data_3NN9
#
_model_server_result.job_id            o5OpcJZ7TdJc4tc_8lzl-g 
_model_server_result.datetime_utc      '2024-11-25 22:23:51' 
_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          3nn9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":476}' 
#
_entry.id    3NN9 
#
_exptl.entry_id    3NN9 
_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         90 
_cell.entry_id            3NN9 
_cell.length_a            185.1 
_cell.length_b            185.1 
_cell.length_c            185.1 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NN9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        211 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 4 3 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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' 15_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 16_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
#
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 
5 ? 2 6 5 MAN MAN C1 O1 . O2 HO2 . sing 
6 ? 2 7 3 MAN 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 B NAG 1 B 1 NAG ? 200 NAG 
2 n B NAG 2 B 2 NAG ? 200 NAG 
2 n B BMA 3 B 3 BMA ? 200 MAN 
2 n B MAN 4 B 4 MAN ? 200 MAN 
2 n B MAN 5 B 5 MAN ? 200 MAN 
2 n B MAN 6 B 6 MAN ? 200 MAN 
2 n B MAN 7 B 7 MAN ? 200 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 11 A CYS 92 1_555 A SG CYS 337 A CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf2 A SG CYS 43 A CYS 124 1_555 A SG CYS 48 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
disulf ? disulf3 A SG CYS 95 A CYS 175 1_555 A SG CYS 113 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
disulf ? disulf4 A SG CYS 103 A CYS 183 1_555 A SG CYS 150 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf5 A SG CYS 152 A CYS 232 1_555 A SG CYS 157 A CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf6 A SG CYS 198 A CYS 278 1_555 A SG CYS 211 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? 
disulf ? disulf7 A SG CYS 200 A CYS 280 1_555 A SG CYS 209 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
disulf ? disulf8 A SG CYS 238 A CYS 318 1_555 A SG CYS 256 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf9 A SG CYS 341 A CYS 421 1_555 A SG CYS 367 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
covale ? covale1 A ND2 ASN 5 A ASN 86 1_555 D C1 NAG . A NAG 477 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.455 ? 
covale ? covale2 A ND2 ASN 65 A ASN 146 1_555 C C1 NAG . A NAG 476 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.479 ? 
covale ? covale3 A ND2 ASN 120 A ASN 200 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? 
covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? 
covale ? covale7 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale8 B O2 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale9 B O2 MAN . B MAN 5 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
metalc ? metalc1 E CA CA . A CA 18 1_555 A O ASP 213 A ASP 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? 
metalc ? metalc2 E CA CA . A CA 18 1_555 A O GLY 217 A GLY 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? 
metalc ? metalc3 E CA CA . A CA 18 1_555 A OD2 ASP 244 A ASP 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? 
metalc ? metalc4 E CA CA . A CA 18 1_555 A O ASN 266 A ASN 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.171 ? 
metalc ? metalc5 E CA CA . A CA 18 1_555 F O HOH . A HOH 485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? 
#
_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 285 n n 
C1 O1 NAG sing 286 n n 
C1 O5 NAG sing 287 n n 
C1 H1 NAG sing 288 n n 
C2 C3 NAG sing 289 n n 
C2 N2 NAG sing 290 n n 
C2 H2 NAG sing 291 n n 
C3 C4 NAG sing 292 n n 
C3 O3 NAG sing 293 n n 
C3 H3 NAG sing 294 n n 
C4 C5 NAG sing 295 n n 
C4 O4 NAG sing 296 n n 
C4 H4 NAG sing 297 n n 
C5 C6 NAG sing 298 n n 
C5 O5 NAG sing 299 n n 
C5 H5 NAG sing 300 n n 
C6 O6 NAG sing 301 n n 
C6 H61 NAG sing 302 n n 
C6 H62 NAG sing 303 n n 
C7 C8 NAG sing 304 n n 
C7 N2 NAG sing 305 n n 
C7 O7 NAG doub 306 n n 
C8 H81 NAG sing 307 n n 
C8 H82 NAG sing 308 n n 
C8 H83 NAG sing 309 n n 
N2 HN2 NAG sing 310 n n 
O1 HO1 NAG sing 311 n n 
O3 HO3 NAG sing 312 n n 
O4 HO4 NAG sing 313 n n 
O6 HO6 NAG sing 314 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                     3NN9 
_atom_sites.fract_transf_matrix[1][1]    0.005402 
_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]    0.005402 
_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]    0.005402 
_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 1 476 146 NAG NAG A 
D 3 NAG A 1 477 86 NAG NAG A 
E 4 CA A 1 18 18 CA CA . 
