data_2ZI7
#
_model_server_result.job_id            FJG1JOQ7iy33BKvx1snElQ 
_model_server_result.datetime_utc      '2024-11-13 05:37:01' 
_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          2zi7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    2ZI7 
#
_exptl.entry_id    2ZI7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            2ZI7 
_cell.length_a            43.8 
_cell.length_b            107.5 
_cell.length_c            110.4 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2ZI7 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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 OE2 GLU 72 B GLU 53 1_555 C O5' GNG . B GNG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
covale ? covale2 B OE2 GLU 72 A GLU 53 1_555 E O5' GNG . A GNG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna 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
N1 C2 UDP sing 392 n n 
N1 C6 UDP sing 393 n n 
N1 C1' UDP sing 394 n n 
C2 N3 UDP sing 395 n n 
C2 O2 UDP doub 396 n n 
N3 C4 UDP sing 397 n n 
N3 HN3 UDP sing 398 n n 
C4 C5 UDP sing 399 n n 
C4 O4 UDP doub 400 n n 
C5 C6 UDP doub 401 n n 
C5 H5 UDP sing 402 n n 
C6 H6 UDP sing 403 n n 
C1' C2' UDP sing 404 n n 
C1' O4' UDP sing 405 n n 
C1' H1' UDP sing 406 n n 
C2' O2' UDP sing 407 n n 
C2' C3' UDP sing 408 n n 
C2' H2' UDP sing 409 n n 
O2' HO2' UDP sing 410 n n 
C3' C4' UDP sing 411 n n 
C3' O3' UDP sing 412 n n 
C3' H3' UDP sing 413 n n 
C4' O4' UDP sing 414 n n 
C4' C5' UDP sing 415 n n 
C4' H4' UDP sing 416 n n 
O3' HO3' UDP sing 417 n n 
C5' O5' UDP sing 418 n n 
C5' "H5'1" UDP sing 419 n n 
C5' "H5'2" UDP sing 420 n n 
O5' PA UDP sing 421 n n 
PA O1A UDP doub 422 n n 
PA O2A UDP sing 423 n n 
PA O3A UDP sing 424 n n 
O2A HOA2 UDP sing 425 n n 
O3A PB UDP sing 426 n n 
PB O1B UDP doub 427 n n 
PB O2B UDP sing 428 n n 
PB O3B UDP sing 429 n n 
O2B HOB2 UDP sing 430 n n 
O3B HOB3 UDP sing 431 n n 
#
_atom_sites.entry_id                     2ZI7 
_atom_sites.fract_transf_matrix[1][1]    0.022831 
_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]    0.009302 
_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]    0.009058 
_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
C 2 GNG B 1 503 503 GNG DGU . 
D 3 UDP B 1 301 301 UDP UDP . 
E 2 GNG A 1 502 502 GNG DGU . 
F 3 UDP A 1 301 301 UDP UDP . 
G 4 HOH B 1 504 3 HOH HOH . 
G 4 HOH B 2 505 4 HOH HOH . 
G 4 HOH B 3 506 5 HOH HOH . 
G 4 HOH B 4 507 7 HOH HOH . 
G 4 HOH B 5 508 8 HOH HOH . 
G 4 HOH B 6 509 12 HOH HOH . 
G 4 HOH B 7 510 14 HOH HOH . 
G 4 HOH B 8 511 15 HOH HOH . 
G 4 HOH B 9 512 16 HOH HOH . 
G 4 HOH B 10 513 26 HOH HOH . 
G 4 HOH B 11 514 27 HOH HOH . 
G 4 HOH B 12 515 28 HOH HOH . 
G 4 HOH B 13 516 37 HOH HOH . 
G 4 HOH B 14 517 38 HOH HOH . 
G 4 HOH B 15 518 39 HOH HOH . 
G 4 HOH B 16 519 41 HOH HOH . 
G 4 HOH B 17 520 42 HOH HOH . 
G 4 HOH B 18 521 46 HOH HOH . 
G 4 HOH B 19 522 49 HOH HOH . 
G 4 HOH B 20 523 50 HOH HOH . 
G 4 HOH B 21 524 52 HOH HOH . 
G 4 HOH B 22 525 53 HOH HOH . 
G 4 HOH B 23 526 57 HOH HOH . 
G 4 HOH B 24 527 58 HOH HOH . 
G 4 HOH B 25 528 59 HOH HOH . 
G 4 HOH B 26 529 61 HOH HOH . 
G 4 HOH B 27 530 62 HOH HOH . 
G 4 HOH B 28 531 65 HOH HOH . 
G 4 HOH B 29 532 67 HOH HOH . 
G 4 HOH B 30 533 68 HOH HOH . 
G 4 HOH B 31 534 69 HOH HOH . 
G 4 HOH B 32 535 71 HOH HOH . 
G 4 HOH B 33 536 73 HOH HOH . 
G 4 HOH B 34 537 76 HOH HOH . 
G 4 HOH B 35 538 79 HOH HOH . 
G 4 HOH B 36 539 86 HOH HOH . 
G 4 HOH B 37 540 87 HOH HOH . 
G 4 HOH B 38 541 88 HOH HOH . 
G 4 HOH B 39 542 92 HOH HOH . 
G 4 HOH B 40 543 93 HOH HOH . 
G 4 HOH B 41 544 94 HOH HOH . 
H 4 HOH A 1 503 1 HOH HOH . 
H 4 HOH A 2 504 2 HOH HOH . 
H 4 HOH A 3 505 6 HOH HOH . 
H 4 HOH A 4 506 9 HOH HOH . 
H 4 HOH A 5 507 10 HOH HOH . 
H 4 HOH A 6 508 11 HOH HOH . 
