data_6HD1
#
_model_server_result.job_id            wlo06xcZbRl0jezHDEuqWg 
_model_server_result.datetime_utc      '2024-12-02 13:26:24' 
_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          6hd1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":501}' 
#
_entry.id    6HD1 
#
_exptl.entry_id    6HD1 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              743.405 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_entity.pdbx_number_of_molecules    3 
_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            6HD1 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6HD1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 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,L,M,N,O,P,Q,R 
_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    ? 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 D N N 
? 2 I N N 
? 2 N 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
covale ? covale1 A ND2 ASN 323 C ASN 323 1_555 G C1 NAG . C NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale2 B ND2 ASN 323 A ASN 323 1_555 L C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale3 C ND2 ASN 323 B ASN 323 1_555 Q C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
metalc ? metalc1 A NE2 HIS 304 C HIS 304 1_555 E FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? 
metalc ? metalc2 A NE2 HIS 397 C HIS 397 1_555 E FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc3 B NE2 HIS 304 A HIS 304 1_555 J FE HEM . A HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc4 B NE2 HIS 397 A HIS 397 1_555 J FE HEM . A HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc5 C NE2 HIS 304 B HIS 304 1_555 O FE HEM . B HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc6 C NE2 HIS 397 B HIS 397 1_555 O FE HEM . B HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
#
_chem_comp.formula           'C21 H28 N7 O17 P3' 
_chem_comp.formula_weight    743.405 
_chem_comp.id                NAP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" 
#
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
PA O1A NAP doub 490 n n 
PA O2A NAP sing 491 n n 
PA O5B NAP sing 492 n n 
PA O3 NAP sing 493 n n 
O2A HOA2 NAP sing 494 n n 
O5B C5B NAP sing 495 n n 
C5B C4B NAP sing 496 n n 
C5B H51A NAP sing 497 n n 
C5B H52A NAP sing 498 n n 
C4B O4B NAP sing 499 n n 
C4B C3B NAP sing 500 n n 
C4B H4B NAP sing 501 n n 
O4B C1B NAP sing 502 n n 
C3B O3B NAP sing 503 n n 
C3B C2B NAP sing 504 n n 
C3B H3B NAP sing 505 n n 
O3B HO3A NAP sing 506 n n 
C2B O2B NAP sing 507 n n 
C2B C1B NAP sing 508 n n 
C2B H2B NAP sing 509 n n 
O2B P2B NAP sing 510 n n 
C1B N9A NAP sing 511 n n 
C1B H1B NAP sing 512 n n 
N9A C8A NAP sing 513 n y 
N9A C4A NAP sing 514 n y 
C8A N7A NAP doub 515 n y 
C8A H8A NAP sing 516 n n 
N7A C5A NAP sing 517 n y 
C5A C6A NAP sing 518 n y 
C5A C4A NAP doub 519 n y 
C6A N6A NAP sing 520 n n 
C6A N1A NAP doub 521 n y 
N6A H61A NAP sing 522 n n 
N6A H62A NAP sing 523 n n 
N1A C2A NAP sing 524 n y 
C2A N3A NAP doub 525 n y 
C2A H2A NAP sing 526 n n 
N3A C4A NAP sing 527 n y 
O3 PN NAP sing 528 n n 
PN O1N NAP doub 529 n n 
PN O2N NAP sing 530 n n 
PN O5D NAP sing 531 n n 
O5D C5D NAP sing 532 n n 
C5D C4D NAP sing 533 n n 
C5D H51N NAP sing 534 n n 
C5D H52N NAP sing 535 n n 
C4D O4D NAP sing 536 n n 
C4D C3D NAP sing 537 n n 
C4D H4D NAP sing 538 n n 
O4D C1D NAP sing 539 n n 
C3D O3D NAP sing 540 n n 
C3D C2D NAP sing 541 n n 
C3D H3D NAP sing 542 n n 
O3D HO3N NAP sing 543 n n 
C2D O2D NAP sing 544 n n 
C2D C1D NAP sing 545 n n 
C2D H2D NAP sing 546 n n 
O2D HO2N NAP sing 547 n n 
C1D N1N NAP sing 548 n n 
C1D H1D NAP sing 549 n n 
N1N C2N NAP sing 550 n y 
N1N C6N NAP doub 551 n y 
C2N C3N NAP doub 552 n y 
C2N H2N NAP sing 553 n n 
C3N C7N NAP sing 554 n n 
C3N C4N NAP sing 555 n y 
C7N O7N NAP doub 556 n n 
C7N N7N NAP sing 557 n n 
N7N H71N NAP sing 558 n n 
N7N H72N NAP sing 559 n n 
C4N C5N NAP doub 560 n y 
C4N H4N NAP sing 561 n n 
C5N C6N NAP sing 562 n y 
C5N H5N NAP sing 563 n n 
C6N H6N NAP sing 564 n n 
P2B O1X NAP doub 565 n n 
P2B O2X NAP sing 566 n n 
P2B O3X NAP sing 567 n n 
O2X HOP2 NAP sing 568 n n 
O3X HOP3 NAP sing 569 n n 
#
_atom_sites.entry_id                     6HD1 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 2 NAP C 1 501 1200 NAP NAP . 
