data_5YDH
#
_model_server_result.job_id            AhyoAeTyAAWszRXD5UMpXA 
_model_server_result.datetime_utc      '2025-02-20 02:46:16' 
_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          5ydh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":807}' 
#
_entry.id    5YDH 
#
_exptl.entry_id    5YDH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              96.063 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SULFATE ION' 
_entity.pdbx_number_of_molecules    26 
_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            5YDH 
_cell.length_a            148.659 
_cell.length_b            148.659 
_cell.length_c            226.021 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YDH 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
B,D,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,PA 1 1 
A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,OA 1 2 
#
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_445 x-y-1,x-1,z+1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 -74.3295 -128.742471 37.670167 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 H N N 
? 4 I N N 
? 4 J N N 
? 4 K N N 
? 4 L N N 
? 4 M N N 
? 4 N N N 
? 4 U N N 
? 4 V N N 
? 4 W N N 
? 4 X N N 
? 4 Y N N 
? 4 Z N N 
? 4 AA N N 
? 4 BA N N 
? 4 CA N N 
? 4 DA N N 
? 4 EA N N 
? 4 FA N N 
? 4 GA N N 
? 4 HA N N 
? 4 IA N N 
? 4 JA N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
2 oligosaccharide 
3 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
5 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
6 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 
7 ? 3 5 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 C NAG 1 C 1 NAG A 812 NAG 
2 n C NAG 2 C 2 NAG A 813 NAG 
2 n C BMA 3 C 3 BMA A 814 BMA 
2 n C MAN 4 C 4 MAN A 815 MAN 
3 n D NAG 1 D 1 NAG B 818 NAG 
3 n D NAG 2 D 2 NAG B 819 NAG 
3 n D BMA 3 D 3 BMA B 820 BMA 
3 n D MAN 4 D 4 MAN B 822 MAN 
3 n D MAN 5 D 5 MAN B 821 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 67 A CYS 228 1_555 A SG CYS 94 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 253 A CYS 414 1_555 A SG CYS 266 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 A SG CYS 401 A CYS 562 1_555 A SG CYS 522 A CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf4 B SG CYS 67 B CYS 228 1_555 B SG CYS 94 B CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 B SG CYS 253 B CYS 414 1_555 B SG CYS 266 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf6 B SG CYS 401 B CYS 562 1_555 B SG CYS 522 B CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
covale ? covale1 A ND2 ASN 59 A ASN 220 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale2 A ND2 ASN 509 A ASN 670 1_555 O C1 NAG . A NAG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale3 B ND2 ASN 59 B ASN 220 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale4 B ND2 ASN 509 B ASN 670 1_555 KA C1 NAG . B NAG 817 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale10 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale11 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
metalc ? metalc1 A NE2 HIS 255 A HIS 416 1_555 T CO CO . A CO 816 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc2 B NE2 HIS 255 B HIS 416 1_555 NA CO CO . B CO 820 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
#
_chem_comp.formula           'O4 S -2' 
_chem_comp.formula_weight    96.063 
_chem_comp.id                SO4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SULFATE ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
S O1 SO4 doub 414 n n 
S O2 SO4 doub 415 n n 
S O3 SO4 sing 416 n n 
S O4 SO4 sing 417 n n 
#
_atom_sites.entry_id                     5YDH 
_atom_sites.fract_transf_matrix[1][1]    0.006727 
_atom_sites.fract_transf_matrix[1][2]    0.003884 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007767 
_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]    0.004424 
_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
E 4 SO4 A 1 801 801 SO4 SO4 . 
F 4 SO4 A 1 802 802 SO4 SO4 . 
G 4 SO4 A 1 803 803 SO4 SO4 . 
H 4 SO4 A 1 804 804 SO4 SO4 . 
I 4 SO4 A 1 805 805 SO4 SO4 . 
J 4 SO4 A 1 806 806 SO4 SO4 . 
K 4 SO4 A 1 807 807 SO4 SO4 . 
L 4 SO4 A 1 808 808 SO4 SO4 . 
M 4 SO4 A 1 809 809 SO4 SO4 . 
N 4 SO4 A 1 810 810 SO4 SO4 . 
O 5 NAG A 1 811 811 NAG NAG . 
P 6 EPE A 1 812 816 EPE EPE . 
Q 6 EPE A 1 813 817 EPE EPE . 
R 7 GOL A 1 814 818 GOL GOL . 
S 7 GOL A 1 815 819 GOL GOL . 
T 8 CO A 1 816 820 CO CO . 
U 4 SO4 B 1 801 801 SO4 SO4 . 
V 4 SO4 B 1 802 802 SO4 SO4 . 
W 4 SO4 B 1 803 803 SO4 SO4 . 
X 4 SO4 B 1 804 804 SO4 SO4 . 
Y 4 SO4 B 1 805 805 SO4 SO4 . 
Z 4 SO4 B 1 806 806 SO4 SO4 . 
AA 4 SO4 B 1 807 807 SO4 SO4 . 
BA 4 SO4 B 1 808 808 SO4 SO4 . 
CA 4 SO4 B 1 809 809 SO4 SO4 . 
DA 4 SO4 B 1 810 810 SO4 SO4 . 
EA 4 SO4 B 1 811 811 SO4 SO4 . 
FA 4 SO4 B 1 812 812 SO4 SO4 . 
GA 4 SO4 B 1 813 813 SO4 SO4 . 
HA 4 SO4 B 1 814 814 SO4 SO4 . 
IA 4 SO4 B 1 815 815 SO4 SO4 . 
JA 4 SO4 B 1 816 816 SO4 SO4 . 
KA 5 NAG B 1 817 817 NAG NAG . 
LA 6 EPE B 1 818 823 EPE EPE . 
MA 7 GOL B 1 819 824 GOL GOL . 
NA 8 CO B 1 820 825 CO CO . 
OA 9 HOH A 1 901 901 HOH HOH . 
OA 9 HOH A 2 902 903 HOH HOH . 
OA 9 HOH A 3 903 907 HOH HOH . 
OA 9 HOH A 4 904 904 HOH HOH . 
OA 9 HOH A 5 905 905 HOH HOH . 
OA 9 HOH A 6 906 906 HOH HOH . 
OA 9 HOH A 7 907 902 HOH HOH . 
PA 9 HOH B 1 901 901 HOH HOH . 
PA 9 HOH B 2 902 902 HOH HOH . 
PA 9 HOH B 3 903 903 HOH HOH . 
PA 9 HOH B 4 904 905 HOH HOH . 
PA 9 HOH B 5 905 904 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 S S SO4 . . . K 4 74.134 -45.102 -15.785 1 168.35 ? S SO4 807 A 1 
HETATM 2 O O1 SO4 . . . K 4 74.415 -46.546 -15.62 1 168.04 ? O1 SO4 807 A 1 
HETATM 3 O O2 SO4 . . . K 4 73.649 -44.847 -17.161 1 169.47 ? O2 SO4 807 A 1 
HETATM 4 O O3 SO4 . . . K 4 73.094 -44.689 -14.816 1 172.46 ? O3 SO4 807 A 1 
HETATM 5 O O4 SO4 . . . K 4 75.371 -44.326 -15.543 1 167.91 ? O4 SO4 807 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           484 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           5 
#