data_4KDQ
#
_model_server_result.job_id            F3hUgaAJW5MhDHP9ziCh-g 
_model_server_result.datetime_utc      '2024-10-16 20:59:11' 
_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          4kdq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":502}' 
#
_entry.id    4KDQ 
#
_exptl.entry_id    4KDQ 
_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    7 
_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            4KDQ 
_cell.length_a            72.049 
_cell.length_b            72.049 
_cell.length_c            365.862 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KDQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 
_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
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M 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 5 A CYS 5 1_555 D SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 A SG CYS 43 A CYS 43 1_555 A SG CYS 275 A CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 A SG CYS 56 A CYS 56 1_555 A SG CYS 68 A CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf4 A SG CYS 91 A CYS 91 1_555 A SG CYS 136 A CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
disulf ? disulf5 A SG CYS 279 A CYS 279 1_555 A SG CYS 303 A CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf6 B SG CYS 5 C CYS 5 1_555 E SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
disulf ? disulf7 B SG CYS 43 C CYS 43 1_555 B SG CYS 275 C CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf8 B SG CYS 56 C CYS 56 1_555 B SG CYS 68 C CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf9 B SG CYS 91 C CYS 91 1_555 B SG CYS 136 C CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
disulf ? disulf10 B SG CYS 279 C CYS 279 1_555 B SG CYS 303 C CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf11 C SG CYS 5 E CYS 5 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf12 C SG CYS 43 E CYS 43 1_555 C SG CYS 275 E CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf13 C SG CYS 56 E CYS 56 1_555 C SG CYS 68 E CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf14 C SG CYS 91 E CYS 91 1_555 C SG CYS 136 E CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf15 C SG CYS 279 E CYS 279 1_555 C SG CYS 303 E CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf16 D SG CYS 144 B CYS 144 1_555 D SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf17 E SG CYS 144 D CYS 144 1_555 E SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale1 A ND2 ASN 24 A ASN 24 1_555 G C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale2 A ND2 ASN 166 A ASN 166 1_555 H C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale3 B ND2 ASN 24 C ASN 24 1_555 I C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale4 B ND2 ASN 166 C ASN 166 1_555 J C1 NAG . C NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? 
covale ? covale5 C ND2 ASN 24 E ASN 24 1_555 K C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale6 C ND2 ASN 155 E ASN 155 1_555 M C1 NAG . E NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale7 C ND2 ASN 166 E ASN 166 1_555 L C1 NAG . E NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
#
_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                     4KDQ 
_atom_sites.fract_transf_matrix[1][1]    0.013879 
_atom_sites.fract_transf_matrix[1][2]    0.008013 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016027 
_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]    0.002733 
_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
G 3 NAG A 1 501 501 NAG NAG . 
H 3 NAG A 1 502 502 NAG NAG . 
I 3 NAG C 1 501 501 NAG NAG . 
J 3 NAG C 1 502 502 NAG NAG . 
K 3 NAG E 1 501 501 NAG NAG . 
L 3 NAG E 1 502 502 NAG NAG . 
M 3 NAG E 1 503 503 NAG NAG . 
N 4 HOH A 1 601 1 HOH HOH . 
N 4 HOH A 2 602 4 HOH HOH . 
N 4 HOH A 3 603 5 HOH HOH . 
N 4 HOH A 4 604 6 HOH HOH . 
N 4 HOH A 5 605 7 HOH HOH . 
N 4 HOH A 6 606 8 HOH HOH . 
N 4 HOH A 7 607 9 HOH HOH . 
N 4 HOH A 8 608 10 HOH HOH . 
N 4 HOH A 9 609 22 HOH HOH . 
N 4 HOH A 10 610 27 HOH HOH . 
N 4 HOH A 11 611 28 HOH HOH . 
N 4 HOH A 12 612 32 HOH HOH . 
N 4 HOH A 13 613 33 HOH HOH . 
N 4 HOH A 14 614 46 HOH HOH . 
N 4 HOH A 15 615 50 HOH HOH . 
N 4 HOH A 16 616 52 HOH HOH . 
N 4 HOH A 17 617 55 HOH HOH . 
N 4 HOH A 18 618 56 HOH HOH . 
N 4 HOH A 19 619 63 HOH HOH . 
N 4 HOH A 20 620 64 HOH HOH . 
N 4 HOH A 21 621 67 HOH HOH . 
N 4 HOH A 22 622 69 HOH HOH . 
N 4 HOH A 23 623 72 HOH HOH . 
O 4 HOH C 1 601 3 HOH HOH . 
O 4 HOH C 2 602 11 HOH HOH . 
O 4 HOH C 3 603 12 HOH HOH . 
O 4 HOH C 4 604 16 HOH HOH . 
