data_8RPH
#
_model_server_result.job_id            t8FoB1KZULd2f8qrbSsgpg 
_model_server_result.datetime_utc      '2024-11-14 19:54:04' 
_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          8rph 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":703}' 
#
_entry.id    8RPH 
#
_exptl.entry_id    8RPH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              527.403 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2~{S})-2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-2-yl]-2-oxidanyl-butanoic acid' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          97.06 
_cell.angle_gamma         90 
_cell.entry_id            8RPH 
_cell.length_a            173.326 
_cell.length_b            118.189 
_cell.length_c            201.166 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8RPH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 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 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,J,K,L,Z 1 1 
C,D,M,N,O,P,Q,R,S,AA 2 1 
E,F,T,U,V,W,X,Y 3 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
? 4 I N N 
? 4 L N N 
? 4 O N N 
? 4 S N N 
? 4 V N N 
? 4 Y 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 A OD1 ASP 460 A ASP 459 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 ? 
metalc ? metalc2 A OD1 ASN 487 A ASN 486 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc3 A O GLY 489 A GLY 488 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc4 H MG MG . A MG 702 1_555 I O2A A1H2A . A A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? 
metalc ? metalc5 H MG MG . A MG 702 1_555 I O3B A1H2A . A A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc6 B OD1 ASP 460 B ASP 459 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc7 B OD1 ASN 487 B ASN 486 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc8 B O GLY 489 B GLY 488 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc9 K MG MG . B MG 702 1_555 L O2A A1H2A . B A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc10 C OD1 ASP 460 C ASP 459 1_555 N MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? 
metalc ? metalc11 C OD1 ASN 487 C ASN 486 1_555 N MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc12 C O GLY 489 C GLY 488 1_555 N MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc13 N MG MG . C MG 702 1_555 O O1B A1H2A . C A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
metalc ? metalc14 N MG MG . C MG 702 1_555 O O2A A1H2A . C A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? 
metalc ? metalc15 N MG MG . C MG 702 1_555 AA O HOH . C HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc16 D OD1 ASP 460 D ASP 459 1_555 Q MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc17 D OD1 ASN 487 D ASN 486 1_555 Q MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc18 D O GLY 489 D GLY 488 1_555 Q MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc19 Q MG MG . D MG 702 1_555 S O3A A1H2A . D A1H2A 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? 
metalc ? metalc20 E OD1 ASP 460 E ASP 459 1_555 U MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc21 E OD1 ASN 487 E ASN 486 1_555 U MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc22 E O GLY 489 E GLY 488 1_555 U MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc23 U MG MG . E MG 702 1_555 V O2A A1H2A . E A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
metalc ? metalc24 U MG MG . E MG 702 1_555 V O2B A1H2A . E A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? 
