data_2RD5
#
_model_server_result.job_id            9sMPaAavQyHVF_FFCSqUFQ 
_model_server_result.datetime_utc      '2024-12-21 16:19:42' 
_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          2rd5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1000}' 
#
_entry.id    2RD5 
#
_exptl.entry_id    2RD5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              175.209 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ARGININE 
_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            2RD5 
_cell.length_a            171.133 
_cell.length_b            171.133 
_cell.length_c            171.133 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2RD5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,O,P,Q,R,S 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 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 I 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 J O1B ADP . B ADP 2000 1_555 H MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc2 J O2A ADP . B ADP 2000 1_555 H MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc3 C O GLY 49 C GLY 48 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc4 M O3G ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc5 M O2A ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc6 M O2B ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc7 M O1A ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? 
metalc ? metalc8 D O GLY 49 D GLY 48 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc9 O O3G ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc10 O O2B ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc11 O O2A ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc12 O O1A ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
#
_chem_comp.formula           'C6 H15 N4 O2 1' 
_chem_comp.formula_weight    175.209 
_chem_comp.id                ARG 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              ARGININE 
_chem_comp.type              'l-peptide linking' 
_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
N CA ARG sing 57 n n 
N H ARG sing 58 n n 
N H2 ARG sing 59 n n 
CA C ARG sing 60 n n 
CA CB ARG sing 61 n n 
CA HA ARG sing 62 n n 
C O ARG doub 63 n n 
C OXT ARG sing 64 n n 
CB CG ARG sing 65 n n 
CB HB2 ARG sing 66 n n 
CB HB3 ARG sing 67 n n 
CG CD ARG sing 68 n n 
CG HG2 ARG sing 69 n n 
CG HG3 ARG sing 70 n n 
CD NE ARG sing 71 n n 
CD HD2 ARG sing 72 n n 
CD HD3 ARG sing 73 n n 
NE CZ ARG sing 74 n n 
NE HE ARG sing 75 n n 
CZ NH1 ARG sing 76 n n 
CZ NH2 ARG doub 77 n n 
NH1 HH11 ARG sing 78 n n 
NH1 HH12 ARG sing 79 n n 
NH2 HH21 ARG sing 80 n n 
NH2 HH22 ARG sing 81 n n 
OXT HXT ARG sing 82 n n 
#
_atom_sites.entry_id                     2RD5 
_atom_sites.fract_transf_matrix[1][1]    0.005843 
_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]    0.005843 
_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]    0.005843 
_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 3 ARG A 1 1000 1000 ARG ARG . 
F 4 ADP A 1 2000 2000 ADP ADP . 
G 5 NLG A 1 2001 2001 NLG NLG . 
H 6 MG B 1 2002 2002 MG MG . 
I 3 ARG B 1 1000 1000 ARG ARG . 
J 4 ADP B 1 2000 2000 ADP ADP . 
K 5 NLG B 1 2001 2001 NLG NLG . 
L 6 MG C 1 1001 1001 MG MG . 
M 7 ATP C 1 1000 1000 ATP ATP . 
N 6 MG D 1 1001 1001 MG MG . 
O 7 ATP D 1 1000 1000 ATP ATP . 
P 8 HOH A 1 2002 10 HOH HOH . 
P 8 HOH A 2 2003 11 HOH HOH . 
P 8 HOH A 3 2004 12 HOH HOH . 
P 8 HOH A 4 2005 19 HOH HOH . 
P 8 HOH A 5 2006 20 HOH HOH . 
P 8 HOH A 6 2007 40 HOH HOH . 
P 8 HOH A 7 2008 41 HOH HOH . 
P 8 HOH A 8 2009 42 HOH HOH . 
P 8 HOH A 9 2010 43 HOH HOH . 
P 8 HOH A 10 2011 44 HOH HOH . 
P 8 HOH A 11 2012 45 HOH HOH . 
P 8 HOH A 12 2013 46 HOH HOH . 
P 8 HOH A 13 2014 47 HOH HOH . 
P 8 HOH A 14 2015 48 HOH HOH . 
P 8 HOH A 15 2016 49 HOH HOH . 
P 8 HOH A 16 2017 53 HOH HOH . 
P 8 HOH A 17 2018 54 HOH HOH . 
P 8 HOH A 18 2019 55 HOH HOH . 
P 8 HOH A 19 2020 56 HOH HOH . 
P 8 HOH A 20 2021 57 HOH HOH . 
