data_5GPN
#
_model_server_result.job_id            IRs51uGMWEULjzK-tA1Tjg 
_model_server_result.datetime_utc      '2025-02-05 12:50:14' 
_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          5gpn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"XC","auth_seq_id":401}' 
#
_entry.id    5GPN 
#
_exptl.entry_id    5GPN 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              745.421 
_entity.id                          69 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    84-meric 
_pdbx_struct_assembly.oligomeric_count      84 
_pdbx_struct_assembly.details               author_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,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      69 
_struct_asym.id                             XC 
_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
covale ? covale1 K CB ARG 11 K ARG 11 1_555 DB CB ALA 26 7 ALA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 W NH2 ARG 101 W ARG 101 1_555 W O VAL 159 W VAL 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? 
covale ? covale3 W CB LYS 161 W LYS 161 1_555 Y CG ASN 285 Z ASN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.642 ? 
covale ? covale4 W CB LYS 161 W LYS 161 1_555 Y OD1 ASN 285 Z ASN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? 
covale ? covale5 Z SD MET 106 a MET 106 1_555 Z CE2 PHE 113 a PHE 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.651 ? 
metalc ? metalc1 X SG CYS 64 Y CYS 64 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? 
metalc ? metalc2 X O ASN 74 Y ASN 74 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? 
metalc ? metalc3 X O CYS 75 Y CYS 75 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc4 X NE2 HIS 124 Y HIS 124 1_555 OC FE2 SF4 . Y SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
metalc ? metalc5 X NE2 HIS 124 Y HIS 124 1_555 OC FE3 SF4 . Y SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? 
metalc ? metalc6 X O ILE 177 Y ILE 177 1_555 PC FE1 SF4 . Y SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc7 Z SG CYS 92 a CYS 92 1_555 RC FE1 SF4 . a SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? 
metalc ? metalc8 Z SG CYS 186 a CYS 186 1_555 RC FE2 SF4 . a SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? 
metalc ? metalc9 AA SG CYS 113 b CYS 113 1_555 SC FE1 SF4 . b SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? 
metalc ? metalc10 AA N CYS 155 b CYS 155 1_555 TC FE4 SF4 . b SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? 
metalc ? metalc11 AA N GLY 156 b GLY 156 1_555 TC FE4 SF4 . b SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? 
metalc ? metalc12 BA O SER 378 c SER 378 1_555 UC FE3 SF4 . c SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc13 BA OG1 THR 423 c THR 423 1_555 UC FE1 SF4 . c SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc14 IB O GLU 198 z GLU 198 1_555 ED CU CU . z CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc15 DD CU CU . z CU 301 1_555 ED CU CU . z CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
#
_chem_comp.formula           'C21 H30 N7 O17 P3' 
_chem_comp.formula_weight    745.421 
_chem_comp.id                NDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_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
PA O1A NDP doub 582 n n 
PA O2A NDP sing 583 n n 
PA O5B NDP sing 584 n n 
PA O3 NDP sing 585 n n 
O2A HOA2 NDP sing 586 n n 
O5B C5B NDP sing 587 n n 
C5B C4B NDP sing 588 n n 
C5B H51A NDP sing 589 n n 