metalc ? metalc25 U MG MG . E MG 702 1_555 V O3A A1H2A . E A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc26 F OD1 ASP 460 F ASP 459 1_555 X MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc27 F OD1 ASN 487 F ASN 486 1_555 X MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc28 F O GLY 489 F GLY 488 1_555 X MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc29 X MG MG . F MG 702 1_555 Y O1B A1H2A . F A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc30 X MG MG . F MG 702 1_555 Y O2A A1H2A . F A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
#
_chem_comp.formula           'C16 H25 N4 O10 P2 S 1' 
_chem_comp.formula_weight    527.403 
_chem_comp.id                A1H2A 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2~{S})-2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-2-yl]-2-oxidanyl-butanoic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Ketobutyryl-thiamine diphosphate' 
#
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
N1' C2' A1H2A doub 1 n y 
N1' C6' A1H2A sing 2 n y 
C2' CM2 A1H2A sing 3 n n 
C2' N3' A1H2A sing 4 n y 
N3' C4' A1H2A doub 5 n y 
C4' N4' A1H2A sing 6 n n 
C4' C5' A1H2A sing 7 n y 
C5' C6' A1H2A doub 8 n y 
C5' C7' A1H2A sing 9 n n 
C7' N3 A1H2A sing 10 n n 
N3 C2 A1H2A doub 11 n y 
N3 C4 A1H2A sing 12 n y 
C2 S1 A1H2A sing 13 n y 
C2 C1 A1H2A sing 14 n n 
S1 C5 A1H2A sing 15 n y 
C5 C4 A1H2A doub 16 n y 
C5 C6 A1H2A sing 17 n n 
C4 CM4 A1H2A sing 18 n n 
C6 C7 A1H2A sing 19 n n 
C7 O7 A1H2A sing 20 n n 
O7 PA A1H2A sing 21 n n 
PA O1A A1H2A doub 22 n n 
PA O2A A1H2A sing 23 n n 
PA O3A A1H2A sing 24 n n 
O3A PB A1H2A sing 25 n n 
PB O1B A1H2A doub 26 n n 
PB O2B A1H2A sing 27 n n 
PB O3B A1H2A sing 28 n n 
C1 O2 A1H2A sing 29 n n 
C1 C3 A1H2A sing 30 n n 
C1 C8 A1H2A sing 31 n n 
C3 O9 A1H2A doub 32 n n 
C3 O10 A1H2A sing 33 n n 
C8 C9 A1H2A sing 34 n n 
O2 HO2 A1H2A sing 35 n n 
C9 H92 A1H2A sing 36 n n 
C9 H91 A1H2A sing 37 n n 
C9 H9 A1H2A sing 38 n n 
C8 H8 A1H2A sing 39 n n 
C8 H81 A1H2A sing 40 n n 
C7 H72 A1H2A sing 41 n n 
C7 H71 A1H2A sing 42 n n 
C6 H61 A1H2A sing 43 n n 
C6 H62 A1H2A sing 44 n n 
C6' H6' A1H2A sing 45 n n 
C7' "H7'1" A1H2A sing 46 n n 
C7' "H7'2" A1H2A sing 47 n n 
CM2 HM21 A1H2A sing 48 n n 
CM2 HM23 A1H2A sing 49 n n 
CM2 HM22 A1H2A sing 50 n n 
CM4 HM42 A1H2A sing 51 n n 
CM4 HM41 A1H2A sing 52 n n 
CM4 HM43 A1H2A sing 53 n n 
N4' HN42 A1H2A sing 54 n n 
N4' HN41 A1H2A sing 55 n n 
O10 H1 A1H2A sing 56 n n 
O2A H2 A1H2A sing 57 n n 
O2B H3 A1H2A sing 58 n n 
O3B H4 A1H2A sing 59 n n 
#
_atom_sites.entry_id                     8RPH 
_atom_sites.fract_transf_matrix[1][1]    0.005769 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000715 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008461 
_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]    0.005009 
_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
G 2 FAD A 1 701 701 FAD FAD . 
H 3 MG A 1 702 702 MG MG . 
I 4 A1H2A A 1 703 701 A1H2A HBT . 
J 2 FAD B 1 701 701 FAD FAD . 
K 3 MG B 1 702 702 MG MG . 
L 4 A1H2A B 1 703 701 A1H2A HBT . 
M 2 FAD C 1 701 701 FAD FAD . 
N 3 MG C 1 702 702 MG MG . 
O 4 A1H2A C 1 703 701 A1H2A HBT . 
P 2 FAD D 1 701 701 FAD FAD . 
Q 3 MG D 1 702 702 MG MG . 
R 5 PGE D 1 703 801 PGE PEG . 
S 4 A1H2A D 1 704 701 A1H2A HBT . 
T 2 FAD E 1 701 701 FAD FAD . 
U 3 MG E 1 702 702 MG MG . 
V 4 A1H2A E 1 703 701 A1H2A HBT . 
W 2 FAD F 1 701 701 FAD FAD . 
X 3 MG F 1 702 702 MG MG . 
Y 4 A1H2A F 1 703 701 A1H2A HBT . 
Z 6 HOH B 1 801 1 HOH HOH . 
