data_4Y7G
#
_model_server_result.job_id            -7Ugu5aZVdpSth4-RhTU9A 
_model_server_result.datetime_utc      '2025-01-10 06:10:03' 
_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          4y7g 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    4Y7G 
#
_exptl.entry_id    4Y7G 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              172.074 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SN-GLYCEROL-3-PHOSPHATE 
_entity.pdbx_number_of_molecules    1 
_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            4Y7G 
_cell.length_a            98.18 
_cell.length_b            98.18 
_cell.length_c            127.34 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Y7G 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 98.18 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 A OD2 ASP 140 A ASP 136 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc3 B MN MN . A MN 401 1_555 D O1A UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc4 B MN MN . A MN 401 1_555 D O2B UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc5 B MN MN . A MN 401 1_555 E O HOH . A HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc6 B MN MN . A MN 401 1_555 E O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
#
_chem_comp.formula           'C3 H9 O6 P' 
_chem_comp.formula_weight    172.074 
_chem_comp.id                G3P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SN-GLYCEROL-3-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
O1 C1 G3P sing 83 n n 
C1 C2 G3P sing 84 n n 
C2 O2 G3P sing 85 n n 
C2 C3 G3P sing 86 n n 
C3 O1P G3P sing 87 n n 
O1P P G3P sing 88 n n 
O4P P G3P sing 89 n n 
O2P P G3P doub 90 n n 
O3P P G3P sing 91 n n 
O1 HO1 G3P sing 92 n n 
C1 H11 G3P sing 93 n n 
C1 H12 G3P sing 94 n n 
C2 H2 G3P sing 95 n n 
O2 HO2 G3P sing 96 n n 
C3 H31 G3P sing 97 n n 
C3 H32 G3P sing 98 n n 
O3P HOP3 G3P sing 99 n n 
O4P HOP4 G3P sing 100 n n 
#
_atom_sites.entry_id                     4Y7G 
_atom_sites.fract_transf_matrix[1][1]    0.010185 
_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]    0.010185 
_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]    0.007853 
_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
B 2 MN A 1 401 1 MN MN . 
C 3 G3P A 1 402 1 G3P G3P . 
D 4 UPG A 1 403 2 UPG UPG . 
E 5 HOH A 1 501 95 HOH HOH . 
E 5 HOH A 2 502 9 HOH HOH . 
E 5 HOH A 3 503 75 HOH HOH . 
E 5 HOH A 4 504 67 HOH HOH . 
E 5 HOH A 5 505 63 HOH HOH . 
E 5 HOH A 6 506 29 HOH HOH . 
E 5 HOH A 7 507 38 HOH HOH . 
E 5 HOH A 8 508 45 HOH HOH . 
E 5 HOH A 9 509 90 HOH HOH . 
E 5 HOH A 10 510 1 HOH HOH . 
E 5 HOH A 11 511 2 HOH HOH . 
E 5 HOH A 12 512 3 HOH HOH . 
E 5 HOH A 13 513 5 HOH HOH . 
E 5 HOH A 14 514 7 HOH HOH . 
E 5 HOH A 15 515 8 HOH HOH . 
E 5 HOH A 16 516 10 HOH HOH . 
E 5 HOH A 17 517 11 HOH HOH . 
E 5 HOH A 18 518 12 HOH HOH . 
E 5 HOH A 19 519 13 HOH HOH . 
E 5 HOH A 20 520 14 HOH HOH . 
E 5 HOH A 21 521 15 HOH HOH . 
E 5 HOH A 22 522 16 HOH HOH . 
E 5 HOH A 23 523 17 HOH HOH . 
E 5 HOH A 24 524 18 HOH HOH . 
E 5 HOH A 25 525 19 HOH HOH . 
E 5 HOH A 26 526 20 HOH HOH . 
E 5 HOH A 27 527 21 HOH HOH . 
E 5 HOH A 28 528 22 HOH HOH . 
E 5 HOH A 29 529 23 HOH HOH . 
E 5 HOH A 30 530 24 HOH HOH . 
E 5 HOH A 31 531 25 HOH HOH . 
E 5 HOH A 32 532 26 HOH HOH . 
E 5 HOH A 33 533 27 HOH HOH . 
E 5 HOH A 34 534 28 HOH HOH . 
E 5 HOH A 35 535 30 HOH HOH . 
