data_2R9K
#
_model_server_result.job_id            RDjA4BGExS15X6WLhv5vWg 
_model_server_result.datetime_utc      '2024-10-14 10:13:33' 
_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          2r9k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":600}' 
#
_entry.id    2R9K 
#
_exptl.entry_id    2R9K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    4 
_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            2R9K 
_cell.length_a            107.059 
_cell.length_b            107.059 
_cell.length_c            312.375 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2R9K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA tetrameric 4 software_defined_assembly 2 
PISA tetrameric 4 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,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 2 1,4 
B,C,L,M,N,O,P,Q,S 3 1,5 
A,D,E,F,G,H,I,J,K,R 3 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_654 x-y+1,x,z-1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 107.059 0 -52.0625 
3 'crystal symmetry operation' 8_665 x-y+1,-y+1,-z 1 0 0 0 -1 0 0 0 -1 53.5295 92.715814 0 
4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 53.5295 92.715814 52.0625 
5 'crystal symmetry operation' 12_554 x,x-y,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 -52.0625 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 L N N 
? 4 M N N 
? 4 N N N 
#
_pdbx_entity_branch.entity_id    3 
_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 ? 3 1 2 NAG NAG C4 H4 . O4 HO4 . sing 
2 ? 3 2 1 NAG NAG C4 H4 . O4 HO4 . 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
3 n C NAG 1 C 1 NAG B 602 NAG 
3 n C NAG 2 C 2 NAG B 605 NAG 
#
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 247 A CYS 247 1_555 B SG CYS 5 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf2 B SG CYS 64 B CYS 311 1_555 B SG CYS 81 B CYS 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf3 B SG CYS 152 B CYS 399 1_555 B SG CYS 165 B CYS 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf4 B SG CYS 191 B CYS 438 1_555 B SG CYS 208 B CYS 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
covale ? covale1 B ND2 ASN 96 B ASN 343 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.275 ? 
covale ? covale2 B ND2 ASN 136 B ASN 383 1_555 M C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.257 ? 
covale ? covale3 C C4 NAG . C NAG 1 1_555 C O4 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale4 C O4 NAG . C NAG 1 1_555 C C4 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.358 ? 
#
_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 250 n n 
C1 O1 NAG sing 251 n n 
C1 O5 NAG sing 252 n n 
C1 H1 NAG sing 253 n n 
C2 C3 NAG sing 254 n n 
C2 N2 NAG sing 255 n n 
C2 H2 NAG sing 256 n n 
C3 C4 NAG sing 257 n n 
C3 O3 NAG sing 258 n n 
C3 H3 NAG sing 259 n n 
C4 C5 NAG sing 260 n n 
C4 O4 NAG sing 261 n n 
C4 H4 NAG sing 262 n n 
C5 C6 NAG sing 263 n n 
C5 O5 NAG sing 264 n n 
C5 H5 NAG sing 265 n n 
C6 O6 NAG sing 266 n n 
C6 H61 NAG sing 267 n n 
C6 H62 NAG sing 268 n n 
C7 C8 NAG sing 269 n n 
C7 N2 NAG sing 270 n n 
C7 O7 NAG doub 271 n n 
C8 H81 NAG sing 272 n n 
C8 H82 NAG sing 273 n n 
C8 H83 NAG sing 274 n n 
N2 HN2 NAG sing 275 n n 
O1 HO1 NAG sing 276 n n 
O3 HO3 NAG sing 277 n n 
O4 HO4 NAG sing 278 n n 
O6 HO6 NAG sing 279 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                     2R9K 
_atom_sites.fract_transf_matrix[1][1]    0.009341 
_atom_sites.fract_transf_matrix[1][2]    0.005393 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010786 
_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]    0.003201 
_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
D 4 NAG A 1 500 500 NAG NAG . 
E 5 SO4 A 1 255 255 SO4 SO4 . 
F 5 SO4 A 1 256 256 SO4 SO4 . 
G 5 SO4 A 1 257 257 SO4 SO4 . 
H 6 GOL A 1 649 649 GOL GOL . 
I 6 GOL A 1 650 650 GOL GOL . 
J 7 CL A 1 258 258 CL CL . 
K 8 SGI A 1 600 600 SGI SGI . 
L 4 NAG B 1 600 600 NAG NAG . 
M 4 NAG B 1 603 603 NAG NAG . 
N 4 NAG B 1 604 604 NAG NAG . 
O 5 SO4 B 1 3 3 SO4 SO4 . 
P 6 GOL B 1 647 647 GOL GOL . 
Q 6 GOL B 1 648 648 GOL GOL . 
R 9 HOH A 1 651 651 HOH HOH . 
R 9 HOH A 2 652 652 HOH HOH . 
R 9 HOH A 3 653 653 HOH HOH . 
R 9 HOH A 4 654 654 HOH HOH . 
R 9 HOH A 5 655 655 HOH HOH . 
R 9 HOH A 6 656 656 HOH HOH . 
R 9 HOH A 7 657 657 HOH HOH . 
R 9 HOH A 8 658 658 HOH HOH . 
R 9 HOH A 9 659 659 HOH HOH . 
R 9 HOH A 10 660 660 HOH HOH . 
R 9 HOH A 11 661 661 HOH HOH . 
R 9 HOH A 12 662 662 HOH HOH . 
R 9 HOH A 13 663 663 HOH HOH . 
R 9 HOH A 14 664 664 HOH HOH . 
