data_4KMY
#
_model_server_result.job_id            I19kcqjo6xb2j4jryY2HuA 
_model_server_result.datetime_utc      '2024-11-27 01:12:49' 
_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          4kmy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    4KMY 
#
_exptl.entry_id    4KMY 
_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    1 
_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            4KMY 
_cell.length_a            75.026 
_cell.length_b            75.026 
_cell.length_c            97.188 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KMY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 10 A CYS 31 1_555 A SG CYS 38 A CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
disulf ? disulf2 A SG CYS 30 A CYS 51 1_555 A SG CYS 78 A CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
disulf ? disulf3 A SG CYS 39 A CYS 60 1_555 A SG CYS 82 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf4 A SG CYS 62 A CYS 83 1_555 A SG CYS 148 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf5 A SG CYS 69 A CYS 90 1_555 A SG CYS 119 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf6 A SG CYS 108 A CYS 129 1_555 A SG CYS 182 A CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf7 A SG CYS 112 A CYS 133 1_555 A SG CYS 162 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
disulf ? disulf8 A SG CYS 125 A CYS 146 1_555 A SG CYS 142 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
covale ? covale1 A ND2 ASN 174 A ASN 195 1_555 C C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
metalc ? metalc1 A OG SER 83 A SER 104 1_555 B K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.113 ? 
metalc ? metalc2 A OD1 ASN 85 A ASN 106 1_555 B K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.373 ? 
#
_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                     4KMY 
_atom_sites.fract_transf_matrix[1][1]    0.013329 
_atom_sites.fract_transf_matrix[1][2]    0.007695 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015391 
_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]    0.010289 
_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
B 2 K A 1 301 251 K K . 
C 3 NAG A 1 302 301 NAG NAG . 
D 4 HOH A 1 401 1 HOH HOH . 
D 4 HOH A 2 402 2 HOH HOH . 
D 4 HOH A 3 403 3 HOH HOH . 
D 4 HOH A 4 404 4 HOH HOH . 
D 4 HOH A 5 405 5 HOH HOH . 
D 4 HOH A 6 406 6 HOH HOH . 
D 4 HOH A 7 407 7 HOH HOH . 
D 4 HOH A 8 408 8 HOH HOH . 
D 4 HOH A 9 409 9 HOH HOH . 
D 4 HOH A 10 410 10 HOH HOH . 
D 4 HOH A 11 411 11 HOH HOH . 
D 4 HOH A 12 412 12 HOH HOH . 
D 4 HOH A 13 413 13 HOH HOH . 
D 4 HOH A 14 414 14 HOH HOH . 
D 4 HOH A 15 415 15 HOH HOH . 
D 4 HOH A 16 416 16 HOH HOH . 
D 4 HOH A 17 417 17 HOH HOH . 
D 4 HOH A 18 418 18 HOH HOH . 
D 4 HOH A 19 419 19 HOH HOH . 
D 4 HOH A 20 420 20 HOH HOH . 
D 4 HOH A 21 421 21 HOH HOH . 
D 4 HOH A 22 422 22 HOH HOH . 
D 4 HOH A 23 423 23 HOH HOH . 
D 4 HOH A 24 424 24 HOH HOH . 
D 4 HOH A 25 425 25 HOH HOH . 
D 4 HOH A 26 426 26 HOH HOH . 
D 4 HOH A 27 427 27 HOH HOH . 
D 4 HOH A 28 428 28 HOH HOH . 
D 4 HOH A 29 429 29 HOH HOH . 
D 4 HOH A 30 430 30 HOH HOH . 
D 4 HOH A 31 431 31 HOH HOH . 
D 4 HOH A 32 432 32 HOH HOH . 
D 4 HOH A 33 433 33 HOH HOH . 
D 4 HOH A 34 434 34 HOH HOH . 
D 4 HOH A 35 435 35 HOH HOH . 
D 4 HOH A 36 436 36 HOH HOH . 
D 4 HOH A 37 437 37 HOH HOH . 
D 4 HOH A 38 438 38 HOH HOH . 
D 4 HOH A 39 439 39 HOH HOH . 
D 4 HOH A 40 440 40 HOH HOH . 
D 4 HOH A 41 441 41 HOH HOH . 
D 4 HOH A 42 442 42 HOH HOH . 
D 4 HOH A 43 443 43 HOH HOH . 
D 4 HOH A 44 444 44 HOH HOH . 
D 4 HOH A 45 445 45 HOH HOH . 
D 4 HOH A 46 446 46 HOH HOH . 
D 4 HOH A 47 447 47 HOH HOH . 
