data_4GVZ
#
_model_server_result.job_id            8TTSAYXY6yU0kBuMZdqI3Q 
_model_server_result.datetime_utc      '2024-11-25 01:58:00' 
_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          4gvz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":404}' 
#
_entry.id    4GVZ 
#
_exptl.entry_id    4GVZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              175.209 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            D-ARGININE 
_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            4GVZ 
_cell.length_a            64.109 
_cell.length_b            65.382 
_cell.length_c            85.912 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4GVZ 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                             E 
_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 O1A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc2 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc3 C MG MG . A MG 402 1_555 D O2 NO3 . A NO3 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc4 C MG MG . A MG 402 1_555 F O HOH . A HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc5 C MG MG . A MG 402 1_555 F O HOH . A HOH 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc6 C MG MG . A MG 402 1_555 F O HOH . A HOH 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
#
_chem_comp.formula           'C6 H15 N4 O2 1' 
_chem_comp.formula_weight    175.209 
_chem_comp.id                DAR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              D-ARGININE 
_chem_comp.type              'd-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 DAR sing 127 n n 
N H DAR sing 128 n n 
N H2 DAR sing 129 n n 
CA CB DAR sing 130 n n 
CA C DAR sing 131 n n 
CA HA DAR sing 132 n n 
CB CG DAR sing 133 n n 
CB HB2 DAR sing 134 n n 
CB HB3 DAR sing 135 n n 
CG CD DAR sing 136 n n 
CG HG2 DAR sing 137 n n 
CG HG3 DAR sing 138 n n 
CD NE DAR sing 139 n n 
CD HD2 DAR sing 140 n n 
CD HD3 DAR sing 141 n n 
NE CZ DAR sing 142 n n 
NE HE DAR sing 143 n n 
CZ NH1 DAR sing 144 n n 
CZ NH2 DAR doub 145 n n 
NH1 HH11 DAR sing 146 n n 
NH1 HH12 DAR sing 147 n n 
NH2 HH21 DAR sing 148 n n 
NH2 HH22 DAR sing 149 n n 
C O DAR doub 150 n n 
C OXT DAR sing 151 n n 
OXT HXT DAR sing 152 n n 
#
_atom_sites.entry_id                     4GVZ 
_atom_sites.fract_transf_matrix[1][1]    0.015598 
_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]    0.015295 
_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]    0.01164 
_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 ADP A 1 401 400 ADP ADP . 
C 3 MG A 1 402 408 MG MG . 
D 4 NO3 A 1 403 401 NO3 NO3 . 
E 5 DAR A 1 404 403 DAR DAR . 
F 6 HOH A 1 501 1 HOH HOH . 
F 6 HOH A 2 502 2 HOH HOH . 
F 6 HOH A 3 503 3 HOH HOH . 
F 6 HOH A 4 504 4 HOH HOH . 
F 6 HOH A 5 505 5 HOH HOH . 
F 6 HOH A 6 506 6 HOH HOH . 
F 6 HOH A 7 507 7 HOH HOH . 
F 6 HOH A 8 508 8 HOH HOH . 
F 6 HOH A 9 509 9 HOH HOH . 
F 6 HOH A 10 510 10 HOH HOH . 
F 6 HOH A 11 511 11 HOH HOH . 
F 6 HOH A 12 512 12 HOH HOH . 
F 6 HOH A 13 513 13 HOH HOH . 
F 6 HOH A 14 514 14 HOH HOH . 
F 6 HOH A 15 515 15 HOH HOH . 
F 6 HOH A 16 516 16 HOH HOH . 
F 6 HOH A 17 517 17 HOH HOH . 
F 6 HOH A 18 518 18 HOH HOH . 
F 6 HOH A 19 519 19 HOH HOH . 
F 6 HOH A 20 520 20 HOH HOH . 
F 6 HOH A 21 521 21 HOH HOH . 
F 6 HOH A 22 522 22 HOH HOH . 
F 6 HOH A 23 523 23 HOH HOH . 
F 6 HOH A 24 524 24 HOH HOH . 
F 6 HOH A 25 525 25 HOH HOH . 
F 6 HOH A 26 526 26 HOH HOH . 
F 6 HOH A 27 527 27 HOH HOH . 
F 6 HOH A 28 528 28 HOH HOH . 
F 6 HOH A 29 529 29 HOH HOH . 
F 6 HOH A 30 530 30 HOH HOH . 
F 6 HOH A 31 531 31 HOH HOH . 
F 6 HOH A 32 532 32 HOH HOH . 
F 6 HOH A 33 533 33 HOH HOH . 
F 6 HOH A 34 534 34 HOH HOH . 