AA 6 HOH C 1 801 2 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 O O2 A1H2A . . . V 4 24.851 -4.722 3.459 1 69.18 ? O2 A1H2A 703 E 1 
HETATM 2 C C9 A1H2A . . . V 4 25.189 -7.538 2.706 1 67.47 ? C9 A1H2A 703 E 1 
HETATM 3 C C8 A1H2A . . . V 4 26.262 -6.472 2.593 1 67.98 ? C8 A1H2A 703 E 1 
HETATM 4 C C7 A1H2A . . . V 4 31.528 -3.425 3.096 1 65.34 ? C7 A1H2A 703 E 1 
HETATM 5 C C6 A1H2A . . . V 4 30.666 -2.946 1.96 1 66.62 ? C6 A1H2A 703 E 1 
HETATM 6 N N3 A1H2A . . . V 4 26.982 -2.776 2.791 1 68.64 ? N3 A1H2A 703 E 1 
HETATM 7 S S1 A1H2A . . . V 4 28.432 -4.624 1.943 1 71.1 ? S1 A1H2A 703 E 1 
HETATM 8 C C5 A1H2A . . . V 4 29.194 -3.124 2.222 1 69.07 ? C5 A1H2A 703 E 1 
HETATM 9 C C4 A1H2A . . . V 4 28.281 -2.231 2.675 1 68.84 ? C4 A1H2A 703 E 1 
HETATM 10 C C3 A1H2A . . . V 4 24.947 -4.917 1.048 1 69.08 ? C3 A1H2A 703 E 1 
HETATM 11 C C1 A1H2A . . . V 4 25.726 -5.033 2.391 1 69.39 ? C1 A1H2A 703 E 1 
HETATM 12 C C2 A1H2A . . . V 4 26.896 -4.103 2.421 1 69.58 ? C2 A1H2A 703 E 1 
HETATM 13 C C2' A1H2A . . . V 4 25.979 -1.363 7.442 1 63.51 ? C2' A1H2A 703 E 1 
HETATM 14 C C4' A1H2A . . . V 4 25.74 -2.822 5.674 1 65.68 ? C4' A1H2A 703 E 1 
HETATM 15 C C5' A1H2A . . . V 4 25.901 -1.771 4.749 1 66.5 ? C5' A1H2A 703 E 1 
HETATM 16 C C6' A1H2A . . . V 4 26.097 -0.519 5.302 1 64.48 ? C6' A1H2A 703 E 1 
HETATM 17 C C7' A1H2A . . . V 4 25.863 -1.965 3.274 1 67.44 ? C7' A1H2A 703 E 1 
HETATM 18 C CM2 A1H2A . . . V 4 26.021 -1.144 8.918 1 62.52 ? CM2 A1H2A 703 E 1 
HETATM 19 C CM4 A1H2A . . . V 4 28.546 -0.808 3.036 1 65.31 ? CM4 A1H2A 703 E 1 
HETATM 20 N N1' A1H2A . . . V 4 26.139 -0.294 6.629 1 63.51 ? N1' A1H2A 703 E 1 
HETATM 21 N N3' A1H2A . . . V 4 25.786 -2.597 7.008 1 63.7 ? N3' A1H2A 703 E 1 
HETATM 22 N N4' A1H2A . . . V 4 25.547 -4.09 5.294 1 66.52 ? N4' A1H2A 703 E 1 
HETATM 23 O O10 A1H2A . . . V 4 24.559 -3.772 0.708 1 67.3 ? O10 A1H2A 703 E 1 
HETATM 24 O O1A A1H2A . . . V 4 33.327 -5.368 4.47 1 66 ? O1A A1H2A 703 E 1 
HETATM 25 O O1B A1H2A . . . V 4 35.747 -6.77 0.811 1 66.47 ? O1B A1H2A 703 E 1 
HETATM 26 O O2A A1H2A . . . V 4 34.712 -3.241 4.094 1 65.16 ? O2A A1H2A 703 E 1 
HETATM 27 O O2B A1H2A . . . V 4 34.447 -4.726 0.096 1 64.89 ? O2B A1H2A 703 E 1 
HETATM 28 O O3A A1H2A . . . V 4 34.873 -5.154 2.508 1 65.72 ? O3A A1H2A 703 E 1 
HETATM 29 O O3B A1H2A . . . V 4 33.259 -6.599 1.211 1 64.98 ? O3B A1H2A 703 E 1 
HETATM 30 O O7 A1H2A . . . V 4 32.816 -3.806 2.566 1 64.42 ? O7 A1H2A 703 E 1 
HETATM 31 O O9 A1H2A . . . V 4 24.768 -5.964 0.382 1 69.08 ? O9 A1H2A 703 E 1 
HETATM 32 P PA A1H2A . . . V 4 33.933 -4.378 3.544 1 64.98 ? PA A1H2A 703 E 1 
HETATM 33 P PB A1H2A . . . V 4 34.566 -5.862 1.087 1 65.03 ? PB A1H2A 703 E 1 
#
_model_server_stats.io_time_ms              76 
_model_server_stats.parse_time_ms           219 
_model_server_stats.create_model_time_ms    194 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           33 
#