E 3 HEM C 1 502 1202 HEM HEM . 
F 4 FAD C 1 503 1203 FAD FAD . 
G 5 NAG C 1 504 1204 NAG NAG . 
H 6 44E C 1 505 1205 44E 44E . 
I 2 NAP A 1 501 1200 NAP NAP . 
J 3 HEM A 1 502 1202 HEM HEM . 
K 4 FAD A 1 503 1203 FAD FAD . 
L 5 NAG A 1 504 1204 NAG NAG . 
M 6 44E A 1 505 1205 44E 44E . 
N 2 NAP B 1 501 1200 NAP NAP . 
O 3 HEM B 1 502 1202 HEM HEM . 
P 4 FAD B 1 503 1203 FAD FAD . 
Q 5 NAG B 1 504 1204 NAG NAG . 
R 6 44E B 1 505 1205 44E 44E . 
#
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 P PA NAP . . . N 2 122.05 91.663 91.161 1 137.44 ? PA NAP 501 B 1 
HETATM 2 O O1A NAP . . . N 2 121.581 92.635 90.111 1 137.44 ? O1A NAP 501 B 1 
HETATM 3 O O2A NAP . . . N 2 120.891 90.844 91.658 1 137.44 ? O2A NAP 501 B 1 
HETATM 4 O O5B NAP . . . N 2 123.158 90.63 90.533 1 137.44 ? O5B NAP 501 B 1 
HETATM 5 C C5B NAP . . . N 2 123.845 91.007 89.384 1 137.44 ? C5B NAP 501 B 1 
HETATM 6 C C4B NAP . . . N 2 122.98 90.787 88.116 1 137.44 ? C4B NAP 501 B 1 
HETATM 7 O O4B NAP . . . N 2 123.75 90.472 87.124 1 137.44 ? O4B NAP 501 B 1 
HETATM 8 C C3B NAP . . . N 2 122.049 89.572 88.255 1 137.44 ? C3B NAP 501 B 1 
HETATM 9 O O3B NAP . . . N 2 120.83 89.98 88.663 1 137.44 ? O3B NAP 501 B 1 
HETATM 10 C C2B NAP . . . N 2 121.929 88.999 86.832 1 137.44 ? C2B NAP 501 B 1 
HETATM 11 O O2B NAP . . . N 2 120.565 89.239 86.288 1 137.44 ? O2B NAP 501 B 1 
HETATM 12 C C1B NAP . . . N 2 122.799 89.655 86.116 1 137.44 ? C1B NAP 501 B 1 
HETATM 13 N N9A NAP . . . N 2 123.606 88.769 85.332 1 137.44 ? N9A NAP 501 B 1 
HETATM 14 C C8A NAP . . . N 2 123.738 88.598 84.022 1 137.44 ? C8A NAP 501 B 1 
HETATM 15 N N7A NAP . . . N 2 124.641 87.645 83.817 1 137.44 ? N7A NAP 501 B 1 
HETATM 16 C C5A NAP . . . N 2 125.065 87.222 85.005 1 137.44 ? C5A NAP 501 B 1 
HETATM 17 C C6A NAP . . . N 2 125.975 86.26 85.351 1 137.44 ? C6A NAP 501 B 1 
HETATM 18 N N6A NAP . . . N 2 126.752 85.413 84.47 1 137.44 ? N6A NAP 501 B 1 
HETATM 19 N N1A NAP . . . N 2 126.24 86.017 86.618 1 137.44 ? N1A NAP 501 B 1 
HETATM 20 C C2A NAP . . . N 2 125.609 86.716 87.584 1 137.44 ? C2A NAP 501 B 1 
HETATM 21 N N3A NAP . . . N 2 124.71 87.661 87.242 1 137.44 ? N3A NAP 501 B 1 
HETATM 22 C C4A NAP . . . N 2 124.435 87.914 85.95 1 137.44 ? C4A NAP 501 B 1 