D 4 HOH A 48 448 48 HOH HOH . 
D 4 HOH A 49 449 49 HOH HOH . 
D 4 HOH A 50 450 50 HOH HOH . 
D 4 HOH A 51 451 51 HOH HOH . 
D 4 HOH A 52 452 52 HOH HOH . 
D 4 HOH A 53 453 53 HOH HOH . 
D 4 HOH A 54 454 54 HOH HOH . 
D 4 HOH A 55 455 55 HOH HOH . 
D 4 HOH A 56 456 56 HOH HOH . 
D 4 HOH A 57 457 57 HOH HOH . 
D 4 HOH A 58 458 58 HOH HOH . 
D 4 HOH A 59 459 59 HOH HOH . 
D 4 HOH A 60 460 60 HOH HOH . 
D 4 HOH A 61 461 61 HOH HOH . 
D 4 HOH A 62 462 62 HOH HOH . 
D 4 HOH A 63 463 63 HOH HOH . 
D 4 HOH A 64 464 64 HOH HOH . 
D 4 HOH A 65 465 65 HOH HOH . 
D 4 HOH A 66 466 66 HOH HOH . 
D 4 HOH A 67 467 67 HOH HOH . 
D 4 HOH A 68 468 68 HOH HOH . 
D 4 HOH A 69 469 69 HOH HOH . 
D 4 HOH A 70 470 70 HOH HOH . 
D 4 HOH A 71 471 71 HOH HOH . 
D 4 HOH A 72 472 72 HOH HOH . 
D 4 HOH A 73 473 73 HOH HOH . 
D 4 HOH A 74 474 74 HOH HOH . 
D 4 HOH A 75 475 75 HOH HOH . 
D 4 HOH A 76 476 76 HOH HOH . 
D 4 HOH A 77 477 79 HOH HOH . 
D 4 HOH A 78 478 80 HOH HOH . 
D 4 HOH A 79 479 81 HOH HOH . 
D 4 HOH A 80 480 82 HOH HOH . 
D 4 HOH A 81 481 83 HOH HOH . 
D 4 HOH A 82 482 84 HOH HOH . 
D 4 HOH A 83 483 85 HOH HOH . 
D 4 HOH A 84 484 86 HOH HOH . 
D 4 HOH A 85 485 87 HOH HOH . 
D 4 HOH A 86 486 88 HOH HOH . 
D 4 HOH A 87 487 89 HOH HOH . 
D 4 HOH A 88 488 90 HOH HOH . 
D 4 HOH A 89 489 91 HOH HOH . 
D 4 HOH A 90 490 92 HOH HOH . 
D 4 HOH A 91 491 93 HOH HOH . 
D 4 HOH A 92 492 94 HOH HOH . 
D 4 HOH A 93 493 95 HOH HOH . 
D 4 HOH A 94 494 96 HOH HOH . 
D 4 HOH A 95 495 97 HOH HOH . 
D 4 HOH A 96 496 98 HOH HOH . 
D 4 HOH A 97 497 99 HOH HOH . 
D 4 HOH A 98 498 100 HOH HOH . 
D 4 HOH A 99 499 101 HOH HOH . 
D 4 HOH A 100 500 102 HOH HOH . 
D 4 HOH A 101 501 103 HOH HOH . 
D 4 HOH A 102 502 104 HOH HOH . 
D 4 HOH A 103 503 105 HOH HOH . 
D 4 HOH A 104 504 106 HOH HOH . 
D 4 HOH A 105 505 107 HOH HOH . 
D 4 HOH A 106 506 108 HOH HOH . 
D 4 HOH A 107 507 109 HOH HOH . 
D 4 HOH A 108 508 110 HOH HOH . 
D 4 HOH A 109 509 111 HOH HOH . 
D 4 HOH A 110 510 112 HOH HOH . 
D 4 HOH A 111 511 113 HOH HOH . 
D 4 HOH A 112 512 114 HOH HOH . 
D 4 HOH A 113 513 116 HOH HOH . 
D 4 HOH A 114 514 117 HOH HOH . 
D 4 HOH A 115 515 118 HOH HOH . 
D 4 HOH A 116 516 119 HOH HOH . 
D 4 HOH A 117 517 120 HOH HOH . 
D 4 HOH A 118 518 121 HOH HOH . 
D 4 HOH A 119 519 122 HOH HOH . 
D 4 HOH A 120 520 123 HOH HOH . 
D 4 HOH A 121 521 124 HOH HOH . 
D 4 HOH A 122 522 125 HOH HOH . 