F 6 HOH A 35 535 35 HOH HOH . 
F 6 HOH A 36 536 36 HOH HOH . 
F 6 HOH A 37 537 37 HOH HOH . 
F 6 HOH A 38 538 38 HOH HOH . 
F 6 HOH A 39 539 39 HOH HOH . 
F 6 HOH A 40 540 40 HOH HOH . 
F 6 HOH A 41 541 41 HOH HOH . 
F 6 HOH A 42 542 42 HOH HOH . 
F 6 HOH A 43 543 43 HOH HOH . 
F 6 HOH A 44 544 44 HOH HOH . 
F 6 HOH A 45 545 45 HOH HOH . 
F 6 HOH A 46 546 46 HOH HOH . 
F 6 HOH A 47 547 47 HOH HOH . 
F 6 HOH A 48 548 48 HOH HOH . 
F 6 HOH A 49 549 49 HOH HOH . 
F 6 HOH A 50 550 50 HOH HOH . 
F 6 HOH A 51 551 51 HOH HOH . 
F 6 HOH A 52 552 52 HOH HOH . 
F 6 HOH A 53 553 53 HOH HOH . 
F 6 HOH A 54 554 54 HOH HOH . 
F 6 HOH A 55 555 55 HOH HOH . 
F 6 HOH A 56 556 56 HOH HOH . 
F 6 HOH A 57 557 57 HOH HOH . 
F 6 HOH A 58 558 58 HOH HOH . 
F 6 HOH A 59 559 59 HOH HOH . 
F 6 HOH A 60 560 60 HOH HOH . 
F 6 HOH A 61 561 61 HOH HOH . 
F 6 HOH A 62 562 62 HOH HOH . 
F 6 HOH A 63 563 63 HOH HOH . 
F 6 HOH A 64 564 64 HOH HOH . 
F 6 HOH A 65 565 65 HOH HOH . 
F 6 HOH A 66 566 66 HOH HOH . 
F 6 HOH A 67 567 67 HOH HOH . 
F 6 HOH A 68 568 68 HOH HOH . 
F 6 HOH A 69 569 69 HOH HOH . 
F 6 HOH A 70 570 70 HOH HOH . 
F 6 HOH A 71 571 71 HOH HOH . 
F 6 HOH A 72 572 72 HOH HOH . 
F 6 HOH A 73 573 73 HOH HOH . 
F 6 HOH A 74 574 74 HOH HOH . 
F 6 HOH A 75 575 75 HOH HOH . 
F 6 HOH A 76 576 76 HOH HOH . 
F 6 HOH A 77 577 77 HOH HOH . 
F 6 HOH A 78 578 78 HOH HOH . 
F 6 HOH A 79 579 79 HOH HOH . 
F 6 HOH A 80 580 80 HOH HOH . 
F 6 HOH A 81 581 81 HOH HOH . 
F 6 HOH A 82 582 82 HOH HOH . 
F 6 HOH A 83 583 83 HOH HOH . 
F 6 HOH A 84 584 84 HOH HOH . 
F 6 HOH A 85 585 85 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 DAR . . . E 5 -10.849 5.285 17.026 1 20.9 ? N DAR 404 A 1 
HETATM 2 C CA DAR . . . E 5 -10.869 4.521 15.775 1 16.67 ? CA DAR 404 A 1 
HETATM 3 C CB DAR . . . E 5 -10.724 3.017 16.117 1 15.8 ? CB DAR 404 A 1 
HETATM 4 C CG DAR . . . E 5 -10.311 2.147 14.922 1 15.93 ? CG DAR 404 A 1 
HETATM 5 C CD DAR . . . E 5 -10.698 0.691 15.217 1 10.97 ? CD DAR 404 A 1 
HETATM 6 N NE DAR . . . E 5 -10.059 0.198 16.438 1 8.79 ? NE DAR 404 A 1 
HETATM 7 C CZ DAR . . . E 5 -10.781 -0.305 17.538 1 7.2 ? CZ DAR 404 A 1 
HETATM 8 N NH1 DAR . . . E 5 -12.175 -0.314 17.424 1 1.91 ? NH1 DAR 404 A 1 
HETATM 9 N NH2 DAR . . . E 5 -10.285 -0.763 18.669 1 10.23 ? NH2 DAR 404 A 1 
HETATM 10 C C DAR . . . E 5 -9.676 4.974 14.869 1 25.29 ? C DAR 404 A 1 
HETATM 11 O O DAR . . . E 5 -9.985 5.679 13.886 1 30.49 ? O DAR 404 A 1 
HETATM 12 O OXT DAR . . . E 5 -8.527 4.618 15.191 1 22.57 ? OXT DAR 404 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           12 
#