data_2YVJ
#
_model_server_result.job_id            DJkquMt6VmkdOK-6_FHiDg 
_model_server_result.datetime_utc      '2024-11-06 01:39:59' 
_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          2yvj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":500}' 
#
_entry.id    2YVJ 
#
_exptl.entry_id    2YVJ 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              175.82 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'FE2/S2 (INORGANIC) CLUSTER' 
_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          115.81 
_cell.angle_gamma         90 
_cell.entry_id            2YVJ 
_cell.length_a            60.596 
_cell.length_b            173.715 
_cell.length_c            60.976 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YVJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             F 
_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 B SG CYS 43 B CYS 43 1_555 F FE1 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? 
metalc ? metalc2 B ND1 HIS 45 B HIS 45 1_555 F FE2 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? 
metalc ? metalc3 B SG CYS 63 B CYS 63 1_555 F FE1 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? 
metalc ? metalc4 B ND1 HIS 66 B HIS 66 1_555 F FE2 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? 
#
_chem_comp.formula           'Fe2 S2' 
_chem_comp.formula_weight    175.82 
_chem_comp.id                FES 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'FE2/S2 (INORGANIC) CLUSTER' 
_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
FE1 S1 FES sing 174 n n 
FE1 S2 FES sing 175 n n 
FE2 S1 FES sing 176 n n 
FE2 S2 FES sing 177 n n 
#
_atom_sites.entry_id                     2YVJ 
_atom_sites.fract_transf_matrix[1][1]    0.016503 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.007981 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005757 
_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]    0.018217 
_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
D 3 FAD A 1 501 501 FAD FAD . 
E 4 NAI A 1 503 503 NAI NAI . 
F 5 FES B 1 500 500 FES FES . 
G 3 FAD P 1 502 502 FAD FAD . 
H 4 NAI P 1 504 504 NAI NAI . 
I 6 HOH A 1 504 1 HOH HOH . 
I 6 HOH A 2 505 2 HOH HOH . 
I 6 HOH A 3 506 3 HOH HOH . 
I 6 HOH A 4 507 4 HOH HOH . 
I 6 HOH A 5 508 7 HOH HOH . 
I 6 HOH A 6 509 10 HOH HOH . 
I 6 HOH A 7 510 11 HOH HOH . 
I 6 HOH A 8 511 13 HOH HOH . 
I 6 HOH A 9 512 16 HOH HOH . 
I 6 HOH A 10 513 19 HOH HOH . 
I 6 HOH A 11 514 21 HOH HOH . 
I 6 HOH A 12 515 24 HOH HOH . 
I 6 HOH A 13 516 25 HOH HOH . 
I 6 HOH A 14 517 28 HOH HOH . 
I 6 HOH A 15 518 31 HOH HOH . 
I 6 HOH A 16 519 33 HOH HOH . 
I 6 HOH A 17 520 43 HOH HOH . 
I 6 HOH A 18 521 44 HOH HOH . 
I 6 HOH A 19 522 46 HOH HOH . 
I 6 HOH A 20 523 50 HOH HOH . 
I 6 HOH A 21 524 51 HOH HOH . 
I 6 HOH A 22 525 52 HOH HOH . 
I 6 HOH A 23 526 54 HOH HOH . 
I 6 HOH A 24 527 55 HOH HOH . 
I 6 HOH A 25 528 57 HOH HOH . 
I 6 HOH A 26 529 60 HOH HOH . 
I 6 HOH A 27 530 61 HOH HOH . 
I 6 HOH A 28 531 62 HOH HOH . 
I 6 HOH A 29 532 66 HOH HOH . 
I 6 HOH A 30 533 68 HOH HOH . 
I 6 HOH A 31 534 70 HOH HOH . 
I 6 HOH A 32 535 77 HOH HOH . 
J 6 HOH B 1 501 5 HOH HOH . 
J 6 HOH B 2 502 56 HOH HOH . 
J 6 HOH B 3 503 64 HOH HOH . 
J 6 HOH B 4 504 78 HOH HOH . 
K 6 HOH P 1 505 6 HOH HOH . 
K 6 HOH P 2 506 8 HOH HOH . 
K 6 HOH P 3 507 9 HOH HOH . 
K 6 HOH P 4 508 12 HOH HOH . 
K 6 HOH P 5 509 14 HOH HOH . 
K 6 HOH P 6 510 15 HOH HOH . 
K 6 HOH P 7 511 17 HOH HOH . 
K 6 HOH P 8 512 18 HOH HOH . 
K 6 HOH P 9 513 20 HOH HOH . 
K 6 HOH P 10 514 22 HOH HOH . 
K 6 HOH P 11 515 23 HOH HOH . 
K 6 HOH P 12 516 26 HOH HOH . 
K 6 HOH P 13 517 27 HOH HOH . 
K 6 HOH P 14 518 29 HOH HOH . 
K 6 HOH P 15 519 30 HOH HOH . 
K 6 HOH P 16 520 32 HOH HOH . 
K 6 HOH P 17 521 34 HOH HOH . 
K 6 HOH P 18 522 35 HOH HOH . 
K 6 HOH P 19 523 36 HOH HOH . 
K 6 HOH P 20 524 37 HOH HOH . 
K 6 HOH P 21 525 38 HOH HOH . 
K 6 HOH P 22 526 39 HOH HOH . 
K 6 HOH P 23 527 40 HOH HOH . 
K 6 HOH P 24 528 41 HOH HOH . 
K 6 HOH P 25 529 42 HOH HOH . 
K 6 HOH P 26 530 45 HOH HOH . 
K 6 HOH P 27 531 47 HOH HOH . 
K 6 HOH P 28 532 48 HOH HOH . 
K 6 HOH P 29 533 49 HOH HOH . 
K 6 HOH P 30 534 53 HOH HOH . 
K 6 HOH P 31 535 58 HOH HOH . 
K 6 HOH P 32 536 59 HOH HOH . 
K 6 HOH P 33 537 63 HOH HOH . 
K 6 HOH P 34 538 65 HOH HOH . 
K 6 HOH P 35 539 67 HOH HOH . 
K 6 HOH P 36 540 69 HOH HOH . 
K 6 HOH P 37 541 71 HOH HOH . 
K 6 HOH P 38 542 72 HOH HOH . 
K 6 HOH P 39 543 73 HOH HOH . 
K 6 HOH P 40 544 74 HOH HOH . 
K 6 HOH P 41 545 75 HOH HOH . 
K 6 HOH P 42 546 76 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 FE FE1 FES . . . F 5 -4.776 -26.991 2.808 1 37.37 ? FE1 FES 500 B 1 
HETATM 2 FE FE2 FES . . . F 5 -4.033 -26.289 5.29 1 35.5 ? FE2 FES 500 B 1 
HETATM 3 S S1 FES . . . F 5 -5.53 -27.814 4.707 1 37.54 ? S1 FES 500 B 1 
HETATM 4 S S2 FES . . . F 5 -3.066 -25.714 3.39 1 34.13 ? S2 FES 500 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           4 
#