data_3ELB # _model_server_result.job_id I6OPt1gZKaXyJhn49wuT4g _model_server_result.datetime_utc '2024-11-02 21:27:56' _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 3elb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 3ELB # _exptl.entry_id 3ELB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 3ELB _cell.length_a 74.179 _cell.length_b 74.179 _cell.length_c 139.723 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ELB _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_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,C,D 1 1 A,B,C,D 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 139.723 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 A C ASP 17 A ASP 32 1_555 A N MSE 18 A MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C MSE 18 A MSE 33 1_555 A N VAL 19 A VAL 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C ALA 32 A ALA 47 1_555 A N MSE 33 A MSE 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 A C MSE 33 A MSE 48 1_555 A N GLY 34 A GLY 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C LYS 63 A LYS 78 1_555 A N MSE 64 A MSE 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 64 A MSE 79 1_555 A N VAL 65 A VAL 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C ARG 137 A ARG 152 1_555 A N MSE 138 A MSE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale8 A C MSE 138 A MSE 153 1_555 A N LEU 139 A LEU 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale9 A C ILE 250 A ILE 265 1_555 A N MSE 251 A MSE 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale10 A C MSE 251 A MSE 266 1_555 A N ASN 252 A ASN 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C5P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-MONOPHOSPHATE" _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 O3P P C5P sing 70 n n O3P HOP3 C5P sing 71 n n P O1P C5P doub 72 n n P O2P C5P sing 73 n n P O5' C5P sing 74 n n O2P HOP2 C5P sing 75 n n O5' C5' C5P sing 76 n n C5' C4' C5P sing 77 n n C5' "H5'1" C5P sing 78 n n C5' "H5'2" C5P sing 79 n n C4' O4' C5P sing 80 n n C4' C3' C5P sing 81 n n C4' H4' C5P sing 82 n n O4' C1' C5P sing 83 n n C3' O3' C5P sing 84 n n C3' C2' C5P sing 85 n n C3' H3' C5P sing 86 n n O3' HO3' C5P sing 87 n n C2' O2' C5P sing 88 n n C2' C1' C5P sing 89 n n C2' "H2'1" C5P sing 90 n n O2' HO2' C5P sing 91 n n C1' N1 C5P sing 92 n n C1' H1' C5P sing 93 n n N1 C2 C5P sing 94 n n N1 C6 C5P sing 95 n n C2 N3 C5P sing 96 n n C2 O2 C5P doub 97 n n N3 C4 C5P doub 98 n n C4 C5 C5P sing 99 n n C4 N4 C5P sing 100 n n C5 C6 C5P doub 101 n n C5 H5 C5P sing 102 n n C6 H6 C5P sing 103 n n N4 HN41 C5P sing 104 n n N4 HN42 C5P sing 105 n n # _atom_sites.entry_id 3ELB _atom_sites.fract_transf_matrix[1][1] 0.013481 _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] 0.013481 _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] 0.007157 _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 B 2 C5P A 1 400 400 C5P C5P . C 3 GOL A 1 500 500 GOL GOL . D 4 HOH A 1 501 1 HOH HOH . D 4 HOH A 2 502 2 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 