data_2A2Z
#
_model_server_result.job_id            JOyRCAV0hWeBZczUFwTc4Q 
_model_server_result.datetime_utc      '2025-03-04 08:06:36' 
_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          2a2z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    2A2Z 
#
_exptl.entry_id    2A2Z 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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            2A2Z 
_cell.length_a            64.18 
_cell.length_b            110.85 
_cell.length_c            155.37 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2A2Z 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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,B,E,F,G,H,I,J,K,S,T 1 1 
C,D,L,M,N,O,P,Q,R,U,V 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
? 5 H N N 
? 5 K N N 
? 5 O N N 
? 5 R 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 OG SER 38 A SER 35 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
metalc ? metalc2 A ND2 ASN 63 A ASN 60 1_555 E CA CA . A CA 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? 
metalc ? metalc3 A OE1 GLU 115 A GLU 127 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc4 A O GLU 218 A GLU 230 4_466 L CA CA . C CA 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.063 ? 
metalc ? metalc5 E CA CA . A CA 261 1_555 C O GLU 218 C GLU 230 4_466 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
metalc ? metalc6 H O1B UDP . A UDP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc7 H O2B UDP . A UDP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.128 ? 
metalc ? metalc8 F MG MG . A MG 302 1_555 S O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc9 F MG MG . A MG 302 1_555 S O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc10 F MG MG . A MG 302 1_555 S O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc11 B OG SER 38 B SER 35 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
metalc ? metalc12 B OE1 GLU 115 B GLU 127 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? 
metalc ? metalc13 K O1B UDP . B UDP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc14 I MG MG . B MG 402 1_555 T O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc15 I MG MG . B MG 402 1_555 T O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc16 I MG MG . B MG 402 1_555 T O HOH . B HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc17 C OG SER 38 C SER 35 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc18 C OD1 ASN 63 C ASN 60 1_555 L CA CA . C CA 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? 
metalc ? metalc19 C OE1 GLU 115 C GLU 127 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc20 O O1B UDP . C UDP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? 
metalc ? metalc21 M MG MG . C MG 502 1_555 U O HOH . C HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc22 M MG MG . C MG 502 1_555 U O HOH . C HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc23 M MG MG . C MG 502 1_555 U O HOH . C HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc24 D OG SER 38 D SER 35 1_555 P MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc25 D OE1 GLU 115 D GLU 127 1_555 P MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? 
metalc ? metalc26 R O1B UDP . D UDP 601 1_555 P MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc27 P MG MG . D MG 602 1_555 V O HOH . D HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc28 P MG MG . D MG 602 1_555 V O HOH . D HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc29 P MG MG . D MG 602 1_555 V O HOH . D HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
#
_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 388 n n 
N1 C6 UDP sing 389 n n 
N1 C1' UDP sing 390 n n 
C2 N3 UDP sing 391 n n 
C2 O2 UDP doub 392 n n 
N3 C4 UDP sing 393 n n 
N3 HN3 UDP sing 394 n n 
C4 C5 UDP sing 395 n n 
C4 O4 UDP doub 396 n n 
C5 C6 UDP doub 397 n n 
C5 H5 UDP sing 398 n n 
C6 H6 UDP sing 399 n n 
C1' C2' UDP sing 400 n n 
C1' O4' UDP sing 401 n n 
C1' H1' UDP sing 402 n n 
C2' O2' UDP sing 403 n n 
C2' C3' UDP sing 404 n n 
C2' H2' UDP sing 405 n n 
O2' HO2' UDP sing 406 n n 
C3' C4' UDP sing 407 n n 
C3' O3' UDP sing 408 n n 
C3' H3' UDP sing 409 n n 
C4' O4' UDP sing 410 n n 
C4' C5' UDP sing 411 n n 
C4' H4' UDP sing 412 n n 
O3' HO3' UDP sing 413 n n 
C5' O5' UDP sing 414 n n 
C5' "H5'1" UDP sing 415 n n 
C5' "H5'2" UDP sing 416 n n 
O5' PA UDP sing 417 n n 
PA O1A UDP doub 418 n n 
PA O2A UDP sing 419 n n 
PA O3A UDP sing 420 n n 
O2A HOA2 UDP sing 421 n n 
O3A PB UDP sing 422 n n 
PB O1B UDP doub 423 n n 
PB O2B UDP sing 424 n n 
PB O3B UDP sing 425 n n 
O2B HOB2 UDP sing 426 n n 
O3B HOB3 UDP sing 427 n n 
#
_atom_sites.entry_id                     2A2Z 
_atom_sites.fract_transf_matrix[1][1]    0.015581 
_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]    0.009021 
_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]    0.006436 
_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 2 CA A 1 261 1 CA CA . 