O 4 HOH C 5 605 19 HOH HOH . 
O 4 HOH C 6 606 21 HOH HOH . 
O 4 HOH C 7 607 31 HOH HOH . 
O 4 HOH C 8 608 34 HOH HOH . 
O 4 HOH C 9 609 36 HOH HOH . 
O 4 HOH C 10 610 39 HOH HOH . 
O 4 HOH C 11 611 41 HOH HOH . 
O 4 HOH C 12 612 48 HOH HOH . 
O 4 HOH C 13 613 49 HOH HOH . 
O 4 HOH C 14 614 53 HOH HOH . 
O 4 HOH C 15 615 61 HOH HOH . 
O 4 HOH C 16 616 62 HOH HOH . 
P 4 HOH E 1 601 13 HOH HOH . 
P 4 HOH E 2 602 14 HOH HOH . 
P 4 HOH E 3 603 15 HOH HOH . 
P 4 HOH E 4 604 26 HOH HOH . 
P 4 HOH E 5 605 29 HOH HOH . 
P 4 HOH E 6 606 30 HOH HOH . 
P 4 HOH E 7 607 35 HOH HOH . 
P 4 HOH E 8 608 42 HOH HOH . 
P 4 HOH E 9 609 43 HOH HOH . 
P 4 HOH E 10 610 45 HOH HOH . 
P 4 HOH E 11 611 54 HOH HOH . 
P 4 HOH E 12 612 65 HOH HOH . 
P 4 HOH E 13 613 68 HOH HOH . 
P 4 HOH E 14 614 70 HOH HOH . 
P 4 HOH E 15 615 73 HOH HOH . 
Q 4 HOH B 1 201 2 HOH HOH . 
Q 4 HOH B 2 202 18 HOH HOH . 
Q 4 HOH B 3 203 24 HOH HOH . 
Q 4 HOH B 4 204 25 HOH HOH . 
Q 4 HOH B 5 205 38 HOH HOH . 
Q 4 HOH B 6 206 40 HOH HOH . 
Q 4 HOH B 7 207 47 HOH HOH . 
Q 4 HOH B 8 208 59 HOH HOH . 
R 4 HOH D 1 201 17 HOH HOH . 
R 4 HOH D 2 202 20 HOH HOH . 
R 4 HOH D 3 203 37 HOH HOH . 
R 4 HOH D 4 204 44 HOH HOH . 
R 4 HOH D 5 205 51 HOH HOH . 
R 4 HOH D 6 206 58 HOH HOH . 
R 4 HOH D 7 207 71 HOH HOH . 
S 4 HOH F 1 201 23 HOH HOH . 
S 4 HOH F 2 202 57 HOH HOH . 
S 4 HOH F 3 203 60 HOH HOH . 
S 4 HOH F 4 204 66 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 . . . H 3 7.291 5.44 -35.428 1 60.84 ? C1 NAG 502 A 1 
HETATM 2 C C2 NAG . . . H 3 6.527 4.117 -35.419 1 58.68 ? C2 NAG 502 A 1 
HETATM 3 C C3 NAG . . . H 3 7.368 2.979 -34.831 1 70.59 ? C3 NAG 502 A 1 
HETATM 4 C C4 NAG . . . H 3 8.766 3.005 -35.445 1 90.12 ? C4 NAG 502 A 1 
HETATM 5 C C5 NAG . . . H 3 9.355 4.401 -35.23 1 83.64 ? C5 NAG 502 A 1 
HETATM 6 C C6 NAG . . . H 3 10.852 4.478 -35.541 1 87.8 ? C6 NAG 502 A 1 
HETATM 7 C C7 NAG . . . H 3 4.11 3.91 -35.056 1 50.24 ? C7 NAG 502 A 1 
HETATM 8 C C8 NAG . . . H 3 3.132 3.553 -33.972 1 42.19 ? C8 NAG 502 A 1 
HETATM 9 N N2 NAG . . . H 3 5.313 4.313 -34.649 1 51.45 ? N2 NAG 502 A 1 
HETATM 10 O O3 NAG . . . H 3 6.75 1.717 -35.018 1 58.16 ? O3 NAG 502 A 1 
HETATM 11 O O4 NAG . . . H 3 9.588 1.998 -34.888 1 95.25 ? O4 NAG 502 A 1 
HETATM 12 O O5 NAG . . . H 3 8.59 5.331 -35.983 1 62.47 ? O5 NAG 502 A 1 
HETATM 13 O O6 NAG . . . H 3 11.098 4.624 -36.921 1 92.74 ? O6 NAG 502 A 1 
HETATM 14 O O7 NAG . . . H 3 3.786 3.827 -36.245 1 60.76 ? O7 NAG 502 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           14 
#