data_5JQB
#
_model_server_result.job_id            foyjt87wz5Y-pD7RS-KzTw 
_model_server_result.datetime_utc      '2024-10-14 05:24:27' 
_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          5jqb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":601}' 
#
_entry.id    5JQB 
#
_exptl.entry_id    5JQB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    4 
_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            5JQB 
_cell.length_a            113.76 
_cell.length_b            113.76 
_cell.length_c            306.15 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JQB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,G,H,I,J,K,L,M,N,O 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -56.88 98.51905 0 
3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -113.76 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 G N N 
#
_pdbx_entity_branch.entity_id    3 
_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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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
3 n C NAG 1 C 1 NAG D 621 NAG 
3 n C NAG 2 C 2 NAG D 622 NAG 
3 n C BMA 3 C 3 BMA D 623 BMA 
#
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 26 A CYS 53 1_555 B SG CYS 108 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 81 A CYS 108 1_555 A SG CYS 108 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 A SG CYS 94 A CYS 121 1_555 A SG CYS 120 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
covale ? covale1 A ND2 ASN 201 A ASN 228 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale2 A ND2 ASN 211 A ASN 238 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale3 A ND2 ASN 230 A ASN 257 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale4 A ND2 ASN 241 A ASN 268 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale5 B ND2 ASN 62 B ASN 563 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                NAG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-beta-D-glucopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE 
#
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 NAG sing 307 n n 
C1 O1 NAG sing 308 n n 
C1 O5 NAG sing 309 n n 
C1 H1 NAG sing 310 n n 
C2 C3 NAG sing 311 n n 
C2 N2 NAG sing 312 n n 
C2 H2 NAG sing 313 n n 
C3 C4 NAG sing 314 n n 
C3 O3 NAG sing 315 n n 
C3 H3 NAG sing 316 n n 
C4 C5 NAG sing 317 n n 
C4 O4 NAG sing 318 n n 
C4 H4 NAG sing 319 n n 
C5 C6 NAG sing 320 n n 
C5 O5 NAG sing 321 n n 
C5 H5 NAG sing 322 n n 
C6 O6 NAG sing 323 n n 
C6 H61 NAG sing 324 n n 
C6 H62 NAG sing 325 n n 
C7 C8 NAG sing 326 n n 
C7 N2 NAG sing 327 n n 
C7 O7 NAG doub 328 n n 
C8 H81 NAG sing 329 n n 
C8 H82 NAG sing 330 n n 
C8 H83 NAG sing 331 n n 
N2 HN2 NAG sing 332 n n 
O1 HO1 NAG sing 333 n n 
O3 HO3 NAG sing 334 n n 
O4 HO4 NAG sing 335 n n 
O6 HO6 NAG sing 336 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 
NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     5JQB 
_atom_sites.fract_transf_matrix[1][1]    0.00879 
_atom_sites.fract_transf_matrix[1][2]    0.005075 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01015 
_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]    0.003266 
_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
D 4 NAG A 1 601 2 NAG NAG . 
E 4 NAG A 1 602 10 NAG NAG . 
F 4 NAG A 1 603 11 NAG NAG . 
G 4 NAG A 1 604 12 NAG NAG . 
H 5 GOL A 1 605 3 GOL GOL . 
I 5 GOL A 1 606 5 GOL GOL . 
J 5 GOL A 1 607 6 GOL GOL . 
K 5 GOL B 1 701 2 GOL GOL . 
L 5 GOL B 1 702 7 GOL GOL . 
M 6 IBP B 1 706 1 IBP IBP . 
N 7 HOH A 1 701 6 HOH HOH . 
N 7 HOH A 2 702 139 HOH HOH . 
N 7 HOH A 3 703 4 HOH HOH . 
N 7 HOH A 4 704 17 HOH HOH . 
N 7 HOH A 5 705 37 HOH HOH . 
N 7 HOH A 6 706 48 HOH HOH . 
N 7 HOH A 7 707 136 HOH HOH . 
N 7 HOH A 8 708 20 HOH HOH . 
N 7 HOH A 9 709 10 HOH HOH . 
N 7 HOH A 10 710 1 HOH HOH . 
N 7 HOH A 11 711 120 HOH HOH . 
N 7 HOH A 12 712 8 HOH HOH . 
N 7 HOH A 13 713 5 HOH HOH . 
N 7 HOH A 14 714 41 HOH HOH . 
N 7 HOH A 15 715 119 HOH HOH . 
N 7 HOH A 16 716 134 HOH HOH . 
N 7 HOH A 17 717 9 HOH HOH . 
N 7 HOH A 18 718 135 HOH HOH . 
N 7 HOH A 19 719 15 HOH HOH . 
N 7 HOH A 20 720 123 HOH HOH . 
N 7 HOH A 21 721 83 HOH HOH . 
N 7 HOH A 22 722 54 HOH HOH . 
N 7 HOH A 23 723 12 HOH HOH . 
