data_8WSA
#
_model_server_result.job_id            VzQonzKNegJUoLvlI5KuGA 
_model_server_result.datetime_utc      '2024-11-05 08:25:47' 
_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          8wsa 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":205}' 
#
_entry.id    8WSA 
#
_exptl.entry_id    8WSA 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              274.162 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate' 
_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            8WSA 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8WSA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,T,U,V,W,X,Y,Z,AA,BA 
_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
? 6 I N N 
? 6 V 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 7 C CYS 25 1_555 A SG CYS 33 C CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 19 C CYS 37 1_555 A SG CYS 130 C CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
disulf ? disulf3 A SG CYS 77 C CYS 95 1_555 A SG CYS 87 C CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf4 B SG CYS 3 A CYS 28 1_555 B SG CYS 14 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf5 B SG CYS 255 A CYS 280 1_555 B SG CYS 279 A CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf6 B SG CYS 363 A CYS 388 1_555 B SG CYS 364 A CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf7 B SG CYS 555 A CYS 580 1_555 B SG CYS 581 A CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf8 C SG CYS 7 D CYS 25 1_555 C SG CYS 33 D CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf9 C SG CYS 19 D CYS 37 1_555 C SG CYS 130 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
disulf ? disulf10 C SG CYS 77 D CYS 95 1_555 C SG CYS 87 D CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf11 D SG CYS 3 B CYS 28 1_555 D SG CYS 14 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf12 D SG CYS 255 B CYS 280 1_555 D SG CYS 279 B CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf13 D SG CYS 363 B CYS 388 1_555 D SG CYS 364 B CYS 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf14 D SG CYS 555 B CYS 580 1_555 D SG CYS 581 B CYS 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
covale ? covale1 A ND2 ASN 96 C ASN 114 1_555 F C1 NAG . C NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale2 A ND2 ASN 132 C ASN 150 1_555 E C1 NAG . C NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale3 G C1 2IL . C 2IL 203 1_555 P N2 GP4 . A GP4 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.287 ? 
covale ? covale4 H O3E 0IL . C 0IL 204 1_555 P C3 GP4 . A GP4 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale5 I C6 X6N . C X6N 205 1_555 J O52 A1L01 . C A1L01 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? 
covale ? covale6 I OXT X6N . C X6N 205 1_555 P C1 GP4 . A GP4 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? 
covale ? covale7 B ND2 ASN 179 A ASN 204 1_555 M C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale8 B ND2 ASN 212 A ASN 237 1_555 N C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale9 B ND2 ASN 499 A ASN 524 1_555 K C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale10 B ND2 ASN 547 A ASN 572 1_555 O C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale11 Q O52 A1L01 . A A1L01 707 1_555 V C6 X6N . D X6N 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? 
covale ? covale12 C ND2 ASN 96 D ASN 114 1_555 S C1 NAG . D NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale13 C ND2 ASN 132 D ASN 150 1_555 R C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale14 T C1 2IL . D 2IL 203 1_555 BA N2 GP4 . B GP4 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.288 ? 
covale ? covale15 U O3E 0IL . D 0IL 204 1_555 BA C3 GP4 . B GP4 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale16 V OXT X6N . D X6N 205 1_555 BA C1 GP4 . B GP4 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? 
covale ? covale17 D ND2 ASN 179 B ASN 204 1_555 Y C1 NAG . B NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale18 D ND2 ASN 212 B ASN 237 1_555 Z C1 NAG . B NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale19 D ND2 ASN 499 B ASN 524 1_555 W C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale20 D ND2 ASN 547 B ASN 572 1_555 AA C1 NAG . B NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
#
_chem_comp.formula           'C7 H15 O9 P' 
_chem_comp.formula_weight    274.162 
_chem_comp.id                X6N 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate' 
_chem_comp.type              'd-saccharide, alpha linking' 
_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
O56 P51 X6N doub 671 n n 
O54 P51 X6N sing 672 n n 
O55 P51 X6N sing 673 n n 
P51 O4 X6N sing 674 n n 
O3 C3 X6N sing 675 n n 
C48 O47 X6N sing 676 n n 
O47 C2 X6N sing 677 n n 
O4 C4 X6N sing 678 n n 
C3 C4 X6N sing 679 n n 
C3 C2 X6N sing 680 n n 
C4 C5 X6N sing 681 n n 
C2 C1 X6N sing 682 n n 
C5 C6 X6N sing 683 n n 
C5 O5 X6N sing 684 n n 
C1 O5 X6N sing 685 n n 
C6 O52 X6N sing 686 n n 
C1 H1 X6N sing 687 n n 
C2 H3 X6N sing 688 n n 
C3 H4 X6N sing 689 n n 
C4 H5 X6N sing 690 n n 
C48 H6 X6N sing 691 n n 
C48 H7 X6N sing 692 n n 
C48 H8 X6N sing 693 n n 
C5 H9 X6N sing 694 n n 
C6 H10 X6N sing 695 n n 
C6 H11 X6N sing 696 n n 
O3 H12 X6N sing 697 n n 
O52 H13 X6N sing 698 n n 
O54 H14 X6N sing 699 n n 
O55 H15 X6N sing 700 n n 
C1 OXT X6N sing 701 n n 
OXT HXT X6N sing 702 n n 
#
_atom_sites.entry_id                     8WSA 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 3 NAG C 1 201 302 NAG NAG . 