F 5 HOH A 1 478 1 HOH HOH . 
F 5 HOH A 2 479 2 HOH HOH . 
F 5 HOH A 3 480 3 HOH HOH . 
F 5 HOH A 4 481 4 HOH HOH . 
F 5 HOH A 5 482 5 HOH HOH . 
F 5 HOH A 6 483 6 HOH HOH . 
F 5 HOH A 7 484 7 HOH HOH . 
F 5 HOH A 8 485 8 HOH HOH . 
F 5 HOH A 9 486 9 HOH HOH . 
F 5 HOH A 10 487 10 HOH HOH . 
F 5 HOH A 11 488 11 HOH HOH . 
F 5 HOH A 12 489 12 HOH HOH . 
F 5 HOH A 13 490 13 HOH HOH . 
F 5 HOH A 14 491 14 HOH HOH . 
F 5 HOH A 15 492 15 HOH HOH . 
F 5 HOH A 16 493 16 HOH HOH . 
F 5 HOH A 17 494 17 HOH HOH . 
F 5 HOH A 18 495 19 HOH HOH . 
F 5 HOH A 19 496 20 HOH HOH . 
F 5 HOH A 20 497 21 HOH HOH . 
F 5 HOH A 21 498 22 HOH HOH . 
F 5 HOH A 22 499 23 HOH HOH . 
F 5 HOH A 23 500 24 HOH HOH . 
F 5 HOH A 24 501 25 HOH HOH . 
F 5 HOH A 25 502 26 HOH HOH . 
F 5 HOH A 26 503 27 HOH HOH . 
F 5 HOH A 27 504 28 HOH HOH . 
F 5 HOH A 28 505 29 HOH HOH . 
F 5 HOH A 29 506 30 HOH HOH . 
F 5 HOH A 30 507 31 HOH HOH . 
F 5 HOH A 31 508 32 HOH HOH . 
F 5 HOH A 32 509 33 HOH HOH . 
F 5 HOH A 33 510 34 HOH HOH . 
F 5 HOH A 34 511 35 HOH HOH . 
F 5 HOH A 35 512 36 HOH HOH . 
F 5 HOH A 36 513 37 HOH HOH . 
F 5 HOH A 37 514 38 HOH HOH . 
F 5 HOH A 38 515 39 HOH HOH . 
F 5 HOH A 39 516 40 HOH HOH . 
F 5 HOH A 40 517 41 HOH HOH . 
F 5 HOH A 41 518 42 HOH HOH . 
F 5 HOH A 42 519 43 HOH HOH . 
F 5 HOH A 43 520 44 HOH HOH . 
F 5 HOH A 44 521 45 HOH HOH . 
F 5 HOH A 45 522 46 HOH HOH . 
F 5 HOH A 46 523 47 HOH HOH . 
F 5 HOH A 47 524 48 HOH HOH . 
F 5 HOH A 48 525 49 HOH HOH . 
F 5 HOH A 49 526 50 HOH HOH . 
F 5 HOH A 50 527 51 HOH HOH . 
F 5 HOH A 51 528 52 HOH HOH . 
F 5 HOH A 52 529 53 HOH HOH . 
F 5 HOH A 53 530 54 HOH HOH . 
F 5 HOH A 54 531 55 HOH HOH . 
F 5 HOH A 55 532 56 HOH HOH . 
