data_4D90
#
_model_server_result.job_id            XYnfHaecQCZ-tb41jrka2Q 
_model_server_result.datetime_utc      '2024-11-05 01:29:34' 
_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          4d90 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    4D90 
#
_exptl.entry_id    4D90 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_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         120 
_cell.entry_id            4D90 
_cell.length_a            82.68 
_cell.length_b            82.68 
_cell.length_c            56.422 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D90 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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 
? monomeric 1 author_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,K 1 1 
B,G,H,I,J,L 2 1 
A,B,C,D,E,F,G,H,I,J,K,L 3 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
? 3 D N N 
? 3 H 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 3 A CYS 26 1_555 A SG CYS 14 A CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 8 A CYS 31 1_555 A SG CYS 25 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 A SG CYS 27 A CYS 50 1_555 A SG CYS 36 A CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf4 A SG CYS 55 A CYS 78 1_555 A SG CYS 66 A CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf5 A SG CYS 60 A CYS 83 1_555 A SG CYS 82 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf6 A SG CYS 84 A CYS 107 1_555 A SG CYS 93 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
disulf ? disulf7 A SG CYS 100 A CYS 123 1_555 A SG CYS 111 A CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
disulf ? disulf8 A SG CYS 105 A CYS 128 1_555 A SG CYS 120 A CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf9 A SG CYS 122 A CYS 145 1_555 A SG CYS 131 A CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
disulf ? disulf10 B SG CYS 3 B CYS 26 1_555 B SG CYS 14 B CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf11 B SG CYS 8 B CYS 31 1_555 B SG CYS 25 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf12 B SG CYS 27 B CYS 50 1_555 B SG CYS 36 B CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf13 B SG CYS 55 B CYS 78 1_555 B SG CYS 66 B CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
disulf ? disulf14 B SG CYS 60 B CYS 83 1_555 B SG CYS 82 B CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf15 B SG CYS 84 B CYS 107 1_555 B SG CYS 93 B CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
disulf ? disulf16 B SG CYS 100 B CYS 123 1_555 B SG CYS 111 B CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
disulf ? disulf17 B SG CYS 105 B CYS 128 1_555 B SG CYS 120 B CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf18 B SG CYS 122 B CYS 145 1_555 B SG CYS 131 B CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
covale ? covale1 A OG1 THR 50 A THR 73 1_555 C C1 NGA . A NGA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale2 A OG1 THR 65 A THR 88 1_555 E C1 FUC . A FUC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? 
covale ? covale3 A ND2 ASN 117 A ASN 140 1_555 D C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale4 B OG1 THR 50 B THR 73 1_555 G C1 NGA . B NGA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale5 B OG1 THR 65 B THR 88 1_555 I C1 FUC . B FUC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? 
covale ? covale6 B ND2 ASN 117 B ASN 140 1_555 H C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
metalc ? metalc1 A OD1 ASN 96 A ASN 119 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc2 A O ILE 97 A ILE 120 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? 
metalc ? metalc3 A OE1 GLU 99 A GLU 122 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? 
metalc ? metalc4 A OD2 ASP 113 A ASP 136 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc5 A OD1 ASP 113 A ASP 136 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? 
metalc ? metalc6 A O LEU 114 A LEU 137 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? 
metalc ? metalc7 F CA CA . A CA 604 1_555 K O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? 
metalc ? metalc8 B OD1 ASN 96 B ASN 119 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? 
metalc ? metalc9 B O ILE 97 B ILE 120 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc10 B OE1 GLU 99 B GLU 122 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? 
metalc ? metalc11 B OD1 ASP 113 B ASP 136 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? 
metalc ? metalc12 B OD2 ASP 113 B ASP 136 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? 
metalc ? metalc13 B O LEU 114 B LEU 137 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? 
metalc ? metalc14 J CA CA . B CA 604 1_555 L O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
#
_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 260 n n 
C1 O1 NAG sing 261 n n 
C1 O5 NAG sing 262 n n 
C1 H1 NAG sing 263 n n 
C2 C3 NAG sing 264 n n 
C2 N2 NAG sing 265 n n 
C2 H2 NAG sing 266 n n 
C3 C4 NAG sing 267 n n 
C3 O3 NAG sing 268 n n 
C3 H3 NAG sing 269 n n 
C4 C5 NAG sing 270 n n 
C4 O4 NAG sing 271 n n 
C4 H4 NAG sing 272 n n 
C5 C6 NAG sing 273 n n 
C5 O5 NAG sing 274 n n 
C5 H5 NAG sing 275 n n 
C6 O6 NAG sing 276 n n 
C6 H61 NAG sing 277 n n 
C6 H62 NAG sing 278 n n 
C7 C8 NAG sing 279 n n 
C7 N2 NAG sing 280 n n 
C7 O7 NAG doub 281 n n 
C8 H81 NAG sing 282 n n 
C8 H82 NAG sing 283 n n 
C8 H83 NAG sing 284 n n 
N2 HN2 NAG sing 285 n n 
O1 HO1 NAG sing 286 n n 
O3 HO3 NAG sing 287 n n 
O4 HO4 NAG sing 288 n n 
O6 HO6 NAG sing 289 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                     4D90 
_atom_sites.fract_transf_matrix[1][1]    0.012095 
_atom_sites.fract_transf_matrix[1][2]    0.006983 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013966 
_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]    0.017724 
_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 NGA A 1 601 601 NGA NGA . 
