data_3VYD
#
_model_server_result.job_id            VQHvYPcJScBp3tgA2dR-LQ 
_model_server_result.datetime_utc      '2025-03-23 15:17:35' 
_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          3vyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    3VYD 
#
_exptl.entry_id    3VYD 
_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            3VYD 
_cell.length_a            141.025 
_cell.length_b            141.025 
_cell.length_c            141.025 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA hexameric 6 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 1 
A,B,C,D,E,F,G,H 3 1,2,3 
#
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' 6_577 z+1/2,-x+5/2,-y+2 0 0 1 -1 0 0 0 -1 0 70.5125 352.5625 282.05 
3 'crystal symmetry operation' 12_774 -y+5/2,-z+2,x-1/2 0 -1 0 0 0 -1 1 0 0 352.5625 282.05 -70.5125 
#
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 E 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 51 A CYS 51 1_555 A SG CYS 58 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf2 A SG CYS 217 A CYS 217 1_555 A SG CYS 221 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? 
disulf ? disulf3 A SG CYS 259 A CYS 259 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 B SG CYS 51 B CYS 51 1_555 B SG CYS 58 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? 
disulf ? disulf5 B SG CYS 217 B CYS 217 1_555 B SG CYS 221 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
disulf ? disulf6 B SG CYS 259 B CYS 259 1_555 B SG CYS 296 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
covale ? covale1 A ND2 ASN 75 A ASN 75 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? 
covale ? covale2 B ND2 ASN 75 B ASN 75 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
#
_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                     3VYD 
_atom_sites.fract_transf_matrix[1][1]    0.007091 
_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]    0.007091 
_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]    0.007091 
_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 1 401 401 NAG NAG . 
D 3 VYD A 1 402 501 VYD UNL . 
E 2 NAG B 1 401 401 NAG NAG . 
F 3 VYD B 1 402 501 VYD UNL . 
G 4 HOH A 1 501 2 HOH HOH . 
G 4 HOH A 2 502 3 HOH HOH . 
G 4 HOH A 3 503 4 HOH HOH . 
G 4 HOH A 4 504 6 HOH HOH . 
G 4 HOH A 5 505 7 HOH HOH . 
G 4 HOH A 6 506 10 HOH HOH . 
G 4 HOH A 7 507 12 HOH HOH . 
G 4 HOH A 8 508 13 HOH HOH . 
G 4 HOH A 9 509 14 HOH HOH . 
G 4 HOH A 10 510 17 HOH HOH . 
G 4 HOH A 11 511 19 HOH HOH . 
G 4 HOH A 12 512 20 HOH HOH . 
G 4 HOH A 13 513 21 HOH HOH . 
G 4 HOH A 14 514 23 HOH HOH . 
G 4 HOH A 15 515 24 HOH HOH . 
G 4 HOH A 16 516 26 HOH HOH . 
G 4 HOH A 17 517 27 HOH HOH . 
G 4 HOH A 18 518 29 HOH HOH . 
G 4 HOH A 19 519 30 HOH HOH . 
G 4 HOH A 20 520 32 HOH HOH . 
G 4 HOH A 21 521 33 HOH HOH . 
G 4 HOH A 22 522 34 HOH HOH . 
G 4 HOH A 23 523 35 HOH HOH . 
G 4 HOH A 24 524 37 HOH HOH . 
G 4 HOH A 25 525 38 HOH HOH . 
G 4 HOH A 26 526 39 HOH HOH . 
G 4 HOH A 27 527 40 HOH HOH . 
G 4 HOH A 28 528 41 HOH HOH . 
G 4 HOH A 29 529 42 HOH HOH . 
G 4 HOH A 30 530 44 HOH HOH . 
G 4 HOH A 31 531 47 HOH HOH . 
G 4 HOH A 32 532 49 HOH HOH . 
G 4 HOH A 33 533 52 HOH HOH . 
G 4 HOH A 34 534 53 HOH HOH . 
G 4 HOH A 35 535 58 HOH HOH . 
G 4 HOH A 36 536 59 HOH HOH . 
G 4 HOH A 37 537 61 HOH HOH . 
G 4 HOH A 38 538 62 HOH HOH . 
G 4 HOH A 39 539 63 HOH HOH . 
G 4 HOH A 40 540 65 HOH HOH . 
G 4 HOH A 41 541 72 HOH HOH . 
G 4 HOH A 42 542 73 HOH HOH . 
G 4 HOH A 43 543 77 HOH HOH . 
G 4 HOH A 44 544 79 HOH HOH . 
G 4 HOH A 45 545 81 HOH HOH . 
G 4 HOH A 46 546 84 HOH HOH . 