E 5 HOH A 36 536 32 HOH HOH . 
E 5 HOH A 37 537 34 HOH HOH . 
E 5 HOH A 38 538 35 HOH HOH . 
E 5 HOH A 39 539 37 HOH HOH . 
E 5 HOH A 40 540 39 HOH HOH . 
E 5 HOH A 41 541 40 HOH HOH . 
E 5 HOH A 42 542 41 HOH HOH . 
E 5 HOH A 43 543 42 HOH HOH . 
E 5 HOH A 44 544 43 HOH HOH . 
E 5 HOH A 45 545 44 HOH HOH . 
E 5 HOH A 46 546 48 HOH HOH . 
E 5 HOH A 47 547 49 HOH HOH . 
E 5 HOH A 48 548 50 HOH HOH . 
E 5 HOH A 49 549 51 HOH HOH . 
E 5 HOH A 50 550 52 HOH HOH . 
E 5 HOH A 51 551 54 HOH HOH . 
E 5 HOH A 52 552 55 HOH HOH . 
E 5 HOH A 53 553 56 HOH HOH . 
E 5 HOH A 54 554 57 HOH HOH . 
E 5 HOH A 55 555 58 HOH HOH . 
E 5 HOH A 56 556 59 HOH HOH . 
E 5 HOH A 57 557 60 HOH HOH . 
E 5 HOH A 58 558 61 HOH HOH . 
E 5 HOH A 59 559 62 HOH HOH . 
E 5 HOH A 60 560 64 HOH HOH . 
E 5 HOH A 61 561 65 HOH HOH . 
E 5 HOH A 62 562 66 HOH HOH . 
E 5 HOH A 63 563 68 HOH HOH . 
E 5 HOH A 64 564 69 HOH HOH . 
E 5 HOH A 65 565 70 HOH HOH . 
E 5 HOH A 66 566 71 HOH HOH . 
E 5 HOH A 67 567 72 HOH HOH . 
E 5 HOH A 68 568 73 HOH HOH . 
E 5 HOH A 69 569 74 HOH HOH . 
E 5 HOH A 70 570 76 HOH HOH . 
E 5 HOH A 71 571 78 HOH HOH . 
E 5 HOH A 72 572 79 HOH HOH . 
E 5 HOH A 73 573 81 HOH HOH . 
E 5 HOH A 74 574 83 HOH HOH . 
E 5 HOH A 75 575 84 HOH HOH . 
E 5 HOH A 76 576 85 HOH HOH . 
E 5 HOH A 77 577 89 HOH HOH . 
E 5 HOH A 78 578 91 HOH HOH . 
E 5 HOH A 79 579 92 HOH HOH . 
E 5 HOH A 80 580 93 HOH HOH . 
E 5 HOH A 81 581 96 HOH HOH . 
E 5 HOH A 82 582 97 HOH HOH . 
E 5 HOH A 83 583 101 HOH HOH . 
E 5 HOH A 84 584 102 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 O1 G3P . . . C 3 40.112 -0.989 27.954 1 97.75 ? O1 G3P 402 A 1 
HETATM 2 C C1 G3P . . . C 3 39.021 -1.186 28.835 1 97.75 ? C1 G3P 402 A 1 
HETATM 3 C C2 G3P . . . C 3 39.218 -0.525 30.212 1 97.75 ? C2 G3P 402 A 1 
HETATM 4 O O2 G3P . . . C 3 37.992 -0.524 30.925 1 97.75 ? O2 G3P 402 A 1 
HETATM 5 C C3 G3P . . . C 3 40.318 -1.31 30.964 1 97.75 ? C3 G3P 402 A 1 
HETATM 6 O O1P G3P . . . C 3 41.327 -0.582 31.645 1 97.75 ? O1P G3P 402 A 1 
HETATM 7 O O4P G3P . . . C 3 42.533 -0.58 33.941 1 97.75 ? O4P G3P 402 A 1 
HETATM 8 O O2P G3P . . . C 3 43.673 -1.568 32.014 1 97.75 ? O2P G3P 402 A 1 
HETATM 9 O O3P G3P . . . C 3 41.774 -2.743 32.999 1 97.75 ? O3P G3P 402 A 1 
HETATM 10 P P G3P . . . C 3 42.327 -1.374 32.66 1 97.75 ? P G3P 402 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           10 
#