data_5E4J
#
_model_server_result.job_id            HjAP8BNrjZQYDS3ZKtfgVA 
_model_server_result.datetime_utc      '2024-11-24 07:51:30' 
_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          5e4j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":601}' 
#
_entry.id    5E4J 
#
_exptl.entry_id    5E4J 
_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            5E4J 
_cell.length_a            111.21 
_cell.length_b            111.21 
_cell.length_c            137.03 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5E4J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_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    1,2 
#
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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 91.353333 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
#
_pdbx_entity_branch.entity_id    2 
_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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 
4 ? 2 5 4 MAN MAN C1 O1 . O2 HO2 . 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 B NAG 1 B 1 NAG A 1539 NAG 
2 n B NAG 2 B 2 NAG A 2107 NAG 
2 n B BMA 3 B 3 BMA A 2108 BMA 
2 n B MAN 4 B 4 MAN A 2109 MAN 
2 n B MAN 5 B 5 MAN A 2110 MAN 
#
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 64 A CYS 67 1_555 A SG CYS 91 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf2 A SG CYS 251 A CYS 254 1_555 A SG CYS 262 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf3 A SG CYS 399 A CYS 402 1_555 A SG CYS 518 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
covale ? covale1 A ND2 ASN 56 A ASN 59 1_555 C C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
covale ? covale2 A ND2 ASN 413 A ASN 416 1_555 D C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale3 A ND2 ASN 454 A ASN 457 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? 
covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale7 B O2 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
#
_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 340 n n 
C1 O1 NAG sing 341 n n 
C1 O5 NAG sing 342 n n 
C1 H1 NAG sing 343 n n 
C2 C3 NAG sing 344 n n 
C2 N2 NAG sing 345 n n 
C2 H2 NAG sing 346 n n 
C3 C4 NAG sing 347 n n 
C3 O3 NAG sing 348 n n 
C3 H3 NAG sing 349 n n 
C4 C5 NAG sing 350 n n 
C4 O4 NAG sing 351 n n 
C4 H4 NAG sing 352 n n 
C5 C6 NAG sing 353 n n 
C5 O5 NAG sing 354 n n 
C5 H5 NAG sing 355 n n 
C6 O6 NAG sing 356 n n 
C6 H61 NAG sing 357 n n 
C6 H62 NAG sing 358 n n 
C7 C8 NAG sing 359 n n 
C7 N2 NAG sing 360 n n 
C7 O7 NAG doub 361 n n 
C8 H81 NAG sing 362 n n 
C8 H82 NAG sing 363 n n 
C8 H83 NAG sing 364 n n 
N2 HN2 NAG sing 365 n n 
O1 HO1 NAG sing 366 n n 
O3 HO3 NAG sing 367 n n 
O4 HO4 NAG sing 368 n n 
O6 HO6 NAG sing 369 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                     5E4J 
_atom_sites.fract_transf_matrix[1][1]    0.008992 
_atom_sites.fract_transf_matrix[1][2]    0.005192 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010383 
_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]    0.007298 
_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 3 NAG A 1 601 1536 NAG NAG . 
D 3 NAG A 1 602 1537 NAG NAG . 
E 4 DME A 1 603 999 DME DME . 
F 5 SO4 A 1 604 701 SO4 SO4 . 
G 5 SO4 A 1 605 702 SO4 SO4 . 
H 5 SO4 A 1 606 703 SO4 SO4 . 
I 5 SO4 A 1 607 704 SO4 SO4 . 
J 5 SO4 A 1 608 705 SO4 SO4 . 
K 5 SO4 A 1 609 706 SO4 SO4 . 
L 5 SO4 A 1 610 707 SO4 SO4 . 
M 5 SO4 A 1 611 708 SO4 SO4 . 
N 5 SO4 A 1 612 709 SO4 SO4 . 
O 5 SO4 A 1 613 710 SO4 SO4 . 
P 6 HOH A 1 701 2011 HOH HOH . 
P 6 HOH A 2 702 2005 HOH HOH . 
P 6 HOH A 3 703 2013 HOH HOH . 
P 6 HOH A 4 704 2007 HOH HOH . 
P 6 HOH A 5 705 2002 HOH HOH . 
P 6 HOH A 6 706 2010 HOH HOH . 
P 6 HOH A 7 707 2003 HOH HOH . 
P 6 HOH A 8 708 2001 HOH HOH . 
P 6 HOH A 9 709 2006 HOH HOH . 
P 6 HOH A 10 710 2012 HOH HOH . 
P 6 HOH A 11 711 2015 HOH HOH . 
P 6 HOH A 12 712 2004 HOH HOH . 
P 6 HOH A 13 713 2014 HOH HOH . 
P 6 HOH A 14 714 2008 HOH HOH . 
P 6 HOH A 15 715 2009 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 . . . C 3 47.44 -57.709 26.251 1 42.77 ? C1 NAG 601 A 1 
HETATM 2 C C2 NAG . . . C 3 46.885 -59.064 25.815 1 45.16 ? C2 NAG 601 A 1 
HETATM 3 C C3 NAG . . . C 3 45.691 -59.552 26.66 1 45.13 ? C3 NAG 601 A 1 
HETATM 4 C C4 NAG . . . C 3 45.928 -59.349 28.162 1 45.04 ? C4 NAG 601 A 1 
HETATM 5 C C5 NAG . . . C 3 46.394 -57.908 28.41 1 44.02 ? C5 NAG 601 A 1 
HETATM 6 C C6 NAG . . . C 3 46.589 -57.586 29.901 1 44.13 ? C6 NAG 601 A 1 
HETATM 7 C C7 NAG . . . C 3 46.995 -59.892 23.519 1 46.7 ? C7 NAG 601 A 1 
HETATM 8 C C8 NAG . . . C 3 46.582 -59.698 22.088 1 47.36 ? C8 NAG 601 A 1 
HETATM 9 N N2 NAG . . . C 3 46.559 -58.99 24.399 1 45.58 ? N2 NAG 601 A 1 
HETATM 10 O O3 NAG . . . C 3 45.43 -60.916 26.403 1 43.44 ? O3 NAG 601 A 1 
HETATM 11 O O4 NAG . . . C 3 44.757 -59.666 28.905 1 45.43 ? O4 NAG 601 A 1 
HETATM 12 O O5 NAG . . . C 3 47.582 -57.664 27.665 1 43.07 ? O5 NAG 601 A 1 
HETATM 13 O O6 NAG . . . C 3 47.946 -57.593 30.299 1 43.78 ? O6 NAG 601 A 1 
HETATM 14 O O7 NAG . . . C 3 47.701 -60.851 23.828 1 45.56 ? O7 NAG 601 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#