G 4 HOH A 47 547 85 HOH HOH . 
G 4 HOH A 48 548 87 HOH HOH . 
G 4 HOH A 49 549 91 HOH HOH . 
G 4 HOH A 50 550 96 HOH HOH . 
G 4 HOH A 51 551 97 HOH HOH . 
G 4 HOH A 52 552 98 HOH HOH . 
G 4 HOH A 53 553 102 HOH HOH . 
G 4 HOH A 54 554 105 HOH HOH . 
G 4 HOH A 55 555 106 HOH HOH . 
G 4 HOH A 56 556 107 HOH HOH . 
G 4 HOH A 57 557 109 HOH HOH . 
G 4 HOH A 58 558 112 HOH HOH . 
G 4 HOH A 59 559 114 HOH HOH . 
G 4 HOH A 60 560 116 HOH HOH . 
G 4 HOH A 61 561 120 HOH HOH . 
G 4 HOH A 62 562 122 HOH HOH . 
G 4 HOH A 63 563 123 HOH HOH . 
G 4 HOH A 64 564 124 HOH HOH . 
G 4 HOH A 65 565 126 HOH HOH . 
G 4 HOH A 66 566 127 HOH HOH . 
G 4 HOH A 67 567 128 HOH HOH . 
G 4 HOH A 68 568 130 HOH HOH . 
G 4 HOH A 69 569 132 HOH HOH . 
G 4 HOH A 70 570 134 HOH HOH . 
G 4 HOH A 71 571 135 HOH HOH . 
G 4 HOH A 72 572 138 HOH HOH . 
G 4 HOH A 73 573 139 HOH HOH . 
G 4 HOH A 74 574 142 HOH HOH . 
G 4 HOH A 75 575 143 HOH HOH . 
G 4 HOH A 76 576 145 HOH HOH . 
G 4 HOH A 77 577 146 HOH HOH . 
G 4 HOH A 78 578 147 HOH HOH . 
G 4 HOH A 79 579 148 HOH HOH . 
G 4 HOH A 80 580 153 HOH HOH . 
G 4 HOH A 81 581 156 HOH HOH . 
G 4 HOH A 82 582 158 HOH HOH . 
G 4 HOH A 83 583 159 HOH HOH . 
G 4 HOH A 84 584 161 HOH HOH . 
G 4 HOH A 85 585 163 HOH HOH . 
G 4 HOH A 86 586 165 HOH HOH . 
G 4 HOH A 87 587 167 HOH HOH . 
G 4 HOH A 88 588 169 HOH HOH . 
H 4 HOH B 1 501 1 HOH HOH . 
H 4 HOH B 2 502 5 HOH HOH . 
H 4 HOH B 3 503 8 HOH HOH . 
H 4 HOH B 4 504 9 HOH HOH . 
H 4 HOH B 5 505 11 HOH HOH . 
H 4 HOH B 6 506 15 HOH HOH . 
H 4 HOH B 7 507 16 HOH HOH . 
H 4 HOH B 8 508 18 HOH HOH . 
H 4 HOH B 9 509 22 HOH HOH . 
H 4 HOH B 10 510 25 HOH HOH . 
H 4 HOH B 11 511 28 HOH HOH . 
H 4 HOH B 12 512 31 HOH HOH . 
H 4 HOH B 13 513 36 HOH HOH . 
H 4 HOH B 14 514 43 HOH HOH . 
H 4 HOH B 15 515 45 HOH HOH . 
H 4 HOH B 16 516 46 HOH HOH . 
H 4 HOH B 17 517 48 HOH HOH . 
H 4 HOH B 18 518 50 HOH HOH . 
H 4 HOH B 19 519 51 HOH HOH . 
H 4 HOH B 20 520 54 HOH HOH . 
H 4 HOH B 21 521 55 HOH HOH . 
H 4 HOH B 22 522 56 HOH HOH . 
H 4 HOH B 23 523 57 HOH HOH . 
H 4 HOH B 24 524 60 HOH HOH . 
H 4 HOH B 25 525 64 HOH HOH . 
H 4 HOH B 26 526 66 HOH HOH . 
H 4 HOH B 27 527 67 HOH HOH . 
H 4 HOH B 28 528 68 HOH HOH . 
H 4 HOH B 29 529 69 HOH HOH . 
H 4 HOH B 30 530 70 HOH HOH . 
H 4 HOH B 31 531 71 HOH HOH . 
H 4 HOH B 32 532 74 HOH HOH . 
H 4 HOH B 33 533 75 HOH HOH . 
H 4 HOH B 34 534 76 HOH HOH . 
H 4 HOH B 35 535 78 HOH HOH . 
