data_4EKK
#
_model_server_result.job_id            Gw00fYslqW4GYP7t_ctM1w 
_model_server_result.datetime_utc      '2024-12-28 08:01:55' 
_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          4ekk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":501}' 
#
_entry.id    4EKK 
#
_exptl.entry_id    4EKK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              506.196 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_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          103.43 
_cell.angle_gamma         90 
_cell.entry_id            4EKK 
_cell.length_a            86.637 
_cell.length_b            55.853 
_cell.length_c            91.402 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4EKK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,G,K 1 1 
B,D,H,I,J,L,M 2 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 
#
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 H 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 C LYS 168 A LYS 307 1_555 A N TPO 169 A TPO 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale2 A C TPO 169 A TPO 308 1_555 A N PHE 170 A PHE 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale3 B C LYS 168 B LYS 307 1_555 B N TPO 169 B TPO 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 B C TPO 169 B TPO 308 1_555 B N PHE 170 B PHE 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
metalc ? metalc1 A OD1 ASN 140 A ASN 279 1_555 F MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc2 A OD2 ASP 153 A ASP 292 1_555 F MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc3 A OD1 ASP 153 A ASP 292 1_555 G MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? 
metalc ? metalc4 A OD2 ASP 153 A ASP 292 1_555 G MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
metalc ? metalc5 E O2A ANP . A ANP 501 1_555 F MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc6 E O1G ANP . A ANP 501 1_555 F MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc7 E O2B ANP . A ANP 501 1_555 G MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc8 E O3G ANP . A ANP 501 1_555 G MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc9 B OD1 ASN 140 B ASN 279 1_555 I MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc10 B OD2 ASP 153 B ASP 292 1_555 J MN MN . B MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? 
metalc ? metalc11 H O2A ANP . B ANP 501 1_555 I MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc12 H N3B ANP . B ANP 501 1_555 I MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
metalc ? metalc13 H O2B ANP . B ANP 501 1_555 J MN MN . B MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
#
_chem_comp.formula           'C10 H17 N6 O12 P3' 
_chem_comp.formula_weight    506.196 
_chem_comp.id                ANP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_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
PG O1G ANP doub 13 n n 
PG O2G ANP sing 14 n n 
PG O3G ANP sing 15 n n 
PG N3B ANP sing 16 n n 
O2G HOG2 ANP sing 17 n n 
O3G HOG3 ANP sing 18 n n 
PB O1B ANP doub 19 n n 
PB O2B ANP sing 20 n n 
PB N3B ANP sing 21 n n 
PB O3A ANP sing 22 n n 
O2B HOB2 ANP sing 23 n n 
N3B HNB1 ANP sing 24 n n 
PA O1A ANP doub 25 n n 
PA O2A ANP sing 26 n n 
PA O3A ANP sing 27 n n 
PA O5' ANP sing 28 n n 
O2A HOA2 ANP sing 29 n n 
O5' C5' ANP sing 30 n n 
C5' C4' ANP sing 31 n n 
C5' "H5'1" ANP sing 32 n n 
C5' "H5'2" ANP sing 33 n n 
C4' O4' ANP sing 34 n n 
C4' C3' ANP sing 35 n n 
C4' H4' ANP sing 36 n n 
O4' C1' ANP sing 37 n n 
C3' O3' ANP sing 38 n n 
C3' C2' ANP sing 39 n n 
C3' H3' ANP sing 40 n n 
O3' HO3' ANP sing 41 n n 
C2' O2' ANP sing 42 n n 
C2' C1' ANP sing 43 n n 
C2' H2' ANP sing 44 n n 
O2' HO2' ANP sing 45 n n 
C1' N9 ANP sing 46 n n 
C1' H1' ANP sing 47 n n 
N9 C8 ANP sing 48 n y 
N9 C4 ANP sing 49 n y 
C8 N7 ANP doub 50 n y 
C8 H8 ANP sing 51 n n 
N7 C5 ANP sing 52 n y 
C5 C6 ANP sing 53 n y 
C5 C4 ANP doub 54 n y 
C6 N6 ANP sing 55 n n 
C6 N1 ANP doub 56 n y 
N6 HN61 ANP sing 57 n n 
N6 HN62 ANP sing 58 n n 
N1 C2 ANP sing 59 n y 
C2 N3 ANP doub 60 n y 
C2 H2 ANP sing 61 n n 
N3 C4 ANP sing 62 n y 
#
_atom_sites.entry_id                     4EKK 
_atom_sites.fract_transf_matrix[1][1]    0.011542 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002756 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017904 
_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]    0.011248 
_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 ANP A 1 501 1 ANP ANP . 
F 4 MN A 1 502 1 MN MN . 
G 4 MN A 1 503 2 MN MN . 
H 3 ANP B 1 501 2 ANP ANP . 
I 4 MN B 1 502 3 MN MN . 
J 4 MN B 1 503 4 MN MN . 
K 5 HOH A 1 601 2 HOH HOH . 
K 5 HOH A 2 602 3 HOH HOH . 
K 5 HOH A 3 603 6 HOH HOH . 