F 3 MG A 1 302 302 MG MO3 . 
G 4 DCZ A 1 304 304 DCZ DCZ . 
H 5 UDP A 1 301 301 UDP UDP . 
I 3 MG B 1 402 402 MG MO3 . 
J 4 DCZ B 1 404 404 DCZ DCZ . 
K 5 UDP B 1 401 401 UDP UDP . 
L 2 CA C 1 261 2 CA CA . 
M 3 MG C 1 502 502 MG MO3 . 
N 4 DCZ C 1 504 504 DCZ DCZ . 
O 5 UDP C 1 501 501 UDP UDP . 
P 3 MG D 1 602 602 MG MO3 . 
Q 4 DCZ D 1 604 604 DCZ DCZ . 
R 5 UDP D 1 601 601 UDP UDP . 
S 6 HOH A 1 305 302 HOH MO3 . 
S 6 HOH A 2 306 302 HOH MO3 . 
S 6 HOH A 3 307 302 HOH MO3 . 
S 6 HOH A 4 308 4 HOH HOH . 
S 6 HOH A 5 309 7 HOH HOH . 
S 6 HOH A 6 310 8 HOH HOH . 
S 6 HOH A 7 311 9 HOH HOH . 
S 6 HOH A 8 312 11 HOH HOH . 
S 6 HOH A 9 313 13 HOH HOH . 
S 6 HOH A 10 314 15 HOH HOH . 
S 6 HOH A 11 315 16 HOH HOH . 
S 6 HOH A 12 316 20 HOH HOH . 
S 6 HOH A 13 317 23 HOH HOH . 
S 6 HOH A 14 318 28 HOH HOH . 
S 6 HOH A 15 319 30 HOH HOH . 
S 6 HOH A 16 320 32 HOH HOH . 
S 6 HOH A 17 321 34 HOH HOH . 
S 6 HOH A 18 322 35 HOH HOH . 
S 6 HOH A 19 323 40 HOH HOH . 
S 6 HOH A 20 324 41 HOH HOH . 
S 6 HOH A 21 325 42 HOH HOH . 
S 6 HOH A 22 326 49 HOH HOH . 
S 6 HOH A 23 327 54 HOH HOH . 
T 6 HOH B 1 405 402 HOH MO3 . 
T 6 HOH B 2 406 402 HOH MO3 . 
T 6 HOH B 3 407 402 HOH MO3 . 
T 6 HOH B 4 408 5 HOH HOH . 
T 6 HOH B 5 409 19 HOH HOH . 
T 6 HOH B 6 410 22 HOH HOH . 
T 6 HOH B 7 411 25 HOH HOH . 
T 6 HOH B 8 412 26 HOH HOH . 
T 6 HOH B 9 413 29 HOH HOH . 
T 6 HOH B 10 414 31 HOH HOH . 
T 6 HOH B 11 415 38 HOH HOH . 
T 6 HOH B 12 416 39 HOH HOH . 
T 6 HOH B 13 417 48 HOH HOH . 
T 6 HOH B 14 418 51 HOH HOH . 
T 6 HOH B 15 419 52 HOH HOH . 
U 6 HOH C 1 505 502 HOH MO3 . 
U 6 HOH C 2 506 502 HOH MO3 . 
U 6 HOH C 3 507 502 HOH MO3 . 
U 6 HOH C 4 508 3 HOH HOH . 
U 6 HOH C 5 509 6 HOH HOH . 
U 6 HOH C 6 510 10 HOH HOH . 
U 6 HOH C 7 511 12 HOH HOH . 
U 6 HOH C 8 512 14 HOH HOH . 
U 6 HOH C 9 513 17 HOH HOH . 
U 6 HOH C 10 514 18 HOH HOH . 
U 6 HOH C 11 515 21 HOH HOH . 
U 6 HOH C 12 516 27 HOH HOH . 
U 6 HOH C 13 517 36 HOH HOH . 
U 6 HOH C 14 518 37 HOH HOH . 
