data_3N8X # _model_server_result.job_id FG0ta5pz5_kEk8Gs7pQkkA _model_server_result.datetime_utc '2024-11-24 11:12:16' _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 3n8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":1661}' # _entry.id 3N8X # _exptl.entry_id 3N8X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 3N8X _cell.length_a 181.709 _cell.length_b 181.709 _cell.length_c 103.454 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # _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,G,H,I,J,K,L,M,N,O,P _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 ? 5 H N N ? 5 K N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 BMA BMA C1 O1 . O6 HO6 . sing 5 ? 3 5 4 BMA BMA C1 O1 . 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 C NAG 1 C 1 NAG A 661 NAG 2 n C NAG 2 C 2 NAG A 662 NAG 3 n D NAG 1 D 1 NAG A 671 NAG 3 n D NAG 2 D 2 NAG A 672 NAG 3 n D BMA 3 D 3 BMA A 673 BMA 3 n D BMA 4 D 4 BMA A 674 BMA 3 n D BMA 5 D 5 BMA A 675 BMA 2 n E NAG 1 E 1 NAG B 1681 NAG 2 n E NAG 2 E 2 NAG B 1682 NAG 2 n F NAG 1 F 1 NAG B 1671 NAG 2 n F NAG 2 F 2 NAG B 1672 NAG # 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 5 A CYS 36 1_555 A SG CYS 16 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf2 A SG CYS 6 A CYS 37 1_555 A SG CYS 128 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf3 A SG CYS 10 A CYS 41 1_555 A SG CYS 26 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? disulf ? disulf4 A SG CYS 28 A CYS 59 1_555 A SG CYS 38 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? disulf ? disulf5 A SG CYS 538 A CYS 569 1_555 A SG CYS 544 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf6 B SG CYS 5 B CYS 36 1_555 B SG CYS 16 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf7 B SG CYS 6 B CYS 37 1_555 B SG CYS 128 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf8 B SG CYS 10 B CYS 41 1_555 B SG CYS 26 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf9 B SG CYS 28 B CYS 59 1_555 B SG CYS 38 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf10 B SG CYS 538 B CYS 569 1_555 B SG CYS 544 B CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? covale ? covale1 A ND2 ASN 37 A ASN 68 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 113 A ASN 144 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A ND2 ASN 379 A ASN 410 1_555 H C1 NAG . A NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale4 B ND2 ASN 37 B ASN 68 1_555 K C1 NAG . B NAG 1661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B ND2 ASN 113 B ASN 144 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale6 B ND2 ASN 379 B ASN 410 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 D O6 BMA . D BMA 3 1_555 D C1 BMA . D BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale11 D O6 BMA . D BMA 4 1_555 D C1 BMA . D BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? metalc ? metalc1 A NE2 HIS 357 A HIS 388 1_555 G FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc2 B NE2 HIS 357 B HIS 388 1_555 J FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc3 P O HOH . B HOH 597 1_555 J FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? # _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 391 n n C1 O1 NAG sing 392 n n C1 O5 NAG sing 393 n n C1 H1 NAG sing 394 n n C2 C3 NAG sing 395 n n C2 N2 NAG sing 396 n n C2 H2 NAG sing 397 n n C3 C4 NAG sing 398 n n C3 O3 NAG sing 399 n n C3 H3 NAG sing 400 n n C4 C5 NAG sing 401 n n C4 O4 NAG sing 402 n n C4 H4 NAG sing 403 n n C5 C6 NAG sing 404 n n C5 O5 NAG sing 405 n n C5 H5 NAG sing 406 n n C6 O6 NAG sing 407 n n C6 H61 NAG sing 408 n n C6 H62 NAG sing 409 n n C7 C8 NAG sing 410 n n C7 N2 NAG sing 411 n n C7 O7 NAG doub 412 n n C8 H81 NAG sing 413 n n C8 H82 NAG sing 414 n n C8 H83 NAG sing 415 n n N2 HN2 NAG sing 416 n n O1 HO1 NAG sing 417 n n O3 HO3 NAG sing 418 n n O4 HO4 NAG sing 419 n n O6 HO6 NAG sing 420 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 3N8X _atom_sites.fract_transf_matrix[1][1] 0.005503 _atom_sites.fract_transf_matrix[1][2] 0.003177 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006355 _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] 0.009666 _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 G 4 HEM A 1 601 601 HEM HEM . H 5 NAG A 1 681 681 NAG NAG . I 6 NIM A 1 701 701 NIM NIM . J 4 HEM B 1 601 601 HEM HEM . K 5 NAG B 1 1661 1661 NAG NAG . L 6 NIM B 1 1701 1701 NIM NIM . M 7 BOG B 1 1751 1751 BOG BOG . N 7 BOG B 1 1752 1752 BOG BOG . O 8 HOH A 1 2 2 HOH HOH . O 8 HOH A 2 3 3 HOH HOH . O 8 HOH A 3 7 7 HOH HOH . O 8 HOH A 4 8 8 HOH HOH . O 8 HOH A 5 9 9 HOH HOH . O 8 HOH A 6 11 11 HOH HOH . O 8 HOH A 7 12 12 HOH HOH . O 8 HOH A 8 13 13 HOH HOH . O 8 HOH A 9 14 14 HOH HOH . O 8 HOH A 10 17 17 HOH HOH . O 8 HOH A 11 19 19 HOH HOH . O 8 HOH A 12 20 20 HOH HOH . O 8 HOH A 13 22 22 HOH HOH . O 8 HOH A 14 26 26 HOH HOH . O 8 HOH A 15 27 27 HOH HOH . O 8 HOH A 16 29 29 HOH HOH . O 8 HOH A 17 30 30 HOH HOH . O 8 HOH A 18 585 585 HOH HOH . O 8 HOH A 19 586 586 HOH HOH . O 8 HOH A 20 587 587 HOH HOH . O 8 HOH A 21 588 588 HOH HOH . O 8 HOH A 22 589 589 HOH HOH . O 8 HOH A 23 590 590 HOH HOH . O 8 HOH A 24 591 591 HOH HOH . O 8 HOH A 25 592 592 HOH HOH . O 8 HOH A 26 593 593 HOH HOH . O 8 HOH A 27 594 594 HOH HOH . O 8 HOH A 28 595 595 HOH HOH . O 8 HOH A 29 596 596 HOH HOH . O 8 HOH A 30 597 597 HOH HOH . O 8 HOH A 31 598 598 HOH HOH . O 8 HOH A 32 599 599 HOH HOH . O 8 HOH A 33 600 600 HOH HOH . O 8 HOH A 34 602 602 HOH HOH . O 8 HOH A 35 603 603 HOH HOH . O 8 HOH A 36 604 604 HOH HOH . O 8 HOH A 37 605 605 HOH HOH . O 8 HOH A 38 606 606 HOH HOH . O 8 HOH A 39 607 607 HOH HOH . O 8 HOH A 40 608 608 HOH HOH . O 8 HOH A 41 609 609 HOH HOH . O 8 HOH A 42 610 610 HOH HOH . O 