R 9 HOH A 15 665 665 HOH HOH . 
R 9 HOH A 16 666 666 HOH HOH . 
R 9 HOH A 17 667 667 HOH HOH . 
R 9 HOH A 18 668 668 HOH HOH . 
R 9 HOH A 19 669 669 HOH HOH . 
R 9 HOH A 20 670 670 HOH HOH . 
R 9 HOH A 21 671 671 HOH HOH . 
R 9 HOH A 22 672 672 HOH HOH . 
R 9 HOH A 23 673 673 HOH HOH . 
R 9 HOH A 24 674 674 HOH HOH . 
R 9 HOH A 25 675 675 HOH HOH . 
R 9 HOH A 26 676 676 HOH HOH . 
R 9 HOH A 27 677 675 HOH HOH . 
S 9 HOH B 1 649 649 HOH HOH . 
S 9 HOH B 2 650 650 HOH HOH . 
S 9 HOH B 3 651 651 HOH HOH . 
S 9 HOH B 4 652 652 HOH HOH . 
S 9 HOH B 5 653 653 HOH HOH . 
S 9 HOH B 6 654 654 HOH HOH . 
S 9 HOH B 7 655 655 HOH HOH . 
S 9 HOH B 8 656 656 HOH HOH . 
S 9 HOH B 9 657 657 HOH HOH . 
S 9 HOH B 10 658 658 HOH HOH . 
S 9 HOH B 11 659 659 HOH HOH . 
S 9 HOH B 12 660 660 HOH HOH . 
S 9 HOH B 13 661 661 HOH HOH . 
S 9 HOH B 14 662 662 HOH HOH . 
S 9 HOH B 15 663 663 HOH HOH . 
S 9 HOH B 16 664 664 HOH HOH . 
S 9 HOH B 17 665 665 HOH HOH . 
S 9 HOH B 18 666 666 HOH HOH . 
S 9 HOH B 19 667 667 HOH HOH . 
S 9 HOH B 20 668 668 HOH HOH . 
S 9 HOH B 21 669 669 HOH HOH . 
S 9 HOH B 22 670 670 HOH HOH . 
S 9 HOH B 23 672 672 HOH HOH . 
S 9 HOH B 24 673 673 HOH HOH . 
S 9 HOH B 25 674 674 HOH HOH . 
S 9 HOH B 26 676 676 HOH HOH . 
S 9 HOH B 27 677 677 HOH HOH . 
S 9 HOH B 28 678 678 HOH HOH . 
S 9 HOH B 29 679 679 HOH HOH . 
S 9 HOH B 30 680 680 HOH HOH . 
S 9 HOH B 31 681 681 HOH HOH . 
S 9 HOH B 32 682 682 HOH HOH . 
S 9 HOH B 33 683 683 HOH HOH . 
S 9 HOH B 34 684 684 HOH HOH . 
S 9 HOH B 35 685 685 HOH HOH . 
S 9 HOH B 36 686 686 HOH HOH . 
S 9 HOH B 37 687 687 HOH HOH . 
S 9 HOH B 38 688 688 HOH HOH . 
S 9 HOH B 39 689 689 HOH HOH . 
S 9 HOH B 40 690 690 HOH HOH . 
S 9 HOH B 41 691 691 HOH HOH . 
S 9 HOH B 42 692 692 HOH HOH . 
S 9 HOH B 43 693 693 HOH HOH . 
S 9 HOH B 44 694 694 HOH HOH . 
S 9 HOH B 45 696 696 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 . . . L 4 66.322 20.996 -9.582 1 83.52 ? C1 NAG 600 B 1 
HETATM 2 C C2 NAG . . . L 4 66.107 20.461 -10.999 1 83.38 ? C2 NAG 600 B 1 
HETATM 3 C C3 NAG . . . L 4 65.734 18.981 -10.885 1 83.66 ? C3 NAG 600 B 1 
HETATM 4 C C4 NAG . . . L 4 66.857 18.21 -10.161 1 84.26 ? C4 NAG 600 B 1 
HETATM 5 C C5 NAG . . . L 4 67.477 18.935 -8.941 1 85 ? C5 NAG 600 B 1 
HETATM 6 C C6 NAG . . . L 4 68.927 18.47 -8.736 1 86.04 ? C6 NAG 600 B 1 
HETATM 7 C C7 NAG . . . L 4 64.964 21.601 -12.865 1 81.04 ? C7 NAG 600 B 1 
HETATM 8 C C8 NAG . . . L 4 63.64 22.078 -13.423 1 80.2 ? C8 NAG 600 B 1 
HETATM 9 N N2 NAG . . . L 4 64.976 21.194 -11.582 1 82 ? N2 NAG 600 B 1 
HETATM 10 O O3 NAG . . . L 4 65.46 18.427 -12.185 1 82.34 ? O3 NAG 600 B 1 
HETATM 11 O O4 NAG . . . L 4 66.361 16.943 -9.708 1 83.64 ? O4 NAG 600 B 1 
HETATM 12 O O5 NAG . . . L 4 67.479 20.377 -9.006 1 84.11 ? O5 NAG 600 B 1 
HETATM 13 O O6 NAG . . . L 4 69.031 17.436 -7.739 1 86.56 ? O6 NAG 600 B 1 
HETATM 14 O O7 NAG . . . L 4 65.982 21.668 -13.567 1 80.07 ? O7 NAG 600 B 1 
#
_model_server_stats.io_time_ms              184 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           14 
#