
F 3 HOH B 15 515 117 HOH HOH . 
F 3 HOH B 16 516 118 HOH HOH . 
F 3 HOH B 17 517 120 HOH HOH . 
F 3 HOH B 18 518 122 HOH HOH . 
F 3 HOH B 19 519 123 HOH HOH . 
F 3 HOH B 20 520 124 HOH HOH . 
F 3 HOH B 21 521 126 HOH HOH . 
F 3 HOH B 22 522 127 HOH HOH . 
F 3 HOH B 23 523 129 HOH HOH . 
F 3 HOH B 24 524 130 HOH HOH . 
F 3 HOH B 25 525 131 HOH HOH . 
F 3 HOH B 26 526 132 HOH HOH . 
F 3 HOH B 27 527 140 HOH HOH . 
F 3 HOH B 28 528 142 HOH HOH . 
F 3 HOH B 29 529 1 HOH HOH . 
F 3 HOH B 30 530 3 HOH HOH . 
F 3 HOH B 31 531 6 HOH HOH . 
F 3 HOH B 32 532 7 HOH HOH . 
F 3 HOH B 33 533 8 HOH HOH . 
F 3 HOH B 34 534 16 HOH HOH . 
F 3 HOH B 35 535 23 HOH HOH . 
F 3 HOH B 36 536 25 HOH HOH . 
F 3 HOH B 37 537 34 HOH HOH . 
F 3 HOH B 38 538 36 HOH HOH . 
F 3 HOH B 39 539 38 HOH HOH . 
F 3 HOH B 40 540 42 HOH HOH . 
F 3 HOH B 41 541 49 HOH HOH . 
F 3 HOH B 42 542 60 HOH HOH . 
F 3 HOH B 43 543 64 HOH HOH . 
F 3 HOH B 44 544 67 HOH HOH . 
F 3 HOH B 45 545 76 HOH HOH . 
F 3 HOH B 46 546 88 HOH HOH . 
F 3 HOH B 47 547 92 HOH HOH . 
F 3 HOH B 48 548 96 HOH HOH . 
F 3 HOH B 49 549 97 HOH HOH . 
F 3 HOH B 50 550 108 HOH HOH . 
F 3 HOH B 51 551 114 HOH HOH . 
F 3 HOH B 52 552 141 HOH HOH . 
F 3 HOH B 53 553 161 HOH HOH . 
F 3 HOH B 54 554 167 HOH HOH . 
F 3 HOH B 55 555 171 HOH HOH . 
F 3 HOH B 56 556 173 HOH HOH . 
F 3 HOH B 57 557 325 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 DSN . . . C 2 23.803 59.39 74.253 1 36.17 ? N DSN 401 A 1 
HETATM 2 C CA DSN . . . C 2 24.825 60.296 73.656 1 36.77 ? CA DSN 401 A 1 
HETATM 3 C C DSN . . . C 2 25.291 59.744 72.327 1 35.88 ? C DSN 401 A 1 
HETATM 4 O O DSN . . . C 2 24.938 60.22 71.248 1 34.37 ? O DSN 401 A 1 
HETATM 5 O OXT DSN . . . C 2 26.054 58.778 72.279 1 36.07 ? OXT DSN 401 A 1 
HETATM 6 C CB DSN . . . C 2 24.209 61.693 73.54 1 37.54 ? CB DSN 401 A 1 
HETATM 7 O OG DSN . . . C 2 24.87 62.59 74.444 1 37.74 ? OG DSN 401 A 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           7 
#