8 HOH A 43 611 611 HOH HOH . O 8 HOH A 44 612 612 HOH HOH . O 8 HOH A 45 613 613 HOH HOH . P 8 HOH B 1 1 1 HOH HOH . P 8 HOH B 2 4 4 HOH HOH . P 8 HOH B 3 5 5 HOH HOH . P 8 HOH B 4 6 6 HOH HOH . P 8 HOH B 5 10 10 HOH HOH . P 8 HOH B 6 15 15 HOH HOH . P 8 HOH B 7 16 16 HOH HOH . P 8 HOH B 8 18 18 HOH HOH . P 8 HOH B 9 21 21 HOH HOH . P 8 HOH B 10 23 23 HOH HOH . P 8 HOH B 11 24 24 HOH HOH . P 8 HOH B 12 25 25 HOH HOH . P 8 HOH B 13 28 28 HOH HOH . P 8 HOH B 14 31 31 HOH HOH . P 8 HOH B 15 585 585 HOH HOH . P 8 HOH B 16 586 586 HOH HOH . P 8 HOH B 17 587 587 HOH HOH . P 8 HOH B 18 588 588 HOH HOH . P 8 HOH B 19 589 589 HOH HOH . P 8 HOH B 20 590 590 HOH HOH . P 8 HOH B 21 591 591 HOH HOH . P 8 HOH B 22 592 592 HOH HOH . P 8 HOH B 23 593 593 HOH HOH . P 8 HOH B 24 594 594 HOH HOH . P 8 HOH B 25 595 595 HOH HOH . P 8 HOH B 26 596 596 HOH HOH . P 8 HOH B 27 597 597 HOH HOH . P 8 HOH B 28 598 598 HOH HOH . P 8 HOH B 29 599 599 HOH HOH . P 8 HOH B 30 600 600 HOH HOH . P 8 HOH B 31 602 602 HOH HOH . P 8 HOH B 32 603 603 HOH HOH . P 8 HOH B 33 604 604 HOH HOH . P 8 HOH B 34 605 605 HOH HOH . P 8 HOH B 35 606 606 HOH HOH . P 8 HOH B 36 607 607 HOH HOH . P 8 HOH B 37 608 608 HOH HOH . P 8 HOH B 38 609 609 HOH HOH . P 8 HOH B 39 610 610 HOH HOH . P 8 HOH B 40 611 611 HOH HOH . P 8 HOH B 41 612 612 HOH HOH . P 8 HOH B 42 613 613 HOH HOH . P 8 HOH B 43 614 614 HOH HOH . P 8 HOH B 44 615 615 HOH HOH . P 8 HOH B 45 616 616 HOH HOH . P 8 HOH B 46 617 617 HOH HOH . P 8 HOH B 47 618 618 HOH HOH . P 8 HOH B 48 619 619 HOH HOH . P 8 HOH B 49 620 620 HOH HOH . P 8 HOH B 50 621 621 HOH HOH . P 8 HOH B 51 622 622 HOH HOH . P 8 HOH B 52 623 623 HOH HOH . P 8 HOH B 53 624 624 HOH HOH . P 8 HOH B 54 625 625 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 . . . K 5 -1.4 -57.133 45.267 1 71.13 ? C1 NAG 1661 B 1 HETATM 2 C C2 NAG . . . K 5 -0.072 -56.995 46.025 1 74 ? C2 NAG 1661 B 1 HETATM 3 C C3 NAG . . . K 5 0.437 -58.335 46.568 1 75.93 ? C3 NAG 1661 B 1 HETATM 4 C C4 NAG . . . K 5 -0.687 -59.131 47.241 1 75.95 ? C4 NAG 1661 B 1 HETATM 5 C C5 NAG . . . K 5 -1.868 -59.23 46.278 1 73.36 ? C5 NAG 1661 B 1 HETATM 6 C C6 NAG . . . K 5 -3.034 -60.011 46.872 1 73.27 ? C6 NAG 1661 B 1 HETATM 7 C C7 NAG . . . K 5 1.289 -55.093 45.202 1 77.67 ? C7 NAG 1661 B 1 HETATM 8 C C8 NAG . . . K 5 2.412 -54.682 44.287 1 78.4 ? C8 NAG 1661 B 1 HETATM 9 N N2 NAG . . . K 5 0.972 -56.401 45.204 1 75.92 ? N2 NAG 1661 B 1 HETATM 10 O O3 NAG . . . K 5 1.493 -58.134 47.492 1 76.3 ? O3 NAG 1661 B 1 HETATM 11 O O4 NAG . . . K 5 -0.232 -60.411 47.665 1 78.17 ? O4 NAG 1661 B 1 HETATM 12 O O5 NAG . . . K 5 -2.312 -57.92 46.004 1 71.56 ? O5 NAG 1661 B 1 HETATM 13 O O6 NAG . . . K 5 -3.952 -59.107 47.462 1 72.16 ? O6 NAG 1661 B 1 HETATM 14 O O7 NAG . . . K 5 0.72 -54.223 45.879 1 77.5 ? O7 NAG 1661 B 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #