data_3LMY
#
_model_server_result.job_id            F2Y2DTfSyFyua9KV3Jexqw 
_model_server_result.datetime_utc      '2024-11-29 07:09:28' 
_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          3lmy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":561}' 
#
_entry.id    3LMY 
#
_exptl.entry_id    3LMY 
_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-alpha-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            3LMY 
_cell.length_a            113.898 
_cell.length_b            113.898 
_cell.length_c            397.427 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LMY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,G,M 1 1,2 
B,D,H,I,J,K,L,N 2 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' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 66.237833 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 J 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 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 3 2 1 NAG 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
2 n C NAG 1 C 1 NAG A 557 NAG 
2 n C NAG 2 C 2 NAG A 558 NAG 
2 n C BMA 3 C 3 BMA A 559 BMA 
3 n D NAG 1 D 1 NAG B 557 NAG 
3 n D NAG 2 D 2 NAG B 558 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 91 A CYS 91 1_555 A SG CYS 137 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
disulf ? disulf2 A SG CYS 309 A CYS 309 1_555 A SG CYS 360 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
disulf ? disulf3 A SG CYS 534 A CYS 534 1_555 A SG CYS 551 A CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
disulf ? disulf4 B SG CYS 91 B CYS 91 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
disulf ? disulf5 B SG CYS 309 B CYS 309 1_555 B SG CYS 360 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
disulf ? disulf6 B SG CYS 534 B CYS 534 1_555 B SG CYS 551 B CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
covale ? covale1 A ND2 ASN 190 A ASN 190 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? 
covale ? covale2 A ND2 ASN 327 A ASN 327 1_555 F C1 NAG . A NAG 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale3 B ND2 ASN 142 B ASN 142 1_555 H C1 NAG . B NAG 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? 
covale ? covale4 B ND2 ASN 190 B ASN 190 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? 
covale ? covale5 B ND2 ASN 327 B ASN 327 1_555 I C1 NAG . B NAG 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? 
covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? 
covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                NDG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-alpha-D-glucopyranose 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     N-acetyl-alpha-D-glucosamine;2-acetamido-2-deoxy-alpha-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE 
#
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 NDG sing 322 n n 
C1 O5 NDG sing 323 n n 
C1 O1 NDG sing 324 n n 
C1 H1 NDG sing 325 n n 
C2 C3 NDG sing 326 n n 
C2 N2 NDG sing 327 n n 
C2 H2 NDG sing 328 n n 
C3 C4 NDG sing 329 n n 
C3 O3 NDG sing 330 n n 
C3 H3 NDG sing 331 n n 
C4 C5 NDG sing 332 n n 
C4 O4 NDG sing 333 n n 
C4 H4 NDG sing 334 n n 
C5 C6 NDG sing 335 n n 
C5 O5 NDG sing 336 n n 
C5 H5 NDG sing 337 n n 
C6 O6 NDG sing 338 n n 
C6 H61 NDG sing 339 n n 
C6 H62 NDG sing 340 n n 
C7 C8 NDG sing 341 n n 
C7 O7 NDG doub 342 n n 
C7 N2 NDG sing 343 n n 
C8 H81 NDG sing 344 n n 
C8 H82 NDG sing 345 n n 
C8 H83 NDG sing 346 n n 
O3 HO3 NDG sing 347 n n 
O4 HO4 NDG sing 348 n n 
O6 HO6 NDG sing 349 n n 
N2 HN2 NDG sing 350 n n 
O1 HO1 NDG sing 351 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
NDG DGlcpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
NDG N-acetyl-a-D-glucopyranosamine 'COMMON NAME' GMML 1 
NDG a-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
NDG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     3LMY 
_atom_sites.fract_transf_matrix[1][1]    0.00878 
_atom_sites.fract_transf_matrix[1][2]    0.005069 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010138 
_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]    0.002516 
_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
E 4 NDG A 1 560 560 NDG NDG . 
F 5 NAG A 1 561 561 NAG NAG . 
G 6 CP6 A 1 562 562 CP6 CP6 . 
H 5 NAG B 1 559 559 NAG NAG . 
I 5 NAG B 1 560 560 NAG NAG . 
J 4 NDG B 1 561 561 NDG NDG . 
K 7 SO4 B 1 562 562 SO4 SO4 . 
L 6 CP6 B 1 563 563 CP6 CP6 . 
M 8 HOH A 1 563 563 HOH HOH . 
M 8 HOH A 2 564 564 HOH HOH . 
M 8 HOH A 3 565 565 HOH HOH . 
M 8 HOH A 4 566 566 HOH HOH . 
M 8 HOH A 5 567 567 HOH HOH . 
M 8 HOH A 6 568 568 HOH HOH . 
M 8 HOH A 7 569 569 HOH HOH . 
M 8 HOH A 8 570 570 HOH HOH . 
M 8 HOH A 9 571 571 HOH HOH . 
M 8 HOH A 10 572 572 HOH HOH . 
M 8 HOH A 11 573 573 HOH HOH . 
M 8 HOH A 12 574 574 HOH HOH . 
M 8 HOH A 13 575 575 HOH HOH . 
M 8 HOH A 14 576 576 HOH HOH . 
M 8 HOH A 15 577 577 HOH HOH . 
M 8 HOH A 16 578 578 HOH HOH . 
M 8 HOH A 17 579 579 HOH HOH . 
M 8 HOH A 18 580 580 HOH HOH . 
M 8 HOH A 19 581 581 HOH HOH . 