HETATM 23 O O3 NAP . . . N 2 122.701 92.473 92.428 1 137.44 ? O3 NAP 501 B 1 
HETATM 24 P PN NAP . . . N 2 122.884 94.102 92.513 1 137.44 ? PN NAP 501 B 1 
HETATM 25 O O1N NAP . . . N 2 122.994 94.487 93.962 1 137.44 ? O1N NAP 501 B 1 
HETATM 26 O O2N NAP . . . N 2 121.725 94.842 91.895 1 137.44 ? O2N NAP 501 B 1 
HETATM 27 O O5D NAP . . . N 2 124.274 94.52 91.75 1 137.44 ? O5D NAP 501 B 1 
HETATM 28 C C5D NAP . . . N 2 124.168 95.042 90.465 1 137.44 ? C5D NAP 501 B 1 
HETATM 29 C C4D NAP . . . N 2 124.95 96.375 90.394 1 137.44 ? C4D NAP 501 B 1 
HETATM 30 O O4D NAP . . . N 2 124.213 97.304 90.926 1 137.44 ? O4D NAP 501 B 1 
HETATM 31 C C3D NAP . . . N 2 126.238 96.305 91.236 1 137.44 ? C3D NAP 501 B 1 
HETATM 32 O O3D NAP . . . N 2 127.284 96.725 90.492 1 137.44 ? O3D NAP 501 B 1 
HETATM 33 C C2D NAP . . . N 2 126.035 97.301 92.381 1 137.44 ? C2D NAP 501 B 1 
HETATM 34 O O2D NAP . . . N 2 127.31 98.012 92.665 1 137.44 ? O2D NAP 501 B 1 
HETATM 35 C C1D NAP . . . N 2 125.175 98.146 91.901 1 137.44 ? C1D NAP 501 B 1 
HETATM 36 N N1N NAP . . . N 2 124.38 98.732 92.943 1 137.44 ? N1N NAP 501 B 1 
HETATM 37 C C2N NAP . . . N 2 123.786 97.973 93.894 1 137.44 ? C2N NAP 501 B 1 
HETATM 38 C C3N NAP . . . N 2 123.029 98.587 94.87 1 137.44 ? C3N NAP 501 B 1 
HETATM 39 C C7N NAP . . . N 2 122.363 97.761 95.959 1 137.44 ? C7N NAP 501 B 1 
HETATM 40 O O7N NAP . . . N 2 122.335 96.585 95.878 1 137.44 ? O7N NAP 501 B 1 
HETATM 41 N N7N NAP . . . N 2 121.774 98.432 97.099 1 137.44 ? N7N NAP 501 B 1 
HETATM 42 C C4N NAP . . . N 2 122.878 99.927 94.872 1 137.44 ? C4N NAP 501 B 1 
HETATM 43 C C5N NAP . . . N 2 123.464 100.682 93.915 1 137.44 ? C5N NAP 501 B 1 
HETATM 44 C C6N NAP . . . N 2 124.223 100.068 92.939 1 137.44 ? C6N NAP 501 B 1 
HETATM 45 P P2B NAP . . . N 2 120.211 88.606 84.812 1 137.44 ? P2B NAP 501 B 1 
HETATM 46 O O1X NAP . . . N 2 120.688 89.525 83.716 1 137.44 ? O1X NAP 501 B 1 
HETATM 47 O O2X NAP . . . N 2 120.902 87.277 84.662 1 137.44 ? O2X NAP 501 B 1 
HETATM 48 O O3X NAP . . . N 2 118.721 88.422 84.701 1 137.44 ? O3X NAP 501 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    55 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           48 
#