data_4RZC
#
_model_server_result.job_id            BnT2-xt02WCiXsTUK7yyxQ 
_model_server_result.datetime_utc      '2024-11-24 04:49:59' 
_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          4rzc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":201}' 
#
_entry.id    4RZC 
#
_exptl.entry_id    4RZC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              260.136 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-O-phosphono-alpha-D-mannopyranose 
_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         90 
_cell.entry_id            4RZC 
_cell.length_a            60.607 
_cell.length_b            128.05 
_cell.length_c            127.295 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4RZC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,S,T 1 1 
C,D,K,L,U,V 2 1 
E,F,M,N,O,W,X 3 1 
G,H,P,Q,R,Y,Z 4 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 I N N 
? 3 K N N 
? 3 M N N 
? 3 P 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 23 H CYS 22 1_555 A SG CYS 97 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 B SG CYS 22 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 C SG CYS 23 A CYS 22 1_555 C SG CYS 97 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf4 D SG CYS 22 B CYS 23 1_555 D SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf5 E SG CYS 23 C CYS 22 1_555 E SG CYS 97 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf6 F SG CYS 22 D CYS 23 1_555 F SG CYS 88 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf7 G SG CYS 23 E CYS 22 1_555 G SG CYS 97 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf8 H SG CYS 22 F CYS 23 1_555 H SG CYS 88 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
#
_chem_comp.formula           'C6 H13 O9 P' 
_chem_comp.formula_weight    260.136 
_chem_comp.id                M6P 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              6-O-phosphono-alpha-D-mannopyranose 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     ALPHA-D-MANNOSE-6-PHOSPHATE;6-O-phosphono-alpha-D-mannose;6-O-phosphono-D-mannose;6-O-phosphono-mannose 
#
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 M6P sing 218 n n 
C1 O1 M6P sing 219 n n 
C1 O5 M6P sing 220 n n 
C1 H1 M6P sing 221 n n 
C2 C3 M6P sing 222 n n 
C2 O2 M6P sing 223 n n 
C2 H2 M6P sing 224 n n 
C3 C4 M6P sing 225 n n 
C3 O3 M6P sing 226 n n 
C3 H3 M6P sing 227 n n 
C4 C5 M6P sing 228 n n 
C4 O4 M6P sing 229 n n 
C4 H4 M6P sing 230 n n 
C5 C6 M6P sing 231 n n 
C5 O5 M6P sing 232 n n 
C5 H5 M6P sing 233 n n 
C6 O6 M6P sing 234 n n 
C6 H61 M6P sing 235 n n 
C6 H62 M6P sing 236 n n 
O1 HO1 M6P sing 237 n n 
O2 HO2 M6P sing 238 n n 
O3 HO3 M6P sing 239 n n 
O4 HO4 M6P sing 240 n n 
O6 P M6P sing 241 n n 
P O1P M6P doub 242 n n 
P O2P M6P sing 243 n n 
P O3P M6P sing 244 n n 
O2P HOP2 M6P sing 245 n n 
O3P HOP3 M6P sing 246 n n 
#
_pdbx_chem_comp_identifier.comp_id            M6P 
_pdbx_chem_comp_identifier.identifier         a-D-Manp6PO3 
_pdbx_chem_comp_identifier.type               'IUPAC CARBOHYDRATE SYMBOL' 
_pdbx_chem_comp_identifier.program            PDB-CARE 
_pdbx_chem_comp_identifier.program_version    1 
#
_atom_sites.entry_id                     4RZC 
_atom_sites.fract_transf_matrix[1][1]    0.0165 
_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]    0.007809 
_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]    0.007856 
_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
I 3 M6P H 1 201 3 M6P M6P . 
J 4 SO4 L 1 201 2 SO4 SO4 . 
K 3 M6P A 1 201 4 M6P M6P . 
L 4 SO4 B 1 201 1 SO4 SO4 . 
M 3 M6P C 1 201 2 M6P M6P . 
