data_3LMK
#
_model_server_result.job_id            PGH22H3ZsYqV8qvKJIro7Q 
_model_server_result.datetime_utc      '2024-11-14 23:25:17' 
_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          3lmk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1}' 
#
_entry.id    3LMK 
#
_exptl.entry_id    3LMK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          2 
_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         90 
_cell.entry_id            3LMK 
_cell.length_a            71.875 
_cell.length_b            98.346 
_cell.length_c            155.239 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LMK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 
_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
? 2 C N N 
? 2 G 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 44 A CYS 57 1_555 A SG CYS 86 A CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 A SG CYS 263 A CYS 276 1_555 A SG CYS 265 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf3 A SG CYS 352 A CYS 365 1_555 A SG CYS 368 A CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf4 A SG CYS 406 A CYS 419 1_555 A SG CYS 413 A CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf5 B SG CYS 44 B CYS 57 1_555 B SG CYS 86 B CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf6 B SG CYS 263 B CYS 276 1_555 B SG CYS 265 B CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf7 B SG CYS 352 B CYS 365 1_555 B SG CYS 368 B CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 B SG CYS 406 B CYS 419 1_555 B SG CYS 413 B CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
covale ? covale1 C C1 NAG . A NAG 1 1_555 A ND2 ASN 432 A ASN 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale2 G C1 NAG . B NAG 1 1_555 B ND2 ASN 432 B ASN 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
metalc ? metalc1 A O ILE 66 A ILE 79 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? 
metalc ? metalc2 A O ASP 69 A ASP 82 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? 
metalc ? metalc3 A O LEU 72 A LEU 85 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc4 A O LEU 73 A LEU 86 1_555 E MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? 
metalc ? metalc5 A OD1 ASP 448 A ASP 461 1_555 F MG MG . A MG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? 
metalc ? metalc6 E MG MG . A MG 507 1_555 J O HOH . A HOH 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? 
metalc ? metalc7 B O ILE 66 B ILE 79 1_555 H MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? 
metalc ? metalc8 B O ASP 69 B ASP 82 1_555 H MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? 
metalc ? metalc9 B O LEU 72 B LEU 85 1_555 H MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc10 B O LEU 73 B LEU 86 1_555 H MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? 
#
_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 237 n n 
C1 O1 NAG sing 238 n n 
C1 O5 NAG sing 239 n n 
C1 H1 NAG sing 240 n n 
C2 C3 NAG sing 241 n n 
C2 N2 NAG sing 242 n n 
C2 H2 NAG sing 243 n n 
C3 C4 NAG sing 244 n n 
C3 O3 NAG sing 245 n n 
C3 H3 NAG sing 246 n n 
C4 C5 NAG sing 247 n n 
C4 O4 NAG sing 248 n n 
C4 H4 NAG sing 249 n n 
C5 C6 NAG sing 250 n n 
C5 O5 NAG sing 251 n n 
C5 H5 NAG sing 252 n n 
C6 O6 NAG sing 253 n n 
C6 H61 NAG sing 254 n n 
C6 H62 NAG sing 255 n n 
C7 C8 NAG sing 256 n n 
C7 N2 NAG sing 257 n n 
C7 O7 NAG doub 258 n n 
C8 H81 NAG sing 259 n n 
C8 H82 NAG sing 260 n n 
C8 H83 NAG sing 261 n n 
N2 HN2 NAG sing 262 n n 
O1 HO1 NAG sing 263 n n 
O3 HO3 NAG sing 264 n n 
O4 HO4 NAG sing 265 n n 
O6 HO6 NAG sing 266 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                     3LMK 
_atom_sites.fract_transf_matrix[1][1]    0.013913 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010168 
_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]    0.006442 
_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 NAG A 1 1 1 NAG NAG . 
D 3 GLU A 1 506 1 GLU GLU . 
E 4 MG A 1 507 1 MG MG . 
F 4 MG A 1 508 1 MG MG . 
G 2 NAG B 1 1 1 NAG NAG . 
H 4 MG B 1 506 1 MG MG . 
I 3 GLU B 1 507 1 GLU GLU . 
J 5 HOH A 1 4 4 HOH HOH . 
J 5 HOH A 2 6 6 HOH HOH . 
J 5 HOH A 3 9 9 HOH HOH . 
J 5 HOH A 4 10 10 HOH HOH . 
J 5 HOH A 5 509 14 HOH HOH . 
J 5 HOH A 6 510 20 HOH HOH . 
J 5 HOH A 7 511 21 HOH HOH . 
J 5 HOH A 8 512 22 HOH HOH . 
J 5 HOH A 9 513 25 HOH HOH . 
J 5 HOH A 10 514 26 HOH HOH . 
J 5 HOH A 11 515 32 HOH HOH . 
J 5 HOH A 12 516 33 HOH HOH . 
J 5 HOH A 13 517 35 HOH HOH . 
J 5 HOH A 14 518 39 HOH HOH . 
J 5 HOH A 15 519 42 HOH HOH . 
J 5 HOH A 16 520 44 HOH HOH . 
J 5 HOH A 17 521 48 HOH HOH . 
J 5 HOH A 18 522 54 HOH HOH . 
J 5 HOH A 19 523 57 HOH HOH . 
J 5 HOH A 20 524 62 HOH HOH . 
J 5 HOH A 21 525 63 HOH HOH . 
J 5 HOH A 22 526 69 HOH HOH . 
J 5 HOH A 23 527 75 HOH HOH . 
J 5 HOH A 24 528 78 HOH HOH . 
J 5 HOH A 25 529 82 HOH HOH . 
J 5 HOH A 26 530 91 HOH HOH . 