D 3 NAG A 1 602 701 NAG NAG . 
E 4 FUC A 1 603 801 FUC FUC . 
F 5 CA A 1 604 901 CA CA . 
G 2 NGA B 1 601 601 NGA NGA . 
H 3 NAG B 1 602 701 NAG NAG . 
I 4 FUC B 1 603 801 FUC FUC . 
J 5 CA B 1 604 901 CA CA . 
K 6 HOH A 1 701 1 HOH HOH . 
K 6 HOH A 2 702 9 HOH HOH . 
K 6 HOH A 3 703 10 HOH HOH . 
K 6 HOH A 4 704 11 HOH HOH . 
K 6 HOH A 5 705 12 HOH HOH . 
K 6 HOH A 6 706 13 HOH HOH . 
K 6 HOH A 7 707 14 HOH HOH . 
K 6 HOH A 8 708 15 HOH HOH . 
K 6 HOH A 9 709 16 HOH HOH . 
K 6 HOH A 10 710 19 HOH HOH . 
K 6 HOH A 11 711 20 HOH HOH . 
K 6 HOH A 12 712 21 HOH HOH . 
K 6 HOH A 13 713 22 HOH HOH . 
K 6 HOH A 14 714 23 HOH HOH . 
K 6 HOH A 15 715 24 HOH HOH . 
K 6 HOH A 16 716 25 HOH HOH . 
K 6 HOH A 17 717 26 HOH HOH . 
K 6 HOH A 18 718 27 HOH HOH . 
K 6 HOH A 19 719 35 HOH HOH . 
K 6 HOH A 20 720 36 HOH HOH . 
K 6 HOH A 21 721 38 HOH HOH . 
K 6 HOH A 22 722 39 HOH HOH . 
K 6 HOH A 23 723 41 HOH HOH . 
K 6 HOH A 24 724 42 HOH HOH . 
K 6 HOH A 25 725 44 HOH HOH . 
K 6 HOH A 26 726 45 HOH HOH . 
K 6 HOH A 27 727 46 HOH HOH . 
K 6 HOH A 28 728 47 HOH HOH . 
K 6 HOH A 29 729 48 HOH HOH . 
K 6 HOH A 30 730 49 HOH HOH . 
K 6 HOH A 31 731 50 HOH HOH . 
L 6 HOH B 1 701 2 HOH HOH . 
L 6 HOH B 2 702 3 HOH HOH . 
L 6 HOH B 3 703 4 HOH HOH . 
L 6 HOH B 4 704 5 HOH HOH . 
L 6 HOH B 5 705 6 HOH HOH . 
L 6 HOH B 6 706 7 HOH HOH . 
L 6 HOH B 7 707 8 HOH HOH . 
L 6 HOH B 8 708 17 HOH HOH . 
L 6 HOH B 9 709 18 HOH HOH . 
L 6 HOH B 10 710 28 HOH HOH . 
L 6 HOH B 11 711 29 HOH HOH . 
L 6 HOH B 12 712 30 HOH HOH . 
L 6 HOH B 13 713 31 HOH HOH . 
L 6 HOH B 14 714 32 HOH HOH . 
L 6 HOH B 15 715 33 HOH HOH . 
L 6 HOH B 16 716 34 HOH HOH . 
L 6 HOH B 17 717 37 HOH HOH . 
L 6 HOH B 18 718 40 HOH HOH . 
L 6 HOH B 19 719 43 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 3 -7.461 -9.571 4.053 1 83.45 ? C1 NAG 602 A 1 
HETATM 2 C C2 NAG . . . D 3 -8.527 -10.334 3.257 1 86.84 ? C2 NAG 602 A 1 
HETATM 3 C C3 NAG . . . D 3 -8.614 -11.833 3.572 1 86.97 ? C3 NAG 602 A 1 
HETATM 4 C C4 NAG . . . D 3 -7.251 -12.468 3.848 1 87.81 ? C4 NAG 602 A 1 
HETATM 5 C C5 NAG . . . D 3 -6.363 -11.57 4.721 1 84.23 ? C5 NAG 602 A 1 
HETATM 6 C C6 NAG . . . D 3 -4.957 -12.144 4.916 1 82.72 ? C6 NAG 602 A 1 
HETATM 7 C C7 NAG . . . D 3 -10.686 -9.605 2.444 1 87.3 ? C7 NAG 602 A 1 
HETATM 8 C C8 NAG . . . D 3 -10.369 -8.568 1.393 1 67.73 ? C8 NAG 602 A 1 
HETATM 9 N N2 NAG . . . D 3 -9.828 -9.712 3.457 1 89.49 ? N2 NAG 602 A 1 
HETATM 10 O O3 NAG . . . D 3 -9.221 -12.491 2.474 1 79.15 ? O3 NAG 602 A 1 
HETATM 11 O O4 NAG . . . D 3 -7.464 -13.722 4.47 1 89.31 ? O4 NAG 602 A 1 
HETATM 12 O O5 NAG . . . D 3 -6.241 -10.289 4.135 1 82.5 ? O5 NAG 602 A 1 
HETATM 13 O O6 NAG . . . D 3 -4.495 -12.775 3.736 1 75.71 ? O6 NAG 602 A 1 
HETATM 14 O O7 NAG . . . D 3 -11.69 -10.321 2.366 1 89.39 ? O7 NAG 602 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#