K 5 HOH A 4 604 7 HOH HOH . 
K 5 HOH A 5 605 8 HOH HOH . 
K 5 HOH A 6 606 11 HOH HOH . 
K 5 HOH A 7 607 15 HOH HOH . 
K 5 HOH A 8 608 16 HOH HOH . 
K 5 HOH A 9 609 22 HOH HOH . 
K 5 HOH A 10 610 25 HOH HOH . 
K 5 HOH A 11 611 26 HOH HOH . 
K 5 HOH A 12 612 28 HOH HOH . 
K 5 HOH A 13 613 30 HOH HOH . 
K 5 HOH A 14 614 31 HOH HOH . 
K 5 HOH A 15 615 32 HOH HOH . 
K 5 HOH A 16 616 33 HOH HOH . 
K 5 HOH A 17 617 36 HOH HOH . 
K 5 HOH A 18 618 37 HOH HOH . 
K 5 HOH A 19 619 38 HOH HOH . 
K 5 HOH A 20 620 43 HOH HOH . 
K 5 HOH A 21 621 45 HOH HOH . 
K 5 HOH A 22 622 46 HOH HOH . 
K 5 HOH A 23 623 47 HOH HOH . 
K 5 HOH A 24 624 48 HOH HOH . 
K 5 HOH A 25 625 49 HOH HOH . 
K 5 HOH A 26 626 51 HOH HOH . 
K 5 HOH A 27 627 52 HOH HOH . 
K 5 HOH A 28 628 55 HOH HOH . 
K 5 HOH A 29 629 57 HOH HOH . 
K 5 HOH A 30 630 58 HOH HOH . 
K 5 HOH A 31 631 62 HOH HOH . 
K 5 HOH A 32 632 63 HOH HOH . 
K 5 HOH A 33 633 64 HOH HOH . 
K 5 HOH A 34 634 65 HOH HOH . 
K 5 HOH A 35 635 66 HOH HOH . 
K 5 HOH A 36 636 67 HOH HOH . 
K 5 HOH A 37 637 68 HOH HOH . 
K 5 HOH A 38 638 70 HOH HOH . 
K 5 HOH A 39 639 73 HOH HOH . 
K 5 HOH A 40 640 76 HOH HOH . 
K 5 HOH A 41 641 78 HOH HOH . 
K 5 HOH A 42 642 79 HOH HOH . 
K 5 HOH A 43 643 80 HOH HOH . 
K 5 HOH A 44 644 83 HOH HOH . 
K 5 HOH A 45 645 84 HOH HOH . 
K 5 HOH A 46 646 87 HOH HOH . 
K 5 HOH A 47 647 89 HOH HOH . 
K 5 HOH A 48 648 90 HOH HOH . 
K 5 HOH A 49 649 91 HOH HOH . 
K 5 HOH A 50 650 94 HOH HOH . 
K 5 HOH A 51 651 95 HOH HOH . 
L 5 HOH B 1 601 1 HOH HOH . 
L 5 HOH B 2 602 4 HOH HOH . 
L 5 HOH B 3 603 5 HOH HOH . 
L 5 HOH B 4 604 9 HOH HOH . 
L 5 HOH B 5 605 10 HOH HOH . 
L 5 HOH B 6 606 12 HOH HOH . 
L 5 HOH B 7 607 13 HOH HOH . 
L 5 HOH B 8 608 14 HOH HOH . 
L 5 HOH B 9 609 17 HOH HOH . 
L 5 HOH B 10 610 18 HOH HOH . 
L 5 HOH B 11 611 19 HOH HOH . 
L 5 HOH B 12 612 20 HOH HOH . 
L 5 HOH B 13 613 21 HOH HOH . 
L 5 HOH B 14 614 23 HOH HOH . 
L 5 HOH B 15 615 27 HOH HOH . 
L 5 HOH B 16 616 29 HOH HOH . 
L 5 HOH B 17 617 34 HOH HOH . 
L 5 HOH B 18 618 35 HOH HOH . 
L 5 HOH B 19 619 39 HOH HOH . 
L 5 HOH B 20 620 40 HOH HOH . 
L 5 HOH B 21 621 41 HOH HOH . 
L 5 HOH B 22 622 42 HOH HOH . 
L 5 HOH B 23 623 44 HOH HOH . 
L 5 HOH B 24 624 50 HOH HOH . 
L 5 HOH B 25 625 53 HOH HOH . 
L 5 HOH B 26 626 54 HOH HOH . 
L 5 HOH B 27 627 56 HOH HOH . 
L 5 HOH B 28 628 59 HOH HOH . 
L 5 HOH B 29 629 60 HOH HOH . 
L 5 HOH B 30 630 61 HOH HOH . 
L 5 HOH B 31 631 69 HOH HOH . 
L 5 HOH B 32 632 71 HOH HOH . 
L 5 HOH B 33 633 72 HOH HOH . 
L 5 HOH B 34 634 74 HOH HOH . 
L 5 HOH B 35 635 75 HOH HOH . 
L 5 HOH B 36 636 77 HOH HOH . 