J 5 HOH A 27 531 93 HOH HOH . 
J 5 HOH A 28 532 95 HOH HOH . 
J 5 HOH A 29 533 101 HOH HOH . 
J 5 HOH A 30 534 105 HOH HOH . 
J 5 HOH A 31 535 107 HOH HOH . 
J 5 HOH A 32 536 112 HOH HOH . 
J 5 HOH A 33 537 115 HOH HOH . 
J 5 HOH A 34 538 122 HOH HOH . 
J 5 HOH A 35 539 131 HOH HOH . 
K 5 HOH B 1 2 2 HOH HOH . 
K 5 HOH B 2 3 3 HOH HOH . 
K 5 HOH B 3 5 5 HOH HOH . 
K 5 HOH B 4 8 8 HOH HOH . 
K 5 HOH B 5 11 11 HOH HOH . 
K 5 HOH B 6 12 12 HOH HOH . 
K 5 HOH B 7 13 13 HOH HOH . 
K 5 HOH B 8 508 1 HOH HOH . 
K 5 HOH B 9 509 15 HOH HOH . 
K 5 HOH B 10 510 16 HOH HOH . 
K 5 HOH B 11 511 18 HOH HOH . 
K 5 HOH B 12 512 19 HOH HOH . 
K 5 HOH B 13 513 23 HOH HOH . 
K 5 HOH B 14 514 24 HOH HOH . 
K 5 HOH B 15 515 27 HOH HOH . 
K 5 HOH B 16 516 28 HOH HOH . 
K 5 HOH B 17 517 29 HOH HOH . 
K 5 HOH B 18 518 34 HOH HOH . 
K 5 HOH B 19 519 36 HOH HOH . 
K 5 HOH B 20 520 41 HOH HOH . 
K 5 HOH B 21 521 43 HOH HOH . 
K 5 HOH B 22 522 45 HOH HOH . 
K 5 HOH B 23 523 46 HOH HOH . 
K 5 HOH B 24 524 47 HOH HOH . 
K 5 HOH B 25 525 50 HOH HOH . 
K 5 HOH B 26 526 51 HOH HOH . 
K 5 HOH B 27 527 53 HOH HOH . 
K 5 HOH B 28 528 56 HOH HOH . 
K 5 HOH B 29 529 58 HOH HOH . 
K 5 HOH B 30 530 59 HOH HOH . 
K 5 HOH B 31 531 60 HOH HOH . 
K 5 HOH B 32 532 64 HOH HOH . 
K 5 HOH B 33 533 68 HOH HOH . 
K 5 HOH B 34 534 70 HOH HOH . 
K 5 HOH B 35 535 71 HOH HOH . 
K 5 HOH B 36 536 76 HOH HOH . 
K 5 HOH B 37 537 77 HOH HOH . 
K 5 HOH B 38 538 79 HOH HOH . 
K 5 HOH B 39 539 80 HOH HOH . 
K 5 HOH B 40 540 86 HOH HOH . 
K 5 HOH B 41 541 87 HOH HOH . 
K 5 HOH B 42 542 89 HOH HOH . 
K 5 HOH B 43 543 90 HOH HOH . 
K 5 HOH B 44 544 92 HOH HOH . 
K 5 HOH B 45 545 96 HOH HOH . 
K 5 HOH B 46 546 99 HOH HOH . 
K 5 HOH B 47 547 100 HOH HOH . 
K 5 HOH B 48 548 114 HOH HOH . 
K 5 HOH B 49 549 117 HOH HOH . 
K 5 HOH B 50 550 118 HOH HOH . 
K 5 HOH B 51 551 119 HOH HOH . 
K 5 HOH B 52 552 126 HOH HOH . 
K 5 HOH B 53 553 133 HOH HOH . 
K 5 HOH B 54 554 134 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 2 29.013 19.458 22.744 1 65.92 ? C1 NAG 1 A 1 
HETATM 2 C C2 NAG . . . C 2 30.477 19.918 22.659 1 69.76 ? C2 NAG 1 A 1 
HETATM 3 C C3 NAG . . . C 2 31.059 20.138 24.063 1 70.05 ? C3 NAG 1 A 1 
HETATM 4 C C4 NAG . . . C 2 30.165 21.044 24.914 1 70.44 ? C4 NAG 1 A 1 
HETATM 5 C C5 NAG . . . C 2 28.723 20.521 24.901 1 70.44 ? C5 NAG 1 A 1 
HETATM 6 C C6 NAG . . . C 2 27.746 21.447 25.632 1 71.15 ? C6 NAG 1 A 1 
HETATM 7 C C7 NAG . . . C 2 31.479 18.988 20.58 1 71.38 ? C7 NAG 1 A 1 
HETATM 8 C C8 NAG . . . C 2 32.431 17.971 20.022 1 71.53 ? C8 NAG 1 A 1 
HETATM 9 N N2 NAG . . . C 2 31.336 18.995 21.912 1 71 ? N2 NAG 1 A 1 
HETATM 10 O O3 NAG . . . C 2 32.361 20.686 23.985 1 70.58 ? O3 NAG 1 A 1 
HETATM 11 O O4 NAG . . . C 2 30.683 21.095 26.227 1 70.49 ? O4 NAG 1 A 1 
HETATM 12 O O5 NAG . . . C 2 28.286 20.372 23.558 1 68.78 ? O5 NAG 1 A 1 
HETATM 13 O O6 NAG . . . C 2 27.092 22.292 24.7 1 72.37 ? O6 NAG 1 A 1 
HETATM 14 O O7 NAG . . . C 2 30.886 19.748 19.81 1 71.61 ? O7 NAG 1 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           362 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           14 
#