data_2GMS
#
_model_server_result.job_id            b4DywqXXYue83r7QoUAzMQ 
_model_server_result.datetime_utc      '2024-10-30 19:25:17' 
_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          2gms 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":400}' 
#
_entry.id    2GMS 
#
_exptl.entry_id    2GMS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              265.157 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[4-(DIHYDROXYMETHYL)-5-HYDROXY-6-METHYLPYRIDIN-3-YL]METHYL 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            2GMS 
_cell.length_a            74.9 
_cell.length_b            88.1 
_cell.length_c            125.8 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2GMS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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
? 3 D N N 
? 3 E N N 
#
_struct_conn.conn_type_id                   metalc 
_struct_conn.details                        ? 
_struct_conn.id                             metalc1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            OE2 
_struct_conn.ptnr1_label_comp_id            GLU 
_struct_conn.ptnr1_label_seq_id             377 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             GLU 
_struct_conn.ptnr1_auth_seq_id              375 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            C 
_struct_conn.ptnr2_label_atom_id            MG 
_struct_conn.ptnr2_label_comp_id            MG 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             MG 
_struct_conn.ptnr2_auth_seq_id              403 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.122 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C8 H12 N O7 P' 
_chem_comp.formula_weight    265.157 
_chem_comp.id                P0P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[4-(DIHYDROXYMETHYL)-5-HYDROXY-6-METHYLPYRIDIN-3-YL]METHYL DIHYDROGEN PHOSPHATE' 
_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
O3 C3 P0P sing 237 n n 
O3 HO3 P0P sing 238 n n 
N1 C2 P0P sing 239 n y 
N1 C6 P0P doub 240 n y 
C2 C2A P0P sing 241 n n 
C2 C3 P0P doub 242 n y 
C2A H2A1 P0P sing 243 n n 
C2A H2A2 P0P sing 244 n n 
C2A H2A3 P0P sing 245 n n 
C3 C4 P0P sing 246 n y 
C4 C4A P0P sing 247 n n 
C4 C5 P0P doub 248 n y 
C4A O4A P0P sing 249 n n 
C4A O4B P0P sing 250 n n 
C4A H4A P0P sing 251 n n 
O4A H1 P0P sing 252 n n 
O4B H4B P0P sing 253 n n 
C5 C6 P0P sing 254 n y 
C5 C5A P0P sing 255 n n 
C6 H6 P0P sing 256 n n 
C5A O4P P0P sing 257 n n 
C5A H5A1 P0P sing 258 n n 
C5A H5A2 P0P sing 259 n n 
O4P P P0P sing 260 n n 
P O1P P0P doub 261 n n 
P O2P P0P sing 262 n n 
P O3P P0P sing 263 n n 
O2P H2P P0P sing 264 n n 
O3P H3P P0P sing 265 n n 
#
_atom_sites.entry_id                     2GMS 
_atom_sites.fract_transf_matrix[1][1]    0.013351 
_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]    0.011351 
_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]    0.007949 
_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
C 2 MG A 1 403 403 MG MG . 
D 3 P0P A 1 400 400 P0P P0P . 
E 3 P0P B 1 401 401 P0P P0P . 
F 4 HOH A 1 492 492 HOH HOH . 
F 4 HOH A 2 493 493 HOH HOH . 
F 4 HOH A 3 494 494 HOH HOH . 
F 4 HOH A 4 495 495 HOH HOH . 
F 4 HOH A 5 496 496 HOH HOH . 
F 4 HOH A 6 497 497 HOH HOH . 
F 4 HOH A 7 498 498 HOH HOH . 
F 4 HOH A 8 499 499 HOH HOH . 
F 4 HOH A 9 500 500 HOH HOH . 
F 4 HOH A 10 501 501 HOH HOH . 
F 4 HOH A 11 502 502 HOH HOH . 
F 4 HOH A 12 503 503 HOH HOH . 
F 4 HOH A 13 504 504 HOH HOH . 
F 4 HOH A 14 505 505 HOH HOH . 
F 4 HOH A 15 506 506 HOH HOH . 
F 4 HOH A 16 507 507 HOH HOH . 
F 4 HOH A 17 508 508 HOH HOH . 
F 4 HOH A 18 509 509 HOH HOH . 
F 4 HOH A 19 510 510 HOH HOH . 
F 4 HOH A 20 511 511 HOH HOH . 
F 4 HOH A 21 512 512 HOH HOH . 
F 4 HOH A 22 513 513 HOH HOH . 
F 4 HOH A 23 514 514 HOH HOH . 
F 4 HOH A 24 515 515 HOH HOH . 
F 4 HOH A 25 516 516 HOH HOH . 