L 5 HOH B 37 637 81 HOH HOH . 
L 5 HOH B 38 638 82 HOH HOH . 
L 5 HOH B 39 639 85 HOH HOH . 
L 5 HOH B 40 640 86 HOH HOH . 
L 5 HOH B 41 641 88 HOH HOH . 
L 5 HOH B 42 642 92 HOH HOH . 
L 5 HOH B 43 643 93 HOH HOH . 
L 5 HOH B 44 644 96 HOH HOH . 
L 5 HOH B 45 645 97 HOH HOH . 
L 5 HOH B 46 646 98 HOH HOH . 
L 5 HOH B 47 647 99 HOH HOH . 
L 5 HOH B 48 648 100 HOH HOH . 
M 5 HOH D 1 101 24 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 P PG ANP . . . H 3 54.536 4.289 21.999 1 76.91 ? PG ANP 501 B 1 
HETATM 2 O O1G ANP . . . H 3 55.14 4.238 23.362 1 76.58 ? O1G ANP 501 B 1 
HETATM 3 O O2G ANP . . . H 3 53.65 3.008 21.685 1 76.23 ? O2G ANP 501 B 1 
HETATM 4 O O3G ANP . . . H 3 53.687 5.612 21.789 1 76.61 ? O3G ANP 501 B 1 
HETATM 5 P PB ANP . . . H 3 55.904 4.913 19.217 1 76.2 ? PB ANP 501 B 1 
HETATM 6 O O1B ANP . . . H 3 54.497 4.914 18.71 1 76.46 ? O1B ANP 501 B 1 
HETATM 7 O O2B ANP . . . H 3 56.522 6.378 19.244 1 76.72 ? O2B ANP 501 B 1 
HETATM 8 N N3B ANP . . . H 3 55.858 4.337 20.863 1 76.44 ? N3B ANP 501 B 1 
HETATM 9 P PA ANP . . . H 3 57.933 2.822 18.427 1 73.65 ? PA ANP 501 B 1 
HETATM 10 O O1A ANP . . . H 3 59.231 3.319 17.875 1 73.48 ? O1A ANP 501 B 1 
HETATM 11 O O2A ANP . . . H 3 58.135 2.41 19.946 1 74.41 ? O2A ANP 501 B 1 
HETATM 12 O O3A ANP . . . H 3 56.816 3.946 18.349 1 74.8 ? O3A ANP 501 B 1 
HETATM 13 O O5' ANP . . . H 3 57.414 1.571 17.593 1 72.69 ? O5' ANP 501 B 1 
HETATM 14 C C5' ANP . . . H 3 56.51 0.576 18.069 1 70.71 ? C5' ANP 501 B 1 
HETATM 15 C C4' ANP . . . H 3 57.095 -0.845 17.937 1 69.63 ? C4' ANP 501 B 1 
HETATM 16 O O4' ANP . . . H 3 57.778 -1.051 16.708 1 68.62 ? O4' ANP 501 B 1 
HETATM 17 C C3' ANP . . . H 3 58.121 -1.227 19.006 1 69.58 ? C3' ANP 501 B 1 
HETATM 18 O O3' ANP . . . H 3 57.506 -1.411 20.27 1 70.67 ? O3' ANP 501 B 1 
HETATM 19 C C2' ANP . . . H 3 58.646 -2.533 18.375 1 68.99 ? C2' ANP 501 B 1 
HETATM 20 O O2' ANP . . . H 3 57.704 -3.588 18.499 1 69.29 ? O2' ANP 501 B 1 
HETATM 21 C C1' ANP . . . H 3 58.709 -2.114 16.895 1 67.79 ? C1' ANP 501 B 1 
HETATM 22 N N9 ANP . . . H 3 60.103 -1.659 16.565 1 65.89 ? N9 ANP 501 B 1 
HETATM 23 C C8 ANP . . . H 3 60.681 -0.384 16.643 1 65.3 ? C8 ANP 501 B 1 
HETATM 24 N N7 ANP . . . H 3 61.948 -0.249 16.293 1 64.2 ? N7 ANP 501 B 1 
HETATM 25 C C5 ANP . . . H 3 62.223 -1.552 15.958 1 63.97 ? C5 ANP 501 B 1 
HETATM 26 C C6 ANP . . . H 3 63.429 -2.128 15.488 1 63.52 ? C6 ANP 501 B 1 
HETATM 27 N N6 ANP . . . H 3 64.473 -1.274 15.344 1 62.95 ? N6 ANP 501 B 1 
HETATM 28 N N1 ANP . . . H 3 63.498 -3.448 15.21 1 63.88 ? N1 ANP 501 B 1 
HETATM 29 C C2 ANP . . . H 3 62.37 -4.169 15.405 1 64.03 ? C2 ANP 501 B 1 
HETATM 30 N N3 ANP . . . H 3 61.168 -3.734 15.846 1 64.37 ? N3 ANP 501 B 1 
HETATM 31 C C4 ANP . . . H 3 61.127 -2.415 16.115 1 64.6 ? C4 ANP 501 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#