D 4 HOH A 123 523 126 HOH HOH . 
D 4 HOH A 124 524 127 HOH HOH . 
D 4 HOH A 125 525 128 HOH HOH . 
D 4 HOH A 126 526 129 HOH HOH . 
D 4 HOH A 127 527 130 HOH HOH . 
D 4 HOH A 128 528 131 HOH HOH . 
D 4 HOH A 129 529 132 HOH HOH . 
D 4 HOH A 130 530 133 HOH HOH . 
D 4 HOH A 131 531 134 HOH HOH . 
D 4 HOH A 132 532 135 HOH HOH . 
D 4 HOH A 133 533 136 HOH HOH . 
D 4 HOH A 134 534 137 HOH HOH . 
D 4 HOH A 135 535 138 HOH HOH . 
D 4 HOH A 136 536 139 HOH HOH . 
D 4 HOH A 137 537 140 HOH HOH . 
D 4 HOH A 138 538 141 HOH HOH . 
D 4 HOH A 139 539 142 HOH HOH . 
D 4 HOH A 140 540 143 HOH HOH . 
D 4 HOH A 141 541 144 HOH HOH . 
D 4 HOH A 142 542 145 HOH HOH . 
D 4 HOH A 143 543 146 HOH HOH . 
D 4 HOH A 144 544 147 HOH HOH . 
D 4 HOH A 145 545 148 HOH HOH . 
D 4 HOH A 146 546 149 HOH HOH . 
D 4 HOH A 147 547 150 HOH HOH . 
D 4 HOH A 148 548 151 HOH HOH . 
D 4 HOH A 149 549 152 HOH HOH . 
D 4 HOH A 150 550 153 HOH HOH . 
D 4 HOH A 151 551 154 HOH HOH . 
D 4 HOH A 152 552 155 HOH HOH . 
D 4 HOH A 153 553 156 HOH HOH . 
D 4 HOH A 154 554 157 HOH HOH . 
D 4 HOH A 155 555 158 HOH HOH . 
D 4 HOH A 156 556 159 HOH HOH . 
D 4 HOH A 157 557 160 HOH HOH . 
D 4 HOH A 158 558 161 HOH HOH . 
D 4 HOH A 159 559 162 HOH HOH . 
D 4 HOH A 160 560 164 HOH HOH . 
D 4 HOH A 161 561 166 HOH HOH . 
D 4 HOH A 162 562 167 HOH HOH . 
D 4 HOH A 163 563 168 HOH HOH . 
D 4 HOH A 164 564 169 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 -5.608 -26.362 13.874 0.6 32.56 ? C1 NAG 302 A 1 
HETATM 2 C C2 NAG . . . C 3 -6.534 -27.442 14.41 0.6 33.64 ? C2 NAG 302 A 1 
HETATM 3 C C3 NAG . . . C 3 -7.953 -27.204 13.908 0.6 40.26 ? C3 NAG 302 A 1 
HETATM 4 C C4 NAG . . . C 3 -8.384 -25.762 14.155 0.6 42.87 ? C4 NAG 302 A 1 
HETATM 5 C C5 NAG . . . C 3 -7.335 -24.789 13.63 0.6 43.09 ? C5 NAG 302 A 1 
HETATM 6 C C6 NAG . . . C 3 -7.72 -23.337 13.913 0.6 46.48 ? C6 NAG 302 A 1 
HETATM 7 C C7 NAG . . . C 3 -5.443 -29.615 14.704 0.6 33.77 ? C7 NAG 302 A 1 
HETATM 8 C C8 NAG . . . C 3 -5.268 -29.237 16.145 0.6 29.81 ? C8 NAG 302 A 1 
HETATM 9 N N2 NAG . . . C 3 -6.063 -28.727 13.942 0.6 33.47 ? N2 NAG 302 A 1 
HETATM 10 O O3 NAG . . . C 3 -8.848 -28.09 14.545 0.6 42.37 ? O3 NAG 302 A 1 
HETATM 11 O O4 NAG . . . C 3 -9.607 -25.515 13.497 0.6 46.54 ? O4 NAG 302 A 1 
HETATM 12 O O5 NAG . . . C 3 -6.079 -25.076 14.211 0.6 36.18 ? O5 NAG 302 A 1 
HETATM 13 O O6 NAG . . . C 3 -7.926 -23.151 15.297 0.6 48.53 ? O6 NAG 302 A 1 
HETATM 14 O O7 NAG . . . C 3 -5.024 -30.69 14.259 0.6 38.39 ? O7 NAG 302 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#