P 8 HOH A 21 2022 58 HOH HOH . 
P 8 HOH A 22 2023 62 HOH HOH . 
P 8 HOH A 23 2024 63 HOH HOH . 
P 8 HOH A 24 2025 64 HOH HOH . 
Q 8 HOH B 1 2003 13 HOH HOH . 
Q 8 HOH B 2 2004 14 HOH HOH . 
Q 8 HOH B 3 2005 15 HOH HOH . 
Q 8 HOH B 4 2006 16 HOH HOH . 
Q 8 HOH B 5 2007 17 HOH HOH . 
Q 8 HOH B 6 2008 18 HOH HOH . 
Q 8 HOH B 7 2009 21 HOH HOH . 
Q 8 HOH B 8 2010 22 HOH HOH . 
Q 8 HOH B 9 2011 23 HOH HOH . 
Q 8 HOH B 10 2012 24 HOH HOH . 
Q 8 HOH B 11 2013 25 HOH HOH . 
Q 8 HOH B 12 2014 26 HOH HOH . 
Q 8 HOH B 13 2015 27 HOH HOH . 
Q 8 HOH B 14 2016 28 HOH HOH . 
Q 8 HOH B 15 2017 29 HOH HOH . 
Q 8 HOH B 16 2018 32 HOH HOH . 
Q 8 HOH B 17 2019 33 HOH HOH . 
Q 8 HOH B 18 2020 35 HOH HOH . 
Q 8 HOH B 19 2021 36 HOH HOH . 
Q 8 HOH B 20 2022 37 HOH HOH . 
Q 8 HOH B 21 2023 38 HOH HOH . 
Q 8 HOH B 22 2024 39 HOH HOH . 
Q 8 HOH B 23 2025 59 HOH HOH . 
Q 8 HOH B 24 2026 60 HOH HOH . 
Q 8 HOH B 25 2027 61 HOH HOH . 
R 8 HOH C 1 1002 2 HOH HOH . 
R 8 HOH C 2 1003 30 HOH HOH . 
R 8 HOH C 3 1004 31 HOH HOH . 
R 8 HOH C 4 1005 34 HOH HOH . 
S 8 HOH D 1 1002 1 HOH HOH . 
S 8 HOH D 2 1003 3 HOH HOH . 
S 8 HOH D 3 1004 4 HOH HOH . 
S 8 HOH D 4 1005 5 HOH HOH . 
S 8 HOH D 5 1006 6 HOH HOH . 
S 8 HOH D 6 1007 7 HOH HOH . 
S 8 HOH D 7 1008 8 HOH HOH . 
S 8 HOH D 8 1009 9 HOH HOH . 
S 8 HOH D 9 1010 50 HOH HOH . 
S 8 HOH D 10 1011 51 HOH HOH . 
S 8 HOH D 11 1012 52 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 N N ARG . . . I 3 94.511 82.799 49.282 1 76.04 ? N ARG 1000 B 1 
HETATM 2 C CA ARG . . . I 3 94.848 84.028 49.982 1 73.95 ? CA ARG 1000 B 1 
HETATM 3 C C ARG . . . I 3 93.653 84.457 50.825 1 73.69 ? C ARG 1000 B 1 
HETATM 4 O O ARG . . . I 3 93.744 84.528 52.048 1 72.69 ? O ARG 1000 B 1 
HETATM 5 C CB ARG . . . I 3 95.207 85.108 48.965 1 74.43 ? CB ARG 1000 B 1 
HETATM 6 C CG ARG . . . I 3 95.802 86.386 49.511 1 73.38 ? CG ARG 1000 B 1 
HETATM 7 C CD ARG . . . I 3 95.298 87.547 48.666 1 73.54 ? CD ARG 1000 B 1 
HETATM 8 N NE ARG . . . I 3 96.261 88.634 48.511 1 69.73 ? NE ARG 1000 B 1 
HETATM 9 C CZ ARG . . . I 3 95.994 89.795 47.915 1 73.33 ? CZ ARG 1000 B 1 
HETATM 10 N NH1 ARG . . . I 3 94.782 90.039 47.421 1 69.74 ? NH1 ARG 1000 B 1 
HETATM 11 N NH2 ARG . . . I 3 96.939 90.723 47.82 1 68.84 ? NH2 ARG 1000 B 1 
HETATM 12 O OXT ARG . . . I 3 92.424 84.721 50.701 1 73 ? OXT ARG 1000 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           12 
#