F 4 HOH A 26 517 517 HOH HOH . 
F 4 HOH A 27 524 524 HOH HOH . 
F 4 HOH A 28 525 525 HOH HOH . 
F 4 HOH A 29 529 529 HOH HOH . 
F 4 HOH A 30 531 531 HOH HOH . 
F 4 HOH A 31 532 532 HOH HOH . 
F 4 HOH A 32 535 535 HOH HOH . 
F 4 HOH A 33 536 536 HOH HOH . 
F 4 HOH A 34 537 537 HOH HOH . 
F 4 HOH A 35 539 539 HOH HOH . 
F 4 HOH A 36 541 541 HOH HOH . 
F 4 HOH A 37 542 542 HOH HOH . 
F 4 HOH A 38 548 548 HOH HOH . 
F 4 HOH A 39 549 549 HOH HOH . 
F 4 HOH A 40 550 550 HOH HOH . 
F 4 HOH A 41 551 551 HOH HOH . 
F 4 HOH A 42 552 552 HOH HOH . 
G 4 HOH B 1 491 491 HOH HOH . 
G 4 HOH B 2 518 518 HOH HOH . 
G 4 HOH B 3 519 519 HOH HOH . 
G 4 HOH B 4 520 520 HOH HOH . 
G 4 HOH B 5 521 521 HOH HOH . 
G 4 HOH B 6 522 522 HOH HOH . 
G 4 HOH B 7 523 523 HOH HOH . 
G 4 HOH B 8 526 526 HOH HOH . 
G 4 HOH B 9 527 527 HOH HOH . 
G 4 HOH B 10 528 528 HOH HOH . 
G 4 HOH B 11 530 530 HOH HOH . 
G 4 HOH B 12 533 533 HOH HOH . 
G 4 HOH B 13 534 534 HOH HOH . 
G 4 HOH B 14 538 538 HOH HOH . 
G 4 HOH B 15 540 540 HOH HOH . 
G 4 HOH B 16 543 543 HOH HOH . 
G 4 HOH B 17 544 544 HOH HOH . 
G 4 HOH B 18 545 545 HOH HOH . 
G 4 HOH B 19 546 546 HOH HOH . 
G 4 HOH B 20 547 547 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 O O3 P0P . . . D 3 -3.495 -3.392 5.323 1 21.71 ? O3 P0P 400 A 1 
HETATM 2 N N1 P0P . . . D 3 -0.891 -4.74 7.331 1 20.16 ? N1 P0P 400 A 1 
HETATM 3 C C2 P0P . . . D 3 -1.954 -4.687 6.553 1 20.97 ? C2 P0P 400 A 1 
HETATM 4 C C2A P0P . . . D 3 -2.686 -5.946 6.157 1 17.81 ? C2A P0P 400 A 1 
HETATM 5 C C3 P0P . . . D 3 -2.405 -3.477 6.104 1 23.36 ? C3 P0P 400 A 1 
HETATM 6 C C4 P0P . . . D 3 -1.728 -2.319 6.481 1 25.28 ? C4 P0P 400 A 1 
HETATM 7 C C4A P0P . . . D 3 -2.262 -0.985 6.012 1 37.67 ? C4A P0P 400 A 1 
HETATM 8 O O4A P0P . . . D 3 -3.593 -1.14 5.588 1 33.07 ? O4A P0P 400 A 1 
HETATM 9 O O4B P0P . . . D 3 -1.499 -0.484 4.957 1 49.92 ? O4B P0P 400 A 1 
HETATM 10 C C5 P0P . . . D 3 -0.543 -2.383 7.25 1 16.83 ? C5 P0P 400 A 1 
HETATM 11 C C6 P0P . . . D 3 -0.213 -3.641 7.69 1 16.6 ? C6 P0P 400 A 1 
HETATM 12 C C5A P0P . . . D 3 -0.037 -1.176 7.63 1 21.29 ? C5A P0P 400 A 1 
HETATM 13 O O4P P0P . . . D 3 -0.489 -0.327 8.585 1 26.52 ? O4P P0P 400 A 1 
HETATM 14 P P P0P . . . D 3 0.161 1.13 8.481 1 17.81 ? P P0P 400 A 1 
HETATM 15 O O1P P0P . . . D 3 -0.262 1.683 7.177 1 18.73 ? O1P P0P 400 A 1 
HETATM 16 O O2P P0P . . . D 3 -0.514 1.963 9.686 1 20.21 ? O2P P0P 400 A 1 
HETATM 17 O O3P P0P . . . D 3 1.765 1.127 8.62 1 17.95 ? O3P P0P 400 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           403 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           17 
#