N 4 SO4 D 1 201 3 SO4 SO4 . 
O 4 SO4 D 1 202 6 SO4 SO4 . 
P 3 M6P E 1 201 1 M6P M6P . 
Q 4 SO4 F 1 201 4 SO4 SO4 . 
R 4 SO4 F 1 202 5 SO4 SO4 . 
S 5 HOH H 1 301 13 HOH HOH . 
S 5 HOH H 2 302 43 HOH HOH . 
S 5 HOH H 3 303 46 HOH HOH . 
S 5 HOH H 4 304 51 HOH HOH . 
S 5 HOH H 5 305 66 HOH HOH . 
S 5 HOH H 6 306 83 HOH HOH . 
S 5 HOH H 7 307 89 HOH HOH . 
S 5 HOH H 8 308 122 HOH HOH . 
S 5 HOH H 9 309 142 HOH HOH . 
S 5 HOH H 10 310 143 HOH HOH . 
T 5 HOH L 1 301 4 HOH HOH . 
T 5 HOH L 2 302 8 HOH HOH . 
T 5 HOH L 3 303 14 HOH HOH . 
T 5 HOH L 4 304 16 HOH HOH . 
T 5 HOH L 5 305 19 HOH HOH . 
T 5 HOH L 6 306 20 HOH HOH . 
T 5 HOH L 7 307 27 HOH HOH . 
T 5 HOH L 8 308 33 HOH HOH . 
T 5 HOH L 9 309 35 HOH HOH . 
T 5 HOH L 10 310 37 HOH HOH . 
T 5 HOH L 11 311 40 HOH HOH . 
T 5 HOH L 12 312 53 HOH HOH . 
T 5 HOH L 13 313 54 HOH HOH . 
T 5 HOH L 14 314 56 HOH HOH . 
T 5 HOH L 15 315 63 HOH HOH . 
T 5 HOH L 16 316 93 HOH HOH . 
T 5 HOH L 17 317 99 HOH HOH . 
T 5 HOH L 18 318 120 HOH HOH . 
T 5 HOH L 19 319 147 HOH HOH . 
T 5 HOH L 20 320 148 HOH HOH . 
T 5 HOH L 21 321 152 HOH HOH . 
U 5 HOH A 1 301 6 HOH HOH . 
U 5 HOH A 2 302 17 HOH HOH . 
U 5 HOH A 3 303 30 HOH HOH . 
U 5 HOH A 4 304 44 HOH HOH . 
U 5 HOH A 5 305 67 HOH HOH . 
U 5 HOH A 6 306 72 HOH HOH . 
U 5 HOH A 7 307 82 HOH HOH . 
U 5 HOH A 8 308 94 HOH HOH . 
U 5 HOH A 9 309 102 HOH HOH . 
U 5 HOH A 10 310 104 HOH HOH . 
U 5 HOH A 11 311 107 HOH HOH . 
U 5 HOH A 12 312 110 HOH HOH . 
U 5 HOH A 13 313 119 HOH HOH . 
U 5 HOH A 14 314 128 HOH HOH . 
U 5 HOH A 15 315 129 HOH HOH . 
U 5 HOH A 16 316 141 HOH HOH . 
V 5 HOH B 1 301 1 HOH HOH . 
V 5 HOH B 2 302 2 HOH HOH . 
V 5 HOH B 3 303 7 HOH HOH . 
V 5 HOH B 4 304 36 HOH HOH . 
V 5 HOH B 5 305 39 HOH HOH . 
V 5 HOH B 6 306 41 HOH HOH . 
V 5 HOH B 7 307 47 HOH HOH . 
V 5 HOH B 8 308 48 HOH HOH . 
V 5 HOH B 9 309 50 HOH HOH . 
V 5 HOH B 10 310 61 HOH HOH . 
V 5 HOH B 11 311 65 HOH HOH . 
V 5 HOH B 12 312 73 HOH HOH . 
V 5 HOH B 13 313 74 HOH HOH . 