F 5 HOH A 56 533 57 HOH HOH . 
F 5 HOH A 57 534 58 HOH HOH . 
F 5 HOH A 58 535 59 HOH HOH . 
F 5 HOH A 59 536 60 HOH HOH . 
F 5 HOH A 60 537 61 HOH HOH . 
F 5 HOH A 61 538 62 HOH HOH . 
F 5 HOH A 62 539 63 HOH HOH . 
F 5 HOH A 63 540 64 HOH HOH . 
F 5 HOH A 64 541 65 HOH HOH . 
F 5 HOH A 65 542 66 HOH HOH . 
F 5 HOH A 66 543 67 HOH HOH . 
F 5 HOH A 67 544 68 HOH HOH . 
F 5 HOH A 68 545 69 HOH HOH . 
F 5 HOH A 69 546 70 HOH HOH . 
F 5 HOH A 70 547 71 HOH HOH . 
F 5 HOH A 71 548 72 HOH HOH . 
F 5 HOH A 72 549 73 HOH HOH . 
F 5 HOH A 73 550 74 HOH HOH . 
F 5 HOH A 74 551 75 HOH HOH . 
F 5 HOH A 75 552 76 HOH HOH . 
F 5 HOH A 76 553 77 HOH HOH . 
F 5 HOH A 77 554 78 HOH HOH . 
F 5 HOH A 78 555 79 HOH HOH . 
F 5 HOH A 79 556 80 HOH HOH . 
F 5 HOH A 80 557 81 HOH HOH . 
F 5 HOH A 81 558 82 HOH HOH . 
F 5 HOH A 82 559 83 HOH HOH . 
F 5 HOH A 83 560 84 HOH HOH . 
F 5 HOH A 84 561 85 HOH HOH . 
F 5 HOH A 85 562 86 HOH HOH . 
F 5 HOH A 86 563 87 HOH HOH . 
F 5 HOH A 87 564 88 HOH HOH . 
F 5 HOH A 88 565 89 HOH HOH . 
F 5 HOH A 89 566 90 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 . . A C 3 18.807 7.385 81.752 1 36.55 ? C1 NAG 476 A 1 
HETATM 2 C C2 NAG . . A C 3 17.974 7.052 82.945 1 38.45 ? C2 NAG 476 A 1 
HETATM 3 C C3 NAG . . A C 3 18.654 7.606 84.191 1 40.91 ? C3 NAG 476 A 1 
HETATM 4 C C4 NAG . . A C 3 20.097 7.069 84.332 1 41.85 ? C4 NAG 476 A 1 
HETATM 5 C C5 NAG . . A C 3 20.869 7.553 83.039 1 42.42 ? C5 NAG 476 A 1 
HETATM 6 C C6 NAG . . A C 3 22.388 7.245 82.921 1 43.81 ? C6 NAG 476 A 1 
HETATM 7 C C7 NAG . . A C 3 15.53 7.067 83.048 1 40.24 ? C7 NAG 476 A 1 
HETATM 8 C C8 NAG . . A C 3 14.241 7.874 83.13 1 41.23 ? C8 NAG 476 A 1 
HETATM 9 N N2 NAG . . A C 3 16.671 7.712 82.822 1 38.97 ? N2 NAG 476 A 1 
HETATM 10 O O3 NAG . . A C 3 17.955 7.362 85.401 1 42.21 ? O3 NAG 476 A 1 
HETATM 11 O O4 NAG . . A C 3 20.586 7.601 85.566 1 45.3 ? O4 NAG 476 A 1 
HETATM 12 O O5 NAG . . A C 3 20.179 6.96 81.892 1 40.04 ? O5 NAG 476 A 1 
HETATM 13 O O6 NAG . . A C 3 22.758 7.236 81.55 1 45.48 ? O6 NAG 476 A 1 
HETATM 14 O O7 NAG . . A C 3 15.511 5.838 83.131 1 42.17 ? O7 NAG 476 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#