data_2G5R
#
_model_server_result.job_id            k9OEVxuI30qFN0w7twdwTw 
_model_server_result.datetime_utc      '2025-04-18 04:25:51' 
_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          2g5r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":145}' 
#
_entry.id    2G5R 
#
_exptl.entry_id    2G5R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              393.347 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' 
_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            2G5R 
_cell.length_a            52.928 
_cell.length_b            52.928 
_cell.length_c            93.236 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2G5R 
_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                      3 
_struct_asym.id                             C 
_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
disulf ? disulf1 A SG CYS 24 A CYS 41 1_555 D SG CYS . A CYS 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 A SG CYS 29 A CYS 46 1_555 A SG CYS 89 A CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
covale ? covale1 B C1 NAG . A NAG 1 1_555 A ND2 ASN 88 A ASN 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
#
_chem_comp.formula           'C14 H23 N3 O10' 
_chem_comp.formula_weight    393.347 
_chem_comp.id                NXD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     'METHYL 5-(ACETYLAMINO)-9-{[AMINO(OXO)ACETYL]AMINO}-3,5,9-TRIDEOXY-D-GLYCERO-ALPHA-D-GLUCO-NON-2-ULOPYRANOSIDONIC ACID;ALPHA METHYL -9-(AMINOOXALYL-AMINO)-9-DEOXYNEU5AC;OXAMIDO-NEU5AC;methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid;methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-D-galacto-non-2-ulosidonic acid;methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-galacto-non-2-ulosidonic acid' 
#
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
C11 C10 NXD sing 267 n n 
C11 H111 NXD sing 268 n n 
C11 H113 NXD sing 269 n n 
C11 H112 NXD sing 270 n n 
C10 O10 NXD doub 271 n n 
C10 N5 NXD sing 272 n n 
N5 C5 NXD sing 273 n n 
N5 HN5 NXD sing 274 n n 
C5 C4 NXD sing 275 n n 
C5 C6 NXD sing 276 n n 
C5 H5 NXD sing 277 n n 
C4 O4 NXD sing 278 n n 
C4 C3 NXD sing 279 n n 
C4 H4 NXD sing 280 n n 
O4 HO4 NXD sing 281 n n 
C3 C2 NXD sing 282 n n 
C3 H32 NXD sing 283 n n 
C3 H31 NXD sing 284 n n 
C2 C1 NXD sing 285 n n 
C2 O2 NXD sing 286 n n 
C2 O6 NXD sing 287 n n 
C1 O1B NXD sing 288 n n 
C1 O1A NXD doub 289 n n 
O1B HO1B NXD sing 290 n n 
O2 CB NXD sing 291 n n 
CB HB1 NXD sing 292 n n 
CB HB2 NXD sing 293 n n 
CB HB3 NXD sing 294 n n 
O6 C6 NXD sing 295 n n 
C6 C7 NXD sing 296 n n 
C6 H6 NXD sing 297 n n 
C7 O7 NXD sing 298 n n 
C7 C8 NXD sing 299 n n 
C7 H7 NXD sing 300 n n 
O7 HO7 NXD sing 301 n n 
C8 O8 NXD sing 302 n n 
C8 C9 NXD sing 303 n n 
C8 H8 NXD sing 304 n n 
O8 HO8 NXD sing 305 n n 
C9 NAB NXD sing 306 n n 
C9 H92 NXD sing 307 n n 
C9 H91 NXD sing 308 n n 
NAB CAC NXD sing 309 n n 
NAB HAB NXD sing 310 n n 
CAC OAD NXD doub 311 n n 
CAC CAF NXD sing 312 n n 
CAF OAG NXD doub 313 n n 
CAF NAK NXD sing 314 n n 
NAK HAK1 NXD sing 315 n n 
NAK HAK2 NXD sing 316 n n 
#
_atom_sites.entry_id                     2G5R 
_atom_sites.fract_transf_matrix[1][1]    0.01889 
_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]    0.01889 
_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]    0.01072 
_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 NAG A 1 1 1 NAG NAG . 
C 3 NXD A 1 145 1 NXD NXD . 
D 4 CYS A 1 1001 1 CYS CYS . 
E 5 HOH A 1 1002 2 HOH HOH . 
E 5 HOH A 2 1003 3 HOH HOH . 
E 5 HOH A 3 1004 4 HOH HOH . 
E 5 HOH A 4 1005 5 HOH HOH . 
E 5 HOH A 5 1006 6 HOH HOH . 
E 5 HOH A 6 1007 7 HOH HOH . 
E 5 HOH A 7 1008 8 HOH HOH . 
E 5 HOH A 8 1009 9 HOH HOH . 
E 5 HOH A 9 1010 10 HOH HOH . 
E 5 HOH A 10 1011 11 HOH HOH . 