H 4 HOH B 36 536 80 HOH HOH . 
H 4 HOH B 37 537 82 HOH HOH . 
H 4 HOH B 38 538 83 HOH HOH . 
H 4 HOH B 39 539 86 HOH HOH . 
H 4 HOH B 40 540 88 HOH HOH . 
H 4 HOH B 41 541 89 HOH HOH . 
H 4 HOH B 42 542 90 HOH HOH . 
H 4 HOH B 43 543 92 HOH HOH . 
H 4 HOH B 44 544 93 HOH HOH . 
H 4 HOH B 45 545 94 HOH HOH . 
H 4 HOH B 46 546 95 HOH HOH . 
H 4 HOH B 47 547 99 HOH HOH . 
H 4 HOH B 48 548 100 HOH HOH . 
H 4 HOH B 49 549 101 HOH HOH . 
H 4 HOH B 50 550 103 HOH HOH . 
H 4 HOH B 51 551 104 HOH HOH . 
H 4 HOH B 52 552 108 HOH HOH . 
H 4 HOH B 53 553 110 HOH HOH . 
H 4 HOH B 54 554 111 HOH HOH . 
H 4 HOH B 55 555 113 HOH HOH . 
H 4 HOH B 56 556 115 HOH HOH . 
H 4 HOH B 57 557 117 HOH HOH . 
H 4 HOH B 58 558 118 HOH HOH . 
H 4 HOH B 59 559 119 HOH HOH . 
H 4 HOH B 60 560 121 HOH HOH . 
H 4 HOH B 61 561 125 HOH HOH . 
H 4 HOH B 62 562 129 HOH HOH . 
H 4 HOH B 63 563 131 HOH HOH . 
H 4 HOH B 64 564 133 HOH HOH . 
H 4 HOH B 65 565 136 HOH HOH . 
H 4 HOH B 66 566 137 HOH HOH . 
H 4 HOH B 67 567 140 HOH HOH . 
H 4 HOH B 68 568 141 HOH HOH . 
H 4 HOH B 69 569 144 HOH HOH . 
H 4 HOH B 70 570 149 HOH HOH . 
H 4 HOH B 71 571 150 HOH HOH . 
H 4 HOH B 72 572 151 HOH HOH . 
H 4 HOH B 73 573 152 HOH HOH . 
H 4 HOH B 74 574 154 HOH HOH . 
H 4 HOH B 75 575 155 HOH HOH . 
H 4 HOH B 76 576 157 HOH HOH . 
H 4 HOH B 77 577 160 HOH HOH . 
H 4 HOH B 78 578 162 HOH HOH . 
H 4 HOH B 79 579 164 HOH HOH . 
H 4 HOH B 80 580 166 HOH HOH . 
H 4 HOH B 81 581 168 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 . . . E 2 167.589 253.259 84.315 1 107.53 ? C1 NAG 401 B 1 
HETATM 2 C C2 NAG . . . E 2 168.643 254.274 84.743 1 113.24 ? C2 NAG 401 B 1 
HETATM 3 C C3 NAG . . . E 2 168.505 255.485 83.838 1 114.74 ? C3 NAG 401 B 1 
HETATM 4 C C4 NAG . . . E 2 168.816 254.981 82.416 1 110.97 ? C4 NAG 401 B 1 
HETATM 5 C C5 NAG . . . E 2 167.914 253.789 82.008 1 106 ? C5 NAG 401 B 1 
HETATM 6 C C6 NAG . . . E 2 168.343 253.069 80.73 1 93.62 ? C6 NAG 401 B 1 
HETATM 7 C C7 NAG . . . E 2 168.676 254.556 87.349 1 113.66 ? C7 NAG 401 B 1 
HETATM 8 C C8 NAG . . . E 2 169.988 255.239 87.667 1 108.48 ? C8 NAG 401 B 1 
HETATM 9 N N2 NAG . . . E 2 168.255 254.317 86.124 1 113.46 ? N2 NAG 401 B 1 
HETATM 10 O O3 NAG . . . E 2 169.414 256.474 84.262 1 110.87 ? O3 NAG 401 B 1 
HETATM 11 O O4 NAG . . . E 2 168.697 256.04 81.493 1 104.39 ? O4 NAG 401 B 1 
HETATM 12 O O5 NAG . . . E 2 167.867 252.782 83.014 1 113.12 ? O5 NAG 401 B 1 
HETATM 13 O O6 NAG . . . E 2 168.763 253.994 79.763 1 94.56 ? O6 NAG 401 B 1 
HETATM 14 O O7 NAG . . . E 2 167.841 254.196 88.188 1 108.11 ? O7 NAG 401 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#