F 3 NAG C 1 202 303 NAG NAG . 
G 4 2IL C 1 203 1 2IL LM5 . 
H 5 0IL C 1 204 1 0IL LM5 . 
I 6 X6N C 1 205 1 X6N LM5 . 
J 7 A1L01 C 1 206 1 A1L01 LM5 . 
K 3 NAG A 1 701 621 NAG NAG . 
L 3 NAG A 1 702 626 NAG NAG . 
M 3 NAG A 1 703 629 NAG NAG . 
N 3 NAG A 1 704 630 NAG NAG . 
O 3 NAG A 1 705 631 NAG NAG . 
P 8 GP4 A 1 706 1 GP4 LM5 . 
Q 7 A1L01 A 1 707 2 A1L01 LM5 . 
R 3 NAG D 1 201 302 NAG NAG . 
S 3 NAG D 1 202 303 NAG NAG . 
T 4 2IL D 1 203 2 2IL LM5 . 
U 5 0IL D 1 204 2 0IL LM5 . 
V 6 X6N D 1 205 2 X6N LM5 . 
W 3 NAG B 1 701 621 NAG NAG . 
X 3 NAG B 1 702 626 NAG NAG . 
Y 3 NAG B 1 703 629 NAG NAG . 
Z 3 NAG B 1 704 630 NAG NAG . 
AA 3 NAG B 1 705 631 NAG NAG . 
BA 8 GP4 B 1 706 2 GP4 LM5 . 
#
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 X6N . . . V 6 189.807 166.151 180.255 1 97.65 ? C1 X6N 205 D 1 
HETATM 2 C C2 X6N . . . V 6 189.859 166.658 181.67 1 97.65 ? C2 X6N 205 D 1 
HETATM 3 C C3 X6N . . . V 6 190.714 165.742 182.523 1 97.65 ? C3 X6N 205 D 1 
HETATM 4 C C4 X6N . . . V 6 190.299 164.275 182.367 1 97.65 ? C4 X6N 205 D 1 
HETATM 5 C C48 X6N . . . V 6 188.259 168.009 182.73 1 97.65 ? C48 X6N 205 D 1 
HETATM 6 C C5 X6N . . . V 6 190.065 163.899 180.897 1 97.65 ? C5 X6N 205 D 1 
HETATM 7 C C6 X6N . . . V 6 189.426 162.523 180.781 1 97.65 ? C6 X6N 205 D 1 
HETATM 8 O O3 X6N . . . V 6 190.601 166.124 183.896 1 97.65 ? O3 X6N 205 D 1 
HETATM 9 O O4 X6N . . . V 6 191.327 163.45 182.898 1 97.65 ? O4 X6N 205 D 1 
HETATM 10 O O47 X6N . . . V 6 188.542 166.715 182.205 1 97.65 ? O47 X6N 205 D 1 
HETATM 11 O O5 X6N . . . V 6 189.223 164.861 180.263 1 97.65 ? O5 X6N 205 D 1 
HETATM 12 O O54 X6N . . . V 6 191.907 162.339 185.308 1 97.65 ? O54 X6N 205 D 1 
HETATM 13 O O55 X6N . . . V 6 189.375 162.202 184.324 1 97.65 ? O55 X6N 205 D 1 
HETATM 14 O O56 X6N . . . V 6 191.376 160.734 183.173 1 97.65 ? O56 X6N 205 D 1 
HETATM 15 P P51 X6N . . . V 6 190.999 162.186 183.939 1 97.65 ? P51 X6N 205 D 1 
HETATM 16 O OXT X6N . . . V 6 191.14 166.066 179.752 1 97.65 ? OXT X6N 205 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           335 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           16 
#