V 5 HOH B 14 314 78 HOH HOH . 
V 5 HOH B 15 315 95 HOH HOH . 
V 5 HOH B 16 316 100 HOH HOH . 
V 5 HOH B 17 317 125 HOH HOH . 
W 5 HOH C 1 301 5 HOH HOH . 
W 5 HOH C 2 302 9 HOH HOH . 
W 5 HOH C 3 303 12 HOH HOH . 
W 5 HOH C 4 304 15 HOH HOH . 
W 5 HOH C 5 305 21 HOH HOH . 
W 5 HOH C 6 306 22 HOH HOH . 
W 5 HOH C 7 307 25 HOH HOH . 
W 5 HOH C 8 308 55 HOH HOH . 
W 5 HOH C 9 309 59 HOH HOH . 
W 5 HOH C 10 310 62 HOH HOH . 
W 5 HOH C 11 311 68 HOH HOH . 
W 5 HOH C 12 312 70 HOH HOH . 
W 5 HOH C 13 313 88 HOH HOH . 
W 5 HOH C 14 314 92 HOH HOH . 
W 5 HOH C 15 315 103 HOH HOH . 
W 5 HOH C 16 316 113 HOH HOH . 
W 5 HOH C 17 317 124 HOH HOH . 
W 5 HOH C 18 318 131 HOH HOH . 
W 5 HOH C 19 319 139 HOH HOH . 
W 5 HOH C 20 320 149 HOH HOH . 
W 5 HOH C 21 321 150 HOH HOH . 
W 5 HOH C 22 322 151 HOH HOH . 
X 5 HOH D 1 301 28 HOH HOH . 
X 5 HOH D 2 302 45 HOH HOH . 
X 5 HOH D 3 303 80 HOH HOH . 
X 5 HOH D 4 304 81 HOH HOH . 
X 5 HOH D 5 305 90 HOH HOH . 
X 5 HOH D 6 306 96 HOH HOH . 
X 5 HOH D 7 307 97 HOH HOH . 
X 5 HOH D 8 308 108 HOH HOH . 
X 5 HOH D 9 309 111 HOH HOH . 
X 5 HOH D 10 310 116 HOH HOH . 
X 5 HOH D 11 311 121 HOH HOH . 
X 5 HOH D 12 312 123 HOH HOH . 
X 5 HOH D 13 313 126 HOH HOH . 
X 5 HOH D 14 314 127 HOH HOH . 
X 5 HOH D 15 315 136 HOH HOH . 
X 5 HOH D 16 316 146 HOH HOH . 
X 5 HOH D 17 317 153 HOH HOH . 
Y 5 HOH E 1 301 10 HOH HOH . 
Y 5 HOH E 2 302 23 HOH HOH . 
Y 5 HOH E 3 303 24 HOH HOH . 
Y 5 HOH E 4 304 26 HOH HOH . 
Y 5 HOH E 5 305 29 HOH HOH . 
Y 5 HOH E 6 306 31 HOH HOH . 
Y 5 HOH E 7 307 32 HOH HOH . 
Y 5 HOH E 8 308 38 HOH HOH . 
Y 5 HOH E 9 309 42 HOH HOH . 
Y 5 HOH E 10 310 49 HOH HOH . 
Y 5 HOH E 11 311 52 HOH HOH . 
Y 5 HOH E 12 312 57 HOH HOH . 
Y 5 HOH E 13 313 60 HOH HOH . 
Y 5 HOH E 14 314 64 HOH HOH . 
Y 5 HOH E 15 315 69 HOH HOH . 
Y 5 HOH E 16 316 71 HOH HOH . 
Y 5 HOH E 17 317 75 HOH HOH . 
Y 5 HOH E 18 318 76 HOH HOH . 
Y 5 HOH E 19 319 85 HOH HOH . 
Y 5 HOH E 20 320 87 HOH HOH . 
Y 5 HOH E 21 321 91 HOH HOH . 
Y 5 HOH E 22 322 106 HOH HOH . 
