data_5BV3
#
_model_server_result.job_id            ABVggSUDF1GC4FvRcOPIbg 
_model_server_result.datetime_utc      '2024-11-05 04:56:02' 
_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          5bv3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    5BV3 
#
_exptl.entry_id    5BV3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              459.243 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               '7-methylguanosine diphosphate' 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5BV3 
_cell.length_a            87.99 
_cell.length_b            104.52 
_cell.length_c            189.96 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5BV3 
_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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,I,J,R,S 1 1 
C,D,K,L,M,N,O,P,Q,T,U 2 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
? 2 E N N 
? 2 K 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 67 A CYS 72 1_555 A SG CYS 73 A CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf2 B SG CYS 67 B CYS 72 1_555 B SG CYS 73 B CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
disulf ? disulf3 C SG CYS 67 C CYS 72 1_555 C SG CYS 73 C CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf4 D SG CYS 67 D CYS 72 1_555 D SG CYS 73 D CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
#
_chem_comp.formula           'C11 H19 N5 O11 P2' 
_chem_comp.formula_weight    459.243 
_chem_comp.id                M7G 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE" 
_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
PA O1A M7G doub 218 n n 
PA O2A M7G sing 219 n n 
PA O3A M7G sing 220 n n 
PA O5' M7G sing 221 n n 
O2A HOA2 M7G sing 222 n n 
O3A PB M7G sing 223 n n 
O5' C5' M7G sing 224 n n 
PB O1B M7G doub 225 n n 
PB O2B M7G sing 226 n n 
PB O3B M7G sing 227 n n 
O2B HOB2 M7G sing 228 n n 
O3B HOB3 M7G sing 229 n n 
C5' C4' M7G sing 230 n n 
C5' "H5'1" M7G sing 231 n n 
C5' "H5'2" M7G sing 232 n n 
C4' O4' M7G sing 233 n n 
C4' C3' M7G sing 234 n n 
C4' H4' M7G sing 235 n n 
O4' C1' M7G sing 236 n n 
C3' O3' M7G sing 237 n n 
C3' C2' M7G sing 238 n n 
C3' H3' M7G sing 239 n n 
O3' HO3' M7G sing 240 n n 
C2' O2' M7G sing 241 n n 
C2' C1' M7G sing 242 n n 
C2' H2' M7G sing 243 n n 
O2' HO2' M7G sing 244 n n 
C1' N9 M7G sing 245 n n 
C1' H1' M7G sing 246 n n 
N9 C8 M7G sing 247 n n 
N9 C4 M7G sing 248 n n 
C8 N7 M7G sing 249 n n 
C8 H81 M7G sing 250 n n 
C8 H82 M7G sing 251 n n 
N7 CM7 M7G sing 252 n n 
N7 C5 M7G sing 253 n n 
CM7 HM71 M7G sing 254 n n 
CM7 HM72 M7G sing 255 n n 
CM7 HM73 M7G sing 256 n n 
C5 C6 M7G sing 257 n n 
C5 C4 M7G doub 258 n n 
C6 O6 M7G doub 259 n n 
C6 N1 M7G sing 260 n n 
N1 C2 M7G sing 261 n n 
N1 HN1 M7G sing 262 n n 
C2 N2 M7G sing 263 n n 
C2 N3 M7G doub 264 n n 
N2 HN21 M7G sing 265 n n 
N2 HN22 M7G sing 266 n n 
N3 C4 M7G sing 267 n n 
#
_atom_sites.entry_id                     5BV3 
_atom_sites.fract_transf_matrix[1][1]    0.011365 
_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]    0.009568 
_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]    0.005264 
_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 2 M7G A 1 401 401 M7G M7G . 
F 3 SO4 A 1 402 1 SO4 SO4 . 
G 3 SO4 A 1 403 1 SO4 SO4 . 
H 4 CL A 1 404 4 CL CL . 
I 3 SO4 B 1 401 1 SO4 SO4 . 
J 3 SO4 B 1 402 1 SO4 SO4 . 
K 2 M7G C 1 401 401 M7G M7G . 
L 3 SO4 C 1 402 1 SO4 SO4 . 
M 4 CL C 1 403 3 CL CL . 
N 3 SO4 D 1 401 1 SO4 SO4 . 
O 3 SO4 D 1 402 1 SO4 SO4 . 