H 4 HOH A 7 509 13 HOH HOH . 
H 4 HOH A 8 510 17 HOH HOH . 
H 4 HOH A 9 511 18 HOH HOH . 
H 4 HOH A 10 512 19 HOH HOH . 
H 4 HOH A 11 513 20 HOH HOH . 
H 4 HOH A 12 514 21 HOH HOH . 
H 4 HOH A 13 515 22 HOH HOH . 
H 4 HOH A 14 516 23 HOH HOH . 
H 4 HOH A 15 517 24 HOH HOH . 
H 4 HOH A 16 518 25 HOH HOH . 
H 4 HOH A 17 519 29 HOH HOH . 
H 4 HOH A 18 520 30 HOH HOH . 
H 4 HOH A 19 521 31 HOH HOH . 
H 4 HOH A 20 522 32 HOH HOH . 
H 4 HOH A 21 523 33 HOH HOH . 
H 4 HOH A 22 524 35 HOH HOH . 
H 4 HOH A 23 525 36 HOH HOH . 
H 4 HOH A 24 526 40 HOH HOH . 
H 4 HOH A 25 527 43 HOH HOH . 
H 4 HOH A 26 528 44 HOH HOH . 
H 4 HOH A 27 529 45 HOH HOH . 
H 4 HOH A 28 530 47 HOH HOH . 
H 4 HOH A 29 531 48 HOH HOH . 
H 4 HOH A 30 532 51 HOH HOH . 
H 4 HOH A 31 533 54 HOH HOH . 
H 4 HOH A 32 534 55 HOH HOH . 
H 4 HOH A 33 535 56 HOH HOH . 
H 4 HOH A 34 536 63 HOH HOH . 
H 4 HOH A 35 537 64 HOH HOH . 
H 4 HOH A 36 538 66 HOH HOH . 
H 4 HOH A 37 539 70 HOH HOH . 
H 4 HOH A 38 540 74 HOH HOH . 
H 4 HOH A 39 541 75 HOH HOH . 
H 4 HOH A 40 542 84 HOH HOH . 
H 4 HOH A 41 543 85 HOH HOH . 
H 4 HOH A 42 544 89 HOH HOH . 
H 4 HOH A 43 545 90 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 N1 UDP . . . D 3 4.263 -8.197 43.803 1 26.45 ? N1 UDP 301 B 1 
HETATM 2 C C2 UDP . . . D 3 4.407 -8.045 45.181 1 27.5 ? C2 UDP 301 B 1 
HETATM 3 N N3 UDP . . . D 3 3.824 -8.927 45.989 1 25.43 ? N3 UDP 301 B 1 
HETATM 4 C C4 UDP . . . D 3 3.117 -9.953 45.437 1 25.91 ? C4 UDP 301 B 1 
HETATM 5 C C5 UDP . . . D 3 2.933 -10.149 44.066 1 26.41 ? C5 UDP 301 B 1 
HETATM 6 C C6 UDP . . . D 3 3.547 -9.214 43.239 1 26.05 ? C6 UDP 301 B 1 
HETATM 7 O O2 UDP . . . D 3 5.042 -7.118 45.671 1 28.47 ? O2 UDP 301 B 1 
HETATM 8 O O4 UDP . . . D 3 2.618 -10.699 46.227 1 28.81 ? O4 UDP 301 B 1 
HETATM 9 C C1' UDP . . . D 3 4.937 -7.214 42.972 1 25.04 ? C1' UDP 301 B 1 
HETATM 10 C C2' UDP . . . D 3 6.02 -7.835 42.108 1 24.81 ? C2' UDP 301 B 1 
HETATM 11 O O2' UDP . . . D 3 7.273 -7.934 42.734 1 26.84 ? O2' UDP 301 B 1 
HETATM 12 C C3' UDP . . . D 3 6.077 -6.894 40.938 1 23.75 ? C3' UDP 301 B 1 
HETATM 13 C C4' UDP . . . D 3 4.599 -6.533 40.833 1 22.86 ? C4' UDP 301 B 1 
HETATM 14 O O4' UDP . . . D 3 3.977 -6.759 42.084 1 22.05 ? O4' UDP 301 B 1 
HETATM 15 O O3' UDP . . . D 3 6.715 -5.687 41.324 1 25.16 ? O3' UDP 301 B 1 
HETATM 16 C C5' UDP . . . D 3 3.843 -7.264 39.718 1 18.71 ? C5' UDP 301 B 1 
HETATM 17 O O5' UDP . . . D 3 3.79 -8.724 39.951 1 21.24 ? O5' UDP 301 B 1 
HETATM 18 P PA UDP . . . D 3 4.133 -9.519 38.629 1 15.96 ? PA UDP 301 B 1 
HETATM 19 O O1A UDP . . . D 3 5.218 -8.969 37.79 1 16.04 ? O1A UDP 301 B 1 
HETATM 20 O O2A UDP . . . D 3 4.327 -10.928 39.002 1 18.25 ? O2A UDP 301 B 1 
HETATM 21 O O3A UDP . . . D 3 2.791 -9.199 37.771 1 18.63 ? O3A UDP 301 B 1 
HETATM 22 P PB UDP . . . D 3 2.167 -9.74 36.316 1 19.2 ? PB UDP 301 B 1 
HETATM 23 O O1B UDP . . . D 3 3.128 -10.692 35.84 1 14.67 ? O1B UDP 301 B 1 
HETATM 24 O O2B UDP . . . D 3 2.059 -8.539 35.47 1 17.12 ? O2B UDP 301 B 1 
HETATM 25 O O3B UDP . . . D 3 0.814 -10.192 36.622 1 18.78 ? O3B UDP 301 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#