C5B H52A NDP sing 590 n n 
C4B O4B NDP sing 591 n n 
C4B C3B NDP sing 592 n n 
C4B H4B NDP sing 593 n n 
O4B C1B NDP sing 594 n n 
C3B O3B NDP sing 595 n n 
C3B C2B NDP sing 596 n n 
C3B H3B NDP sing 597 n n 
O3B HO3A NDP sing 598 n n 
C2B O2B NDP sing 599 n n 
C2B C1B NDP sing 600 n n 
C2B H2B NDP sing 601 n n 
O2B P2B NDP sing 602 n n 
C1B N9A NDP sing 603 n n 
C1B H1B NDP sing 604 n n 
N9A C8A NDP sing 605 n y 
N9A C4A NDP sing 606 n y 
C8A N7A NDP doub 607 n y 
C8A H8A NDP sing 608 n n 
N7A C5A NDP sing 609 n y 
C5A C6A NDP sing 610 n y 
C5A C4A NDP doub 611 n y 
C6A N6A NDP sing 612 n n 
C6A N1A NDP doub 613 n y 
N6A H61A NDP sing 614 n n 
N6A H62A NDP sing 615 n n 
N1A C2A NDP sing 616 n y 
C2A N3A NDP doub 617 n y 
C2A H2A NDP sing 618 n n 
N3A C4A NDP sing 619 n y 
O3 PN NDP sing 620 n n 
PN O1N NDP doub 621 n n 
PN O2N NDP sing 622 n n 
PN O5D NDP sing 623 n n 
O2N H21N NDP sing 624 n n 
O5D C5D NDP sing 625 n n 
C5D C4D NDP sing 626 n n 
C5D H51N NDP sing 627 n n 
C5D H52N NDP sing 628 n n 
C4D O4D NDP sing 629 n n 
C4D C3D NDP sing 630 n n 
C4D H4D NDP sing 631 n n 
O4D C1D NDP sing 632 n n 
C3D O3D NDP sing 633 n n 
C3D C2D NDP sing 634 n n 
C3D H3D NDP sing 635 n n 
O3D HO3N NDP sing 636 n n 
C2D O2D NDP sing 637 n n 
C2D C1D NDP sing 638 n n 
C2D H2D NDP sing 639 n n 
O2D HO2N NDP sing 640 n n 
C1D N1N NDP sing 641 n n 
C1D H1D NDP sing 642 n n 
N1N C2N NDP sing 643 n n 
N1N C6N NDP sing 644 n n 
C2N C3N NDP doub 645 n n 
C2N H2N NDP sing 646 n n 
C3N C7N NDP sing 647 n n 
C3N C4N NDP sing 648 n n 
C7N O7N NDP doub 649 n n 
C7N N7N NDP sing 650 n n 
N7N H71N NDP sing 651 n n 
N7N H72N NDP sing 652 n n 
C4N C5N NDP sing 653 n n 
C4N H41N NDP sing 654 n n 
C4N H42N NDP sing 655 n n 
C5N C6N NDP doub 656 n n 
C5N H5N NDP sing 657 n n 
C6N H6N NDP sing 658 n n 
P2B O1X NDP doub 659 n n 
P2B O2X NDP sing 660 n n 
P2B O3X NDP sing 661 n n 
O2X HOP2 NDP sing 662 n n 
O3X HOP3 NDP sing 663 n n 
#
_atom_sites.entry_id                     5GPN 
_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
GC 64 HEM C 1 401 380 HEM HEM . 
HC 64 HEM C 1 402 381 HEM HEM . 
IC 65 HEC D 1 301 242 HEC HEC . 
JC 66 FES E 1 201 197 FES FES . 
KC 64 HEM O 1 401 380 HEM HEM . 
LC 64 HEM O 1 402 381 HEM HEM . 
MC 65 HEC P 1 301 242 HEC HEC . 
NC 66 FES Q 1 201 197 FES FES . 
OC 67 SF4 Y 1 801 717 SF4 SF4 . 
PC 67 SF4 Y 1 802 718 SF4 SF4 . 
QC 66 FES Y 1 803 719 FES FES . 
RC 67 SF4 a 1 301 208 SF4 SF4 . 
SC 67 SF4 b 1 301 213 SF4 SF4 . 
TC 67 SF4 b 1 302 214 SF4 SF4 . 
UC 67 SF4 c 1 501 457 SF4 SF4 . 
VC 68 FMN c 1 502 458 FMN FMN . 
WC 66 FES d 1 301 217 FES FES . 
XC 69 NDP p 1 401 378 NDP NDP . 
YC 70 ZN 3 1 101 99 ZN ZN . 
ZC 71 HEA y 1 601 515 HEA HEA . 
AD 71 HEA y 1 602 516 HEA HEA . 
BD 72 CU y 1 603 517 CU CU . 
CD 73 MG y 1 604 518 MG MG . 
DD 72 CU z 1 301 228 CU CU . 
ED 72 CU z 1 302 229 CU CU . 
#
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 NDP . . . XC 69 185.375 196.089 275.725 1 84.44 ? PA NDP 401 p 1 
HETATM 2 O O1A NDP . . . XC 69 184.644 195.911 274.431 1 84.44 ? O1A NDP 401 p 1 
HETATM 3 O O2A NDP . . . XC 69 186.746 195.515 275.886 1 84.44 ? O2A NDP 401 p 1 
HETATM 4 O O5B NDP . . . XC 69 184.433 195.573 276.91 1 84.44 ? O5B NDP 401 p 1 
HETATM 5 C C5B NDP . . . XC 69 183.054 195.351 276.673 1 84.44 ? C5B NDP 401 p 1 
HETATM 6 C C4B NDP . . . XC 69 182.715 193.918 277.014 1 84.44 ? C4B NDP 401 p 1 
HETATM 7 O O4B NDP . . . XC 69 181.334 193.863 277.332 1 84.44 ? O4B NDP 401 p 1 