P 4 CL D 1 403 1 CL CL . 
Q 4 CL D 1 404 2 CL CL . 
R 5 HOH A 1 501 55 HOH HOH . 
R 5 HOH A 2 502 19 HOH HOH . 
R 5 HOH A 3 503 162 HOH HOH . 
R 5 HOH A 4 504 13 HOH HOH . 
R 5 HOH A 5 505 21 HOH HOH . 
R 5 HOH A 6 506 61 HOH HOH . 
R 5 HOH A 7 507 148 HOH HOH . 
R 5 HOH A 8 508 65 HOH HOH . 
R 5 HOH A 9 509 22 HOH HOH . 
R 5 HOH A 10 510 165 HOH HOH . 
R 5 HOH A 11 511 56 HOH HOH . 
R 5 HOH A 12 512 42 HOH HOH . 
R 5 HOH A 13 513 1 HOH HOH . 
R 5 HOH A 14 514 159 HOH HOH . 
R 5 HOH A 15 515 6 HOH HOH . 
R 5 HOH A 16 516 62 HOH HOH . 
R 5 HOH A 17 517 3 HOH HOH . 
R 5 HOH A 18 518 25 HOH HOH . 
R 5 HOH A 19 519 72 HOH HOH . 
R 5 HOH A 20 520 4 HOH HOH . 
R 5 HOH A 21 521 43 HOH HOH . 
R 5 HOH A 22 522 51 HOH HOH . 
R 5 HOH A 23 523 153 HOH HOH . 
R 5 HOH A 24 524 58 HOH HOH . 
R 5 HOH A 25 525 29 HOH HOH . 
R 5 HOH A 26 526 59 HOH HOH . 
R 5 HOH A 27 527 30 HOH HOH . 
R 5 HOH A 28 528 23 HOH HOH . 
R 5 HOH A 29 529 45 HOH HOH . 
R 5 HOH A 30 530 26 HOH HOH . 
R 5 HOH A 31 531 36 HOH HOH . 
R 5 HOH A 32 532 170 HOH HOH . 
R 5 HOH A 33 533 139 HOH HOH . 
R 5 HOH A 34 534 16 HOH HOH . 
R 5 HOH A 35 535 39 HOH HOH . 
R 5 HOH A 36 536 152 HOH HOH . 
R 5 HOH A 37 537 140 HOH HOH . 
R 5 HOH A 38 538 18 HOH HOH . 
R 5 HOH A 39 539 141 HOH HOH . 
R 5 HOH A 40 540 169 HOH HOH . 
R 5 HOH A 41 541 46 HOH HOH . 
R 5 HOH A 42 542 12 HOH HOH . 
R 5 HOH A 43 543 64 HOH HOH . 
R 5 HOH A 44 544 5 HOH HOH . 
R 5 HOH A 45 545 77 HOH HOH . 
R 5 HOH A 46 546 168 HOH HOH . 
R 5 HOH A 47 547 11 HOH HOH . 
R 5 HOH A 48 548 10 HOH HOH . 
R 5 HOH A 49 549 44 HOH HOH . 
R 5 HOH A 50 550 40 HOH HOH . 
R 5 HOH A 51 551 166 HOH HOH . 
R 5 HOH A 52 552 94 HOH HOH . 
S 5 HOH B 1 501 167 HOH HOH . 
S 5 HOH B 2 502 76 HOH HOH . 
S 5 HOH B 3 503 20 HOH HOH . 
S 5 HOH B 4 504 138 HOH HOH . 
S 5 HOH B 5 505 31 HOH HOH . 
S 5 HOH B 6 506 84 HOH HOH . 
S 5 HOH B 7 507 81 HOH HOH . 
S 5 HOH B 8 508 57 HOH HOH . 
S 5 HOH B 9 509 95 HOH HOH . 
S 5 HOH B 10 510 32 HOH HOH . 
S 5 HOH B 11 511 60 HOH HOH . 
S 5 HOH B 12 512 7 HOH HOH . 
S 5 HOH B 13 513 27 HOH HOH . 
S 5 HOH B 14 514 92 HOH HOH . 
S 5 HOH B 15 515 9 HOH HOH . 
S 5 HOH B 16 516 85 HOH HOH . 
S 5 HOH B 17 517 69 HOH HOH . 
