data_4RKV
#
_model_server_result.job_id            nE1NaT4RvBSVw2eLss5vXQ 
_model_server_result.datetime_utc      '2024-12-26 12:40:06' 
_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          4rkv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2103}' 
#
_entry.id    4RKV 
#
_exptl.entry_id    4RKV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_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            4RKV 
_cell.length_a            36.645 
_cell.length_b            36.645 
_cell.length_c            37.078 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4RKV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        90 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 4 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,L,M,N 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 36.645 0 0 
3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 18.3225 -18.3225 0 
4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 18.3225 18.3225 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 J 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
metalc ? metalc1 A O6 G 2 A G 1002 1_555 D SR SR . A SR 9002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? 
metalc ? metalc2 A O6 G 3 A G 1003 1_555 D SR SR . A SR 9002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? 
metalc ? metalc3 A O6 G 4 A G 1004 1_555 C SR SR . A SR 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? 
metalc ? metalc4 A O6 G 5 A G 1005 1_555 C SR SR . A SR 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? 
metalc ? metalc5 A OP1 G 5 A G 1005 1_555 G SR SR . A SR 9005 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.637 ? 
metalc ? metalc6 A O4 U 6 A U 1006 1_555 E NA NA . A NA 9003 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc7 A O3' U 6 A U 1006 1_555 F SR SR . A SR 9004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? 
metalc ? metalc8 A O2' U 6 A U 1006 1_555 F SR SR . A SR 9004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? 
metalc ? metalc9 F SR SR . A SR 9004 1_555 M O HOH . A HOH 9103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? 
metalc ? metalc10 F SR SR . A SR 9004 1_555 M O HOH . A HOH 9108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc11 F SR SR . A SR 9004 1_555 M O HOH . A HOH 9110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? 
metalc ? metalc12 F SR SR . A SR 9004 1_555 M O HOH . A HOH 9111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? 
metalc ? metalc13 F SR SR . A SR 9004 1_555 M O HOH . A HOH 9124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
metalc ? metalc14 G SR SR . A SR 9005 1_555 M O HOH . A HOH 9115 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.695 ? 
metalc ? metalc15 G SR SR . A SR 9005 1_555 M O HOH . A HOH 9116 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.627 ? 
metalc ? metalc16 B O6 G 2 B G 2002 1_555 H SR SR . B SR 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? 
metalc ? metalc17 B O3' G 2 B G 2002 1_555 K CA CA . B CA 2104 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.11 ? 
metalc ? metalc18 B OP2 G 2 B G 2002 1_555 L CA CA . B CA 2105 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc19 B O6 G 3 B G 2003 1_555 H SR SR . B SR 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? 
metalc ? metalc20 B OP1 G 3 B G 2003 1_555 K CA CA . B CA 2104 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.512 ? 
metalc ? metalc21 B O6 G 4 B G 2004 1_555 I SR SR . B SR 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc22 B O6 G 5 B G 2005 1_555 I SR SR . B SR 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? 
metalc ? metalc23 B O4 U 6 B U 2006 1_555 J NA NA . B NA 2103 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc24 J NA NA . B NA 2103 1_555 N O HOH . B HOH 2225 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.199 ? 
metalc ? metalc25 K CA CA . B CA 2104 1_555 N O HOH . B HOH 2210 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.441 ? 
metalc ? metalc26 K CA CA . B CA 2104 1_555 N O HOH . B HOH 2215 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.662 ? 
metalc ? metalc27 L CA CA . B CA 2105 1_555 N O HOH . B HOH 2207 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc28 L CA CA . B CA 2105 1_555 N O HOH . B HOH 2214 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc29 L CA CA . B CA 2105 1_555 N O HOH . B HOH 2224 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.45 ? 
hydrog 'G-U MISPAIR' hydrog1 A N2 G 3 A G 1003 1_555 B O2 U 1 B U 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'Na 1' 
_chem_comp.formula_weight    22.99 
_chem_comp.id                NA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SODIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     4RKV 
_atom_sites.fract_transf_matrix[1][1]    0.027289 
_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]    0.027289 
_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]    0.02697 
_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 SR A 1 9001 9001 SR SR . 
D 2 SR A 1 9002 9002 SR SR . 