M 8 HOH A 20 582 582 HOH HOH . 
M 8 HOH A 21 583 583 HOH HOH . 
M 8 HOH A 22 584 584 HOH HOH . 
M 8 HOH A 23 585 585 HOH HOH . 
M 8 HOH A 24 586 586 HOH HOH . 
M 8 HOH A 25 587 587 HOH HOH . 
M 8 HOH A 26 588 588 HOH HOH . 
M 8 HOH A 27 589 589 HOH HOH . 
M 8 HOH A 28 590 590 HOH HOH . 
M 8 HOH A 29 591 591 HOH HOH . 
M 8 HOH A 30 592 592 HOH HOH . 
M 8 HOH A 31 593 593 HOH HOH . 
M 8 HOH A 32 594 594 HOH HOH . 
M 8 HOH A 33 595 595 HOH HOH . 
M 8 HOH A 34 596 596 HOH HOH . 
M 8 HOH A 35 597 597 HOH HOH . 
M 8 HOH A 36 598 598 HOH HOH . 
M 8 HOH A 37 599 599 HOH HOH . 
M 8 HOH A 38 600 600 HOH HOH . 
M 8 HOH A 39 601 601 HOH HOH . 
M 8 HOH A 40 602 602 HOH HOH . 
M 8 HOH A 41 603 603 HOH HOH . 
M 8 HOH A 42 604 604 HOH HOH . 
M 8 HOH A 43 605 605 HOH HOH . 
N 8 HOH B 1 564 564 HOH HOH . 
N 8 HOH B 2 565 565 HOH HOH . 
N 8 HOH B 3 566 566 HOH HOH . 
N 8 HOH B 4 567 567 HOH HOH . 
N 8 HOH B 5 568 568 HOH HOH . 
N 8 HOH B 6 569 569 HOH HOH . 
N 8 HOH B 7 570 570 HOH HOH . 
N 8 HOH B 8 571 571 HOH HOH . 
N 8 HOH B 9 572 572 HOH HOH . 
N 8 HOH B 10 573 573 HOH HOH . 
N 8 HOH B 11 574 574 HOH HOH . 
N 8 HOH B 12 575 575 HOH HOH . 
N 8 HOH B 13 576 576 HOH HOH . 
N 8 HOH B 14 577 577 HOH HOH . 
N 8 HOH B 15 578 578 HOH HOH . 
N 8 HOH B 16 579 579 HOH HOH . 
N 8 HOH B 17 580 580 HOH HOH . 
N 8 HOH B 18 581 581 HOH HOH . 
N 8 HOH B 19 582 582 HOH HOH . 
N 8 HOH B 20 583 583 HOH HOH . 
N 8 HOH B 21 584 584 HOH HOH . 
N 8 HOH B 22 585 585 HOH HOH . 
N 8 HOH B 23 586 586 HOH HOH . 
N 8 HOH B 24 587 587 HOH HOH . 
N 8 HOH B 25 588 588 HOH HOH . 
N 8 HOH B 26 589 589 HOH HOH . 
N 8 HOH B 27 590 590 HOH HOH . 
N 8 HOH B 28 591 591 HOH HOH . 
N 8 HOH B 29 592 592 HOH HOH . 
N 8 HOH B 30 593 593 HOH HOH . 
N 8 HOH B 31 594 594 HOH HOH . 
N 8 HOH B 32 595 595 HOH HOH . 
N 8 HOH B 33 596 596 HOH HOH . 
N 8 HOH B 34 597 597 HOH HOH . 
N 8 HOH B 35 598 598 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 NDG . . . J 4 26.928 60.705 55.199 1 89.17 ? C1 NDG 561 B 1 
HETATM 2 C C2 NDG . . . J 4 27.684 61.98 54.683 1 96.25 ? C2 NDG 561 B 1 
HETATM 3 C C3 NDG . . . J 4 29.17 62.041 55.156 1 96.06 ? C3 NDG 561 B 1 
HETATM 4 C C4 NDG . . . J 4 29.508 60.825 56.057 1 95.41 ? C4 NDG 561 B 1 
HETATM 5 C C5 NDG . . . J 4 29.102 59.538 55.301 1 94.32 ? C5 NDG 561 B 1 
HETATM 6 C C6 NDG . . . J 4 29.649 58.27 55.944 1 94.06 ? C6 NDG 561 B 1 
HETATM 7 C C7 NDG . . . J 4 27.852 63.124 52.389 1 103 ? C7 NDG 561 B 1 
HETATM 8 C C8 NDG . . . J 4 27.548 62.906 50.914 1 102.22 ? C8 NDG 561 B 1 
HETATM 9 O O5 NDG . . . J 4 27.673 59.454 55.118 1 92.86 ? O5 NDG 561 B 1 
HETATM 10 O O3 NDG . . . J 4 29.5 63.303 55.745 1 95.75 ? O3 NDG 561 B 1 
HETATM 11 O O4 NDG . . . J 4 30.858 60.785 56.496 1 95.84 ? O4 NDG 561 B 1 
HETATM 12 O O6 NDG . . . J 4 29.27 58.207 57.3 1 94.61 ? O6 NDG 561 B 1 
HETATM 13 O O7 NDG . . . J 4 28.376 64.189 52.777 1 104.57 ? O7 NDG 561 B 1 
HETATM 14 N N2 NDG . . . J 4 27.531 62.099 53.213 1 99.98 ? N2 NDG 561 B 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           249 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#