S 5 HOH B 18 518 41 HOH HOH . 
S 5 HOH B 19 519 47 HOH HOH . 
S 5 HOH B 20 520 24 HOH HOH . 
S 5 HOH B 21 521 93 HOH HOH . 
S 5 HOH B 22 522 71 HOH HOH . 
S 5 HOH B 23 523 158 HOH HOH . 
S 5 HOH B 24 524 89 HOH HOH . 
S 5 HOH B 25 525 52 HOH HOH . 
S 5 HOH B 26 526 75 HOH HOH . 
S 5 HOH B 27 527 82 HOH HOH . 
S 5 HOH B 28 528 67 HOH HOH . 
S 5 HOH B 29 529 156 HOH HOH . 
S 5 HOH B 30 530 88 HOH HOH . 
S 5 HOH B 31 531 14 HOH HOH . 
S 5 HOH B 32 532 28 HOH HOH . 
S 5 HOH B 33 533 147 HOH HOH . 
S 5 HOH B 34 534 78 HOH HOH . 
S 5 HOH B 35 535 157 HOH HOH . 
S 5 HOH B 36 536 91 HOH HOH . 
S 5 HOH B 37 537 49 HOH HOH . 
S 5 HOH B 38 538 80 HOH HOH . 
S 5 HOH B 39 539 68 HOH HOH . 
S 5 HOH B 40 540 87 HOH HOH . 
S 5 HOH B 41 541 15 HOH HOH . 
S 5 HOH B 42 542 17 HOH HOH . 
S 5 HOH B 43 543 2 HOH HOH . 
S 5 HOH B 44 544 70 HOH HOH . 
S 5 HOH B 45 545 8 HOH HOH . 
T 5 HOH C 1 501 160 HOH HOH . 
T 5 HOH C 2 502 114 HOH HOH . 
T 5 HOH C 3 503 124 HOH HOH . 
T 5 HOH C 4 504 116 HOH HOH . 
T 5 HOH C 5 505 112 HOH HOH . 
T 5 HOH C 6 506 111 HOH HOH . 
T 5 HOH C 7 507 102 HOH HOH . 
T 5 HOH C 8 508 125 HOH HOH . 
T 5 HOH C 9 509 163 HOH HOH . 
T 5 HOH C 10 510 128 HOH HOH . 
T 5 HOH C 11 511 103 HOH HOH . 
T 5 HOH C 12 512 104 HOH HOH . 
T 5 HOH C 13 513 105 HOH HOH . 
T 5 HOH C 14 514 129 HOH HOH . 
T 5 HOH C 15 515 126 HOH HOH . 
T 5 HOH C 16 516 146 HOH HOH . 
T 5 HOH C 17 517 134 HOH HOH . 
T 5 HOH C 18 518 106 HOH HOH . 
T 5 HOH C 19 519 164 HOH HOH . 
T 5 HOH C 20 520 115 HOH HOH . 
T 5 HOH C 21 521 118 HOH HOH . 
T 5 HOH C 22 522 120 HOH HOH . 
T 5 HOH C 23 523 97 HOH HOH . 
T 5 HOH C 24 524 161 HOH HOH . 
T 5 HOH C 25 525 110 HOH HOH . 
T 5 HOH C 26 526 121 HOH HOH . 
T 5 HOH C 27 527 119 HOH HOH . 
U 5 HOH D 1 501 98 HOH HOH . 
U 5 HOH D 2 502 143 HOH HOH . 
U 5 HOH D 3 503 136 HOH HOH . 
U 5 HOH D 4 504 127 HOH HOH . 
U 5 HOH D 5 505 108 HOH HOH . 
U 5 HOH D 6 506 100 HOH HOH . 
U 5 HOH D 7 507 144 HOH HOH . 
U 5 HOH D 8 508 130 HOH HOH . 
U 5 HOH D 9 509 137 HOH HOH . 
U 5 HOH D 10 510 113 HOH HOH . 
U 5 HOH D 11 511 131 HOH HOH . 
U 5 HOH D 12 512 107 HOH HOH . 
U 5 HOH D 13 513 99 HOH HOH . 
U 5 HOH D 14 514 145 HOH HOH . 
U 5 HOH D 15 515 133 HOH HOH . 
U 5 HOH D 16 516 123 HOH HOH . 
U 5 HOH D 17 517 142 HOH HOH . 