U 6 HOH C 15 519 43 HOH HOH . 
U 6 HOH C 16 520 44 HOH HOH . 
U 6 HOH C 17 521 45 HOH HOH . 
U 6 HOH C 18 522 46 HOH HOH . 
U 6 HOH C 19 523 47 HOH HOH . 
U 6 HOH C 20 524 50 HOH HOH . 
U 6 HOH C 21 525 53 HOH HOH . 
U 6 HOH C 22 526 55 HOH HOH . 
V 6 HOH D 1 605 602 HOH MO3 . 
V 6 HOH D 2 606 602 HOH MO3 . 
V 6 HOH D 3 607 602 HOH MO3 . 
V 6 HOH D 4 608 24 HOH HOH . 
V 6 HOH D 5 609 33 HOH HOH . 
V 6 HOH D 6 610 56 HOH HOH . 
V 6 HOH D 7 611 57 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 . . . H 5 34.902 84.814 56.222 1 56.36 ? N1 UDP 301 A 1 
HETATM 2 C C2 UDP . . . H 5 34.795 85.239 57.557 1 58.43 ? C2 UDP 301 A 1 
HETATM 3 N N3 UDP . . . H 5 35.486 86.408 57.893 1 58.96 ? N3 UDP 301 A 1 
HETATM 4 C C4 UDP . . . H 5 36.269 87.205 57.024 1 59.76 ? C4 UDP 301 A 1 
HETATM 5 C C5 UDP . . . H 5 36.399 86.714 55.596 1 59.57 ? C5 UDP 301 A 1 
HETATM 6 C C6 UDP . . . H 5 35.7 85.487 55.265 1 57.34 ? C6 UDP 301 A 1 
HETATM 7 O O2 UDP . . . H 5 34.124 84.613 58.399 1 60.58 ? O2 UDP 301 A 1 
HETATM 8 O O4 UDP . . . H 5 36.808 88.216 57.394 1 62 ? O4 UDP 301 A 1 
HETATM 9 C C1' UDP . . . H 5 34.1 83.59 55.818 1 53.57 ? C1' UDP 301 A 1 
HETATM 10 C C2' UDP . . . H 5 32.739 84.107 55.283 1 52.81 ? C2' UDP 301 A 1 
HETATM 11 O O2' UDP . . . H 5 31.788 84.245 56.351 1 53.83 ? O2' UDP 301 A 1 
HETATM 12 C C3' UDP . . . H 5 32.345 83.039 54.28 1 52.33 ? C3' UDP 301 A 1 
HETATM 13 C C4' UDP . . . H 5 33.683 82.435 53.817 1 50.29 ? C4' UDP 301 A 1 
HETATM 14 O O4' UDP . . . H 5 34.69 83.001 54.692 1 52.05 ? O4' UDP 301 A 1 
HETATM 15 O O3' UDP . . . H 5 31.491 82.055 54.895 1 54.36 ? O3' UDP 301 A 1 
HETATM 16 C C5' UDP . . . H 5 34.11 82.72 52.366 1 46.49 ? C5' UDP 301 A 1 
HETATM 17 O O5' UDP . . . H 5 34.338 84.137 52.164 1 39.32 ? O5' UDP 301 A 1 
HETATM 18 P PA UDP . . . H 5 33.915 84.737 50.764 1 41.09 ? PA UDP 301 A 1 
HETATM 19 O O1A UDP . . . H 5 32.45 84.527 50.555 1 39.9 ? O1A UDP 301 A 1 
HETATM 20 O O2A UDP . . . H 5 34.364 86.167 50.766 1 40.32 ? O2A UDP 301 A 1 
HETATM 21 O O3A UDP . . . H 5 34.758 83.84 49.68 1 39.17 ? O3A UDP 301 A 1 
HETATM 22 P PB UDP . . . H 5 35.537 84.434 48.34 1 38.06 ? PB UDP 301 A 1 
HETATM 23 O O1B UDP . . . H 5 34.567 85.432 47.706 1 36.11 ? O1B UDP 301 A 1 
HETATM 24 O O2B UDP . . . H 5 35.765 83.174 47.538 1 33.72 ? O2B UDP 301 A 1 
HETATM 25 O O3B UDP . . . H 5 36.787 85.132 48.799 1 35.23 ? O3B UDP 301 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#