N 7 HOH A 24 724 137 HOH HOH . 
N 7 HOH A 25 725 33 HOH HOH . 
N 7 HOH A 26 726 69 HOH HOH . 
N 7 HOH A 27 727 72 HOH HOH . 
N 7 HOH A 28 728 22 HOH HOH . 
N 7 HOH A 29 729 140 HOH HOH . 
N 7 HOH A 30 730 68 HOH HOH . 
N 7 HOH A 31 731 80 HOH HOH . 
N 7 HOH A 32 732 107 HOH HOH . 
N 7 HOH A 33 733 127 HOH HOH . 
N 7 HOH A 34 734 130 HOH HOH . 
N 7 HOH A 35 735 121 HOH HOH . 
N 7 HOH A 36 736 118 HOH HOH . 
N 7 HOH A 37 737 131 HOH HOH . 
N 7 HOH A 38 738 40 HOH HOH . 
N 7 HOH A 39 739 53 HOH HOH . 
N 7 HOH A 40 740 111 HOH HOH . 
O 7 HOH B 1 801 74 HOH HOH . 
O 7 HOH B 2 802 104 HOH HOH . 
O 7 HOH B 3 803 52 HOH HOH . 
O 7 HOH B 4 804 59 HOH HOH . 
O 7 HOH B 5 805 18 HOH HOH . 
O 7 HOH B 6 806 3 HOH HOH . 
O 7 HOH B 7 807 87 HOH HOH . 
O 7 HOH B 8 808 113 HOH HOH . 
O 7 HOH B 9 809 19 HOH HOH . 
O 7 HOH B 10 810 77 HOH HOH . 
O 7 HOH B 11 811 65 HOH HOH . 
O 7 HOH B 12 812 102 HOH HOH . 
O 7 HOH B 13 813 64 HOH HOH . 
O 7 HOH B 14 814 55 HOH HOH . 
O 7 HOH B 15 815 144 HOH HOH . 
O 7 HOH B 16 816 21 HOH HOH . 
O 7 HOH B 17 817 143 HOH HOH . 
O 7 HOH B 18 818 24 HOH HOH . 
O 7 HOH B 19 819 133 HOH HOH . 
O 7 HOH B 20 820 27 HOH HOH . 
O 7 HOH B 21 821 128 HOH HOH . 
O 7 HOH B 22 822 108 HOH HOH . 
O 7 HOH B 23 823 84 HOH HOH . 
O 7 HOH B 24 824 126 HOH HOH . 
O 7 HOH B 25 825 129 HOH HOH . 
O 7 HOH B 26 826 49 HOH HOH . 
O 7 HOH B 27 827 99 HOH HOH . 
O 7 HOH B 28 828 105 HOH HOH . 
O 7 HOH B 29 829 36 HOH HOH . 
O 7 HOH B 30 830 60 HOH HOH . 
O 7 HOH B 31 831 141 HOH HOH . 
O 7 HOH B 32 832 63 HOH HOH . 
O 7 HOH B 33 833 142 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 NAG . . . D 4 -37.858 -0.881 -40.265 1 69.49 ? C1 NAG 601 A 1 
HETATM 2 C C2 NAG . . . D 4 -37.793 0.289 -39.289 1 73.78 ? C2 NAG 601 A 1 
HETATM 3 C C3 NAG . . . D 4 -36.966 1.402 -39.924 1 74.59 ? C3 NAG 601 A 1 
HETATM 4 C C4 NAG . . . D 4 -35.575 0.864 -40.25 1 74 ? C4 NAG 601 A 1 
HETATM 5 C C5 NAG . . . D 4 -35.671 -0.392 -41.119 1 73.02 ? C5 NAG 601 A 1 
HETATM 6 C C6 NAG . . . D 4 -34.312 -1.041 -41.368 1 72.91 ? C6 NAG 601 A 1 
HETATM 7 C C7 NAG . . . D 4 -39.482 1.125 -37.695 1 77.35 ? C7 NAG 601 A 1 
HETATM 8 C C8 NAG . . . D 4 -40.922 1.52 -37.53 1 77.94 ? C8 NAG 601 A 1 
HETATM 9 N N2 NAG . . . D 4 -39.137 0.724 -38.926 1 75.07 ? N2 NAG 601 A 1 
HETATM 10 O O3 NAG . . . D 4 -36.867 2.53 -39.047 1 76.91 ? O3 NAG 601 A 1 
HETATM 11 O O4 NAG . . . D 4 -34.82 1.876 -40.922 1 77.06 ? O4 NAG 601 A 1 
HETATM 12 O O5 NAG . . . D 4 -36.527 -1.353 -40.495 1 71.5 ? O5 NAG 601 A 1 
HETATM 13 O O6 NAG . . . D 4 -33.753 -1.531 -40.144 1 73.18 ? O6 NAG 601 A 1 
HETATM 14 O O7 NAG . . . D 4 -38.702 1.183 -36.753 1 78.37 ? O7 NAG 601 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           370 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#