U 5 HOH D 18 518 135 HOH HOH . 
U 5 HOH D 19 519 132 HOH HOH . 
U 5 HOH D 20 520 35 HOH HOH . 
U 5 HOH D 21 521 90 HOH HOH . 
U 5 HOH D 22 522 101 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 P PA M7G . . . E 2 43.258 5.518 31.931 1 36.37 ? PA M7G 401 A 1 
HETATM 2 O O1A M7G . . . E 2 44.711 5.782 31.87 1 25 ? O1A M7G 401 A 1 
HETATM 3 O O2A M7G . . . E 2 42.346 6.511 32.541 1 44.67 ? O2A M7G 401 A 1 
HETATM 4 O O3A M7G . . . E 2 43.148 4.053 32.598 1 61.11 ? O3A M7G 401 A 1 
HETATM 5 O O5' M7G . . . E 2 42.655 5.189 30.492 1 46.08 ? O5' M7G 401 A 1 
HETATM 6 P PB M7G . . . E 2 42.233 3.676 33.853 1 45.36 ? PB M7G 401 A 1 
HETATM 7 O O1B M7G . . . E 2 40.776 3.811 33.601 1 36.1 ? O1B M7G 401 A 1 
HETATM 8 O O2B M7G . . . E 2 42.748 4.648 35.006 1 49.33 ? O2B M7G 401 A 1 
HETATM 9 O O3B M7G . . . E 2 42.613 2.223 34.195 1 61.48 ? O3B M7G 401 A 1 
HETATM 10 C C5' M7G . . . E 2 43.135 4.056 29.791 1 42.78 ? C5' M7G 401 A 1 
HETATM 11 C C4' M7G . . . E 2 42.002 3.336 29.087 1 36.77 ? C4' M7G 401 A 1 
HETATM 12 O O4' M7G . . . E 2 42.703 2.455 28.183 1 42.17 ? O4' M7G 401 A 1 
HETATM 13 C C3' M7G . . . E 2 41.263 2.458 30.095 1 32.22 ? C3' M7G 401 A 1 
HETATM 14 O O3' M7G . . . E 2 39.849 2.62 29.887 1 27.69 ? O3' M7G 401 A 1 
HETATM 15 C C2' M7G . . . E 2 41.71 1.026 29.758 1 32.06 ? C2' M7G 401 A 1 
HETATM 16 O O2' M7G . . . E 2 40.59 0.154 29.796 1 27.66 ? O2' M7G 401 A 1 
HETATM 17 C C1' M7G . . . E 2 42.129 1.139 28.306 1 43.79 ? C1' M7G 401 A 1 
HETATM 18 N N9 M7G . . . E 2 43.171 0.191 27.902 1 37.12 ? N9 M7G 401 A 1 
HETATM 19 C C8 M7G . . . E 2 44.322 -0.071 28.745 1 41.24 ? C8 M7G 401 A 1 
HETATM 20 N N7 M7G . . . E 2 45.182 -0.813 27.828 1 33.32 ? N7 M7G 401 A 1 
HETATM 21 C CM7 M7G . . . E 2 46.516 -1.309 28.264 1 36.09 ? CM7 M7G 401 A 1 
HETATM 22 C C5 M7G . . . E 2 44.577 -0.985 26.641 1 42.12 ? C5 M7G 401 A 1 
HETATM 23 C C6 M7G . . . E 2 44.978 -1.635 25.474 1 35.85 ? C6 M7G 401 A 1 
HETATM 24 O O6 M7G . . . E 2 46.048 -2.212 25.282 1 33.55 ? O6 M7G 401 A 1 
HETATM 25 N N1 M7G . . . E 2 44.022 -1.583 24.444 1 29.12 ? N1 M7G 401 A 1 
HETATM 26 C C2 M7G . . . E 2 42.803 -0.961 24.578 1 33.21 ? C2 M7G 401 A 1 
HETATM 27 N N2 M7G . . . E 2 41.982 -0.987 23.532 1 37.97 ? N2 M7G 401 A 1 
HETATM 28 N N3 M7G . . . E 2 42.412 -0.338 25.699 1 31.46 ? N3 M7G 401 A 1 
HETATM 29 C C4 M7G . . . E 2 43.322 -0.389 26.679 1 29.16 ? C4 M7G 401 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           29 
#