E 5 HOH A 11 1012 12 HOH HOH . 
E 5 HOH A 12 1013 13 HOH HOH . 
E 5 HOH A 13 1014 14 HOH HOH . 
E 5 HOH A 14 1015 15 HOH HOH . 
E 5 HOH A 15 1016 16 HOH HOH . 
E 5 HOH A 16 1017 17 HOH HOH . 
E 5 HOH A 17 1018 18 HOH HOH . 
E 5 HOH A 18 1019 19 HOH HOH . 
E 5 HOH A 19 1020 20 HOH HOH . 
E 5 HOH A 20 1021 21 HOH HOH . 
E 5 HOH A 21 1022 22 HOH HOH . 
E 5 HOH A 22 1023 23 HOH HOH . 
E 5 HOH A 23 1024 24 HOH HOH . 
E 5 HOH A 24 1025 25 HOH HOH . 
E 5 HOH A 25 1026 26 HOH HOH . 
E 5 HOH A 26 1027 27 HOH HOH . 
E 5 HOH A 27 1028 28 HOH HOH . 
E 5 HOH A 28 1029 29 HOH HOH . 
E 5 HOH A 29 1030 30 HOH HOH . 
E 5 HOH A 30 1031 32 HOH HOH . 
E 5 HOH A 31 1032 33 HOH HOH . 
E 5 HOH A 32 1033 34 HOH HOH . 
E 5 HOH A 33 1034 35 HOH HOH . 
E 5 HOH A 34 1035 36 HOH HOH . 
E 5 HOH A 35 1036 37 HOH HOH . 
E 5 HOH A 36 1037 38 HOH HOH . 
E 5 HOH A 37 1038 39 HOH HOH . 
E 5 HOH A 38 1039 40 HOH HOH . 
E 5 HOH A 39 1040 41 HOH HOH . 
E 5 HOH A 40 1041 42 HOH HOH . 
E 5 HOH A 41 1042 43 HOH HOH . 
E 5 HOH A 42 1043 44 HOH HOH . 
E 5 HOH A 43 1044 45 HOH HOH . 
E 5 HOH A 44 1045 46 HOH HOH . 
E 5 HOH A 45 1046 47 HOH HOH . 
E 5 HOH A 46 1047 48 HOH HOH . 
E 5 HOH A 47 1048 49 HOH HOH . 
E 5 HOH A 48 1049 50 HOH HOH . 
E 5 HOH A 49 1050 51 HOH HOH . 
E 5 HOH A 50 1051 52 HOH HOH . 
E 5 HOH A 51 1052 53 HOH HOH . 
E 5 HOH A 52 1053 54 HOH HOH . 
E 5 HOH A 53 1054 55 HOH HOH . 
E 5 HOH A 54 1055 56 HOH HOH . 
E 5 HOH A 55 1056 57 HOH HOH . 
E 5 HOH A 56 1057 58 HOH HOH . 
E 5 HOH A 57 1058 59 HOH HOH . 
E 5 HOH A 58 1059 60 HOH HOH . 
E 5 HOH A 59 1060 62 HOH HOH . 
E 5 HOH A 60 1061 63 HOH HOH . 
E 5 HOH A 61 1062 64 HOH HOH . 
E 5 HOH A 62 1063 65 HOH HOH . 
E 5 HOH A 63 1064 66 HOH HOH . 
E 5 HOH A 64 1065 67 HOH HOH . 
E 5 HOH A 65 1066 68 HOH HOH . 
E 5 HOH A 66 1067 69 HOH HOH . 
E 5 HOH A 67 1068 70 HOH HOH . 
E 5 HOH A 68 1069 71 HOH HOH . 
E 5 HOH A 69 1070 72 HOH HOH . 
E 5 HOH A 70 1071 73 HOH HOH . 
E 5 HOH A 71 1072 74 HOH HOH . 
E 5 HOH A 72 1073 75 HOH HOH . 
E 5 HOH A 73 1074 76 HOH HOH . 
E 5 HOH A 74 1075 77 HOH HOH . 
E 5 HOH A 75 1076 78 HOH HOH . 
E 5 HOH A 76 1077 79 HOH HOH . 
E 5 HOH A 77 1078 80 HOH HOH . 
E 5 HOH A 78 1079 81 HOH HOH . 
E 5 HOH A 79 1080 82 HOH HOH . 
E 5 HOH A 80 1081 83 HOH HOH . 
E 5 HOH A 81 1082 84 HOH HOH . 
E 5 HOH A 82 1083 85 HOH HOH . 
E 5 HOH A 83 1084 91 HOH HOH . 
E 5 HOH A 84 1085 95 HOH HOH . 
E 5 HOH A 85 1086 99 HOH HOH . 
E 5 HOH A 86 1087 110 HOH HOH . 
E 5 HOH A 87 1088 111 HOH HOH . 
E 5 HOH A 88 1089 112 HOH HOH . 
E 5 HOH A 89 1090 114 HOH HOH . 
E 5 HOH A 90 1091 115 HOH HOH . 
E 5 HOH A 91 1092 117 HOH HOH . 
E 5 HOH A 92 1093 118 HOH HOH . 
E 5 HOH A 93 1094 121 HOH HOH . 
E 5 HOH A 94 1095 124 HOH HOH . 
E 5 HOH A 95 1096 125 HOH HOH . 
E 5 HOH A 96 1097 127 HOH HOH . 
E 5 HOH A 97 1098 128 HOH HOH . 
E 5 HOH A 98 1099 130 HOH HOH . 
E 5 HOH A 99 1100 134 HOH HOH . 
E 5 HOH A 100 1101 136 HOH HOH . 
E 5 HOH A 101 1102 144 HOH HOH . 
E 5 HOH A 102 1103 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 C C11 NXD . . . C 3 -5.337 13.357 30.493 1 43.31 ? C11 NXD 145 A 1 
HETATM 2 C C10 NXD . . . C 3 -3.822 13.569 30.313 1 44.15 ? C10 NXD 145 A 1 
HETATM 3 O O10 NXD . . . C 3 -3.294 14.628 30.654 1 43.63 ? O10 NXD 145 A 1 
HETATM 4 N N5 NXD . . . C 3 -3.135 12.554 29.782 1 42.66 ? N5 NXD 145 A 1 
HETATM 5 C C5 NXD . . . C 3 -3.736 11.283 29.348 1 42.99 ? C5 NXD 145 A 1 
HETATM 6 C C4 NXD . . . C 3 -3.254 10.133 30.233 1 43.04 ? C4 NXD 145 A 1 
HETATM 7 O O4 NXD . . . C 3 -3.683 10.361 31.576 1 43.51 ? O4 NXD 145 A 1 
HETATM 8 C C3 NXD . . . C 3 -3.805 8.781 29.733 1 43.18 ? C3 NXD 145 A 1 
HETATM 9 C C2 NXD . . . C 3 -3.504 8.562 28.23 1 42.46 ? C2 NXD 145 A 1 
HETATM 10 C C1 NXD . . . C 3 -2 8.274 28.042 1 42.27 ? C1 NXD 145 A 1 
HETATM 11 O O1B NXD . . . C 3 -1.427 7.467 28.773 1 40.99 ? O1B NXD 145 A 1 
HETATM 12 O O1A NXD . . . C 3 -1.36 8.848 27.16 1 40.8 ? O1A NXD 145 A 1 
HETATM 13 O O2 NXD . . . C 3 -4.28 7.426 27.769 1 43.3 ? O2 NXD 145 A 1 
HETATM 14 C CB NXD . . . C 3 -4.238 7.196 26.338 1 44.04 ? CB NXD 145 A 1 
HETATM 15 O O6 NXD . . . C 3 -3.91 9.735 27.45 1 42.32 ? O6 NXD 145 A 1 
HETATM 16 C C6 NXD . . . C 3 -3.348 11.004 27.884 1 42.41 ? C6 NXD 145 A 1 
HETATM 17 C C7 NXD . . . C 3 -3.791 12.083 26.885 1 42.83 ? C7 NXD 145 A 1 
HETATM 18 O O7 NXD . . . C 3 -5.23 12.152 26.834 1 42.28 ? O7 NXD 145 A 1 
HETATM 19 C C8 NXD . . . C 3 -3.222 11.837 25.477 1 43.12 ? C8 NXD 145 A 1 
HETATM 20 O O8 NXD . . . C 3 -1.928 11.216 25.547 1 41.45 ? O8 NXD 145 A 1 
HETATM 21 C C9 NXD . . . C 3 -3.125 13.162 24.728 1 44.1 ? C9 NXD 145 A 1 
HETATM 22 N NAB NXD . . . C 3 -2.927 12.963 23.287 1 46.07 ? NAB NXD 145 A 1 
HETATM 23 C CAC NXD . . . C 3 -3.918 12.704 22.433 1 47.8 ? CAC NXD 145 A 1 
HETATM 24 O OAD NXD . . . C 3 -5.101 12.593 22.763 1 48.13 ? OAD NXD 145 A 1 
HETATM 25 C CAF NXD . . . C 3 -3.538 12.534 20.962 1 48.39 ? CAF NXD 145 A 1 
HETATM 26 O OAG NXD . . . C 3 -2.35 12.656 20.674 1 49.96 ? OAG NXD 145 A 1 
HETATM 27 N NAK NXD . . . C 3 -4.48 12.271 20.056 1 48.73 ? NAK NXD 145 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#