Y 5 HOH E 23 323 114 HOH HOH . 
Y 5 HOH E 24 324 115 HOH HOH . 
Y 5 HOH E 25 325 117 HOH HOH . 
Y 5 HOH E 26 326 118 HOH HOH . 
Y 5 HOH E 27 327 132 HOH HOH . 
Y 5 HOH E 28 328 133 HOH HOH . 
Y 5 HOH E 29 329 137 HOH HOH . 
Y 5 HOH E 30 330 138 HOH HOH . 
Y 5 HOH E 31 331 140 HOH HOH . 
Z 5 HOH F 1 301 3 HOH HOH . 
Z 5 HOH F 2 302 11 HOH HOH . 
Z 5 HOH F 3 303 18 HOH HOH . 
Z 5 HOH F 4 304 34 HOH HOH . 
Z 5 HOH F 5 305 58 HOH HOH . 
Z 5 HOH F 6 306 77 HOH HOH . 
Z 5 HOH F 7 307 79 HOH HOH . 
Z 5 HOH F 8 308 84 HOH HOH . 
Z 5 HOH F 9 309 86 HOH HOH . 
Z 5 HOH F 10 310 98 HOH HOH . 
Z 5 HOH F 11 311 101 HOH HOH . 
Z 5 HOH F 12 312 105 HOH HOH . 
Z 5 HOH F 13 313 109 HOH HOH . 
Z 5 HOH F 14 314 112 HOH HOH . 
Z 5 HOH F 15 315 130 HOH HOH . 
Z 5 HOH F 16 316 134 HOH HOH . 
Z 5 HOH F 17 317 135 HOH HOH . 
Z 5 HOH F 18 318 144 HOH HOH . 
Z 5 HOH F 19 319 145 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 M6P . . . P 3 29.639 -22.409 36.954 1 22.13 ? C1 M6P 201 E 1 
HETATM 2 C C2 M6P . . . P 3 29.761 -20.918 36.887 1 22.57 ? C2 M6P 201 E 1 
HETATM 3 C C3 M6P . . . P 3 30.834 -20.45 37.852 1 22.36 ? C3 M6P 201 E 1 
HETATM 4 C C4 M6P . . . P 3 30.53 -20.96 39.252 1 21.79 ? C4 M6P 201 E 1 
HETATM 5 C C5 M6P . . . P 3 30.354 -22.487 39.212 1 21.26 ? C5 M6P 201 E 1 
HETATM 6 C C6 M6P . . . P 3 29.959 -23.002 40.578 1 20.26 ? C6 M6P 201 E 1 
HETATM 7 O O1 M6P . . . P 3 30.857 -22.959 36.485 1 22.72 ? O1 M6P 201 E 1 
HETATM 8 O O2 M6P . . . P 3 28.494 -20.328 37.173 1 22.66 ? O2 M6P 201 E 1 
HETATM 9 O O3 M6P . . . P 3 30.9 -19.039 37.847 1 22.69 ? O3 M6P 201 E 1 
HETATM 10 O O4 M6P . . . P 3 31.592 -20.601 40.076 1 21.1 ? O4 M6P 201 E 1 
HETATM 11 O O5 M6P . . . P 3 29.351 -22.842 38.274 1 21.98 ? O5 M6P 201 E 1 
HETATM 12 O O6 M6P . . . P 3 29.834 -24.422 40.53 1 18.97 ? O6 M6P 201 E 1 
HETATM 13 P P M6P . . . P 3 30.59 -25.38 41.57 1 16.62 ? P M6P 201 E 1 
HETATM 14 O O1P M6P . . . P 3 30.347 -24.923 42.977 1 15.55 ? O1P M6P 201 E 1 
HETATM 15 O O2P M6P . . . P 3 30.028 -26.756 41.404 1 16.71 ? O2P M6P 201 E 1 
HETATM 16 O O3P M6P . . . P 3 32.073 -25.404 41.217 1 16.91 ? O3P M6P 201 E 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           16 
#