HETATM 8 C C3B NDP . . . XC 69 182.908 193.006 275.821 1 84.44 ? C3B NDP 401 p 1 
HETATM 9 O O3B NDP . . . XC 69 183.381 191.748 276.301 1 84.44 ? O3B NDP 401 p 1 
HETATM 10 C C2B NDP . . . XC 69 181.518 192.831 275.26 1 84.44 ? C2B NDP 401 p 1 
HETATM 11 O O2B NDP . . . XC 69 181.359 191.611 274.526 1 84.44 ? O2B NDP 401 p 1 
HETATM 12 C C1B NDP . . . XC 69 180.678 192.905 276.512 1 84.44 ? C1B NDP 401 p 1 
HETATM 13 N N9A NDP . . . XC 69 179.286 193.325 276.257 1 84.44 ? N9A NDP 401 p 1 
HETATM 14 C C8A NDP . . . XC 69 178.764 194.517 276.557 1 84.44 ? C8A NDP 401 p 1 
HETATM 15 N N7A NDP . . . XC 69 177.457 194.57 276.215 1 84.44 ? N7A NDP 401 p 1 
HETATM 16 C C5A NDP . . . XC 69 177.13 193.388 275.693 1 84.44 ? C5A NDP 401 p 1 
HETATM 17 C C6A NDP . . . XC 69 175.918 192.779 275.137 1 84.44 ? C6A NDP 401 p 1 
HETATM 18 N N6A NDP . . . XC 69 174.771 193.485 275.077 1 84.44 ? N6A NDP 401 p 1 
HETATM 19 N N1A NDP . . . XC 69 175.987 191.509 274.691 1 84.44 ? N1A NDP 401 p 1 
HETATM 20 C C2A NDP . . . XC 69 177.127 190.801 274.745 1 84.44 ? C2A NDP 401 p 1 
HETATM 21 N N3A NDP . . . XC 69 178.269 191.299 275.244 1 84.44 ? N3A NDP 401 p 1 
HETATM 22 C C4A NDP . . . XC 69 178.335 192.565 275.725 1 84.44 ? C4A NDP 401 p 1 
HETATM 23 O O3 NDP . . . XC 69 185.514 197.637 276.063 1 84.44 ? O3 NDP 401 p 1 
HETATM 24 P PN NDP . . . XC 69 186.548 197.98 277.225 1 84.44 ? PN NDP 401 p 1 
HETATM 25 O O1N NDP . . . XC 69 186.342 196.95 278.291 1 84.44 ? O1N NDP 401 p 1 
HETATM 26 O O2N NDP . . . XC 69 187.893 198.166 276.593 1 84.44 ? O2N NDP 401 p 1 
HETATM 27 O O5D NDP . . . XC 69 186.074 199.383 277.828 1 84.44 ? O5D NDP 401 p 1 
HETATM 28 C C5D NDP . . . XC 69 185.332 199.427 279.045 1 84.44 ? C5D NDP 401 p 1 
HETATM 29 C C4D NDP . . . XC 69 184.223 200.471 278.961 1 84.44 ? C4D NDP 401 p 1 
HETATM 30 O O4D NDP . . . XC 69 184.74 201.748 279.325 1 84.44 ? O4D NDP 401 p 1 
HETATM 31 C C3D NDP . . . XC 69 183.677 200.586 277.55 1 84.44 ? C3D NDP 401 p 1 
HETATM 32 O O3D NDP . . . XC 69 182.254 200.432 277.588 1 84.44 ? O3D NDP 401 p 1 
HETATM 33 C C2D NDP . . . XC 69 184.138 201.945 277.05 1 84.44 ? C2D NDP 401 p 1 
HETATM 34 O O2D NDP . . . XC 69 183.11 202.683 276.385 1 84.44 ? O2D NDP 401 p 1 
HETATM 35 C C1D NDP . . . XC 69 184.585 202.703 278.281 1 84.44 ? C1D NDP 401 p 1 
HETATM 36 N N1N NDP . . . XC 69 185.854 203.382 278.028 1 84.44 ? N1N NDP 401 p 1 
HETATM 37 C C2N NDP . . . XC 69 186.838 202.756 277.388 1 84.44 ? C2N NDP 401 p 1 
HETATM 38 C C3N NDP . . . XC 69 188.052 203.375 277.134 1 84.44 ? C3N NDP 401 p 1 
HETATM 39 C C7N NDP . . . XC 69 189.136 202.635 276.418 1 84.44 ? C7N NDP 401 p 1 
HETATM 40 O O7N NDP . . . XC 69 188.907 201.54 275.946 1 84.44 ? O7N NDP 401 p 1 
HETATM 41 N N7N NDP . . . XC 69 190.336 203.193 276.321 1 84.44 ? N7N NDP 401 p 1 
HETATM 42 C C4N NDP . . . XC 69 188.318 204.786 277.569 1 84.44 ? C4N NDP 401 p 1 
HETATM 43 C C5N NDP . . . XC 69 187.169 205.346 278.252 1 84.44 ? C5N NDP 401 p 1 
HETATM 44 C C6N NDP . . . XC 69 186.001 204.631 278.451 1 84.44 ? C6N NDP 401 p 1 
HETATM 45 P P2B NDP . . . XC 69 181.405 190.138 275.17 1 84.44 ? P2B NDP 401 p 1 
HETATM 46 O O1X NDP . . . XC 69 182.607 189.508 274.526 1 84.44 ? O1X NDP 401 p 1 
HETATM 47 O O2X NDP . . . XC 69 181.545 190.35 276.651 1 84.44 ? O2X NDP 401 p 1 
HETATM 48 O O3X NDP . . . XC 69 180.09 189.546 274.742 1 84.44 ? O3X NDP 401 p 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    101 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           48 
#