E 3 NA A 1 9003 9005 NA NA . 
F 2 SR A 1 9004 9101 SR SR . 
G 2 SR A 1 9005 9105 SR SR . 
H 2 SR B 1 2101 9003 SR SR . 
I 2 SR B 1 2102 9004 SR SR . 
J 3 NA B 1 2103 9006 NA NA . 
K 4 CA B 1 2104 9103 CA CA . 
L 4 CA B 1 2105 9104 CA CA . 
M 5 HOH A 1 9101 9108 HOH HOH . 
M 5 HOH A 2 9102 9502 HOH HOH . 
M 5 HOH A 3 9103 9503 HOH HOH . 
M 5 HOH A 4 9104 9505 HOH HOH . 
M 5 HOH A 5 9105 9506 HOH HOH . 
M 5 HOH A 6 9106 9510 HOH HOH . 
M 5 HOH A 7 9107 9512 HOH HOH . 
M 5 HOH A 8 9108 9513 HOH HOH . 
M 5 HOH A 9 9109 9517 HOH HOH . 
M 5 HOH A 10 9110 9520 HOH HOH . 
M 5 HOH A 11 9111 9524 HOH HOH . 
M 5 HOH A 12 9112 9525 HOH HOH . 
M 5 HOH A 13 9113 9536 HOH HOH . 
M 5 HOH A 14 9114 9537 HOH HOH . 
M 5 HOH A 15 9115 9540 HOH HOH . 
M 5 HOH A 16 9116 9545 HOH HOH . 
M 5 HOH A 17 9117 9547 HOH HOH . 
M 5 HOH A 18 9118 9556 HOH HOH . 
M 5 HOH A 19 9119 9567 HOH HOH . 
M 5 HOH A 20 9120 9571 HOH HOH . 
M 5 HOH A 21 9121 9574 HOH HOH . 
M 5 HOH A 22 9122 9576 HOH HOH . 
M 5 HOH A 23 9123 9581 HOH HOH . 
M 5 HOH A 24 9124 9585 HOH HOH . 
M 5 HOH A 25 9125 9586 HOH HOH . 
M 5 HOH A 26 9126 9591 HOH HOH . 
N 5 HOH B 1 2201 9504 HOH HOH . 
N 5 HOH B 2 2202 9532 HOH HOH . 
N 5 HOH B 3 2203 9106 HOH HOH . 
N 5 HOH B 4 2204 9107 HOH HOH . 
N 5 HOH B 5 2205 9501 HOH HOH . 
N 5 HOH B 6 2206 9508 HOH HOH . 
N 5 HOH B 7 2207 9509 HOH HOH . 
N 5 HOH B 8 2208 9511 HOH HOH . 
N 5 HOH B 9 2209 9515 HOH HOH . 
N 5 HOH B 10 2210 9516 HOH HOH . 
N 5 HOH B 11 2211 9518 HOH HOH . 
N 5 HOH B 12 2212 9521 HOH HOH . 
N 5 HOH B 13 2213 9523 HOH HOH . 
N 5 HOH B 14 2214 9526 HOH HOH . 
N 5 HOH B 15 2215 9529 HOH HOH . 
N 5 HOH B 16 2216 9534 HOH HOH . 
N 5 HOH B 17 2217 9538 HOH HOH . 
N 5 HOH B 18 2218 9543 HOH HOH . 
N 5 HOH B 19 2219 9546 HOH HOH . 
N 5 HOH B 20 2220 9548 HOH HOH . 
N 5 HOH B 21 2221 9549 HOH HOH . 
N 5 HOH B 22 2222 9561 HOH HOH . 
N 5 HOH B 23 2223 9563 HOH HOH . 
N 5 HOH B 24 2224 9565 HOH HOH . 
N 5 HOH B 25 2225 9573 HOH HOH . 
N 5 HOH B 26 2226 9583 HOH HOH . 
N 5 HOH B 27 2227 9588 HOH HOH . 
N 5 HOH B 28 2228 9590 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 NA NA NA . A . J 3 18.322 0 7.856 0.05 8.89 ? NA NA 2103 B 1 
HETATM 2 NA NA NA . B . J 3 18.322 0 10.229 0.2 13.52 ? NA NA 2103 B 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           235 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           2 
#