5 HOH HOH . D 4 HOH A 6 506 6 HOH HOH . D 4 HOH A 7 507 7 HOH HOH . D 4 HOH A 8 508 8 HOH HOH . D 4 HOH A 9 509 9 HOH HOH . D 4 HOH A 10 510 10 HOH HOH . D 4 HOH A 11 511 11 HOH HOH . D 4 HOH A 12 512 12 HOH HOH . D 4 HOH A 13 513 13 HOH HOH . D 4 HOH A 14 514 14 HOH HOH . D 4 HOH A 15 515 15 HOH HOH . D 4 HOH A 16 516 16 HOH HOH . D 4 HOH A 17 517 17 HOH HOH . D 4 HOH A 18 518 18 HOH HOH . D 4 HOH A 19 519 19 HOH HOH . D 4 HOH A 20 520 20 HOH HOH . D 4 HOH A 21 521 21 HOH HOH . D 4 HOH A 22 522 22 HOH HOH . D 4 HOH A 23 523 23 HOH HOH . D 4 HOH A 24 524 24 HOH HOH . D 4 HOH A 25 525 25 HOH HOH . D 4 HOH A 26 526 26 HOH HOH . D 4 HOH A 27 527 27 HOH HOH . D 4 HOH A 28 528 28 HOH HOH . D 4 HOH A 29 529 29 HOH HOH . D 4 HOH A 30 530 30 HOH HOH . D 4 HOH A 31 531 31 HOH HOH . D 4 HOH A 32 532 32 HOH HOH . D 4 HOH A 33 533 33 HOH HOH . D 4 HOH A 34 534 34 HOH HOH . D 4 HOH A 35 535 35 HOH HOH . D 4 HOH A 36 536 36 HOH HOH . D 4 HOH A 37 537 37 HOH HOH . D 4 HOH A 38 538 38 HOH HOH . D 4 HOH A 39 539 39 HOH HOH . D 4 HOH A 40 540 40 HOH HOH . D 4 HOH A 41 541 41 HOH HOH . D 4 HOH A 42 542 42 HOH HOH . D 4 HOH A 43 543 43 HOH HOH . D 4 HOH A 44 544 44 HOH HOH . D 4 HOH A 45 545 45 HOH HOH . D 4 HOH A 46 546 46 HOH HOH . D 4 HOH A 47 547 47 HOH HOH . D 4 HOH A 48 548 48 HOH HOH . D 4 HOH A 49 549 49 HOH HOH . D 4 HOH A 50 550 50 HOH HOH . D 4 HOH A 51 551 51 HOH HOH . D 4 HOH A 52 552 52 HOH HOH . D 4 HOH A 53 553 53 HOH HOH . D 4 HOH A 54 554 54 HOH HOH . D 4 HOH A 55 555 55 HOH HOH . D 4 HOH A 56 556 56 HOH HOH . D 4 HOH A 57 557 57 HOH HOH . D 4 HOH A 58 558 58 HOH HOH . D 4 HOH A 59 559 59 HOH HOH . D 4 HOH A 60 560 60 HOH HOH . D 4 HOH A 61 561 61 HOH HOH . D 4 HOH A 62 562 62 HOH HOH . D 4 HOH A 63 563 63 HOH HOH . D 4 HOH A 64 564 64 HOH HOH . D 4 HOH A 65 565 65 HOH HOH . D 4 HOH A 66 566 66 HOH HOH . D 4 HOH A 67 567 67 HOH HOH . D 4 HOH A 68 568 68 HOH HOH . D 4 HOH A 69 569 69 HOH HOH . D 4 HOH A 70 570 70 HOH HOH . D 4 HOH A 71 571 71 HOH HOH . D 4 HOH A 72 572 72 HOH HOH . D 4 HOH A 73 573 73 HOH HOH . D 4 HOH A 74 574 74 HOH HOH . D 4 HOH A 75 575 75 HOH HOH . D 4 HOH A 76 576 76 HOH HOH . D 4 HOH A 77 577 77 HOH HOH . D 4 HOH A 78 578 78 HOH HOH . D 4 HOH A 79 579 79 HOH HOH . D 4 HOH A 80 580 80 HOH HOH . D 4 HOH A 81 581 81 HOH HOH . D 4 HOH A 82 582 82 HOH HOH . D 4 HOH A 83 583 83 HOH HOH . D 4 HOH A 84 584 84 HOH HOH . D 4 HOH A 85 585 85 HOH HOH . D 4 HOH A 86 586 86 HOH HOH . D 4 HOH A 87 587 87 HOH HOH . D 4 HOH A 88 588 88 HOH HOH . D 4 HOH A 89 589 89 HOH HOH . D 4 HOH A 90 590 90 HOH HOH . D 4 HOH A 91 591 91 HOH HOH . D 4 HOH A 92 592 92 HOH HOH . D 4 HOH A 93 593 93 HOH HOH . D 4 HOH A 94 594 94 HOH HOH . D 4 HOH A 95 595 95 HOH HOH . D 4 HOH A 96 596 96 HOH HOH . D 4 HOH A 97 597 97 HOH HOH . D 4 HOH A 98 598 98 HOH HOH . D 4 HOH A 99 599 99 HOH HOH . D 4 HOH A 100 600 100 HOH HOH . D 4 HOH A 101 601 101 HOH HOH . D 4 HOH A 102 602 102 HOH HOH . D 4 HOH A 103 603 103 HOH HOH . D 4 HOH A 104 604 104 HOH HOH . D 4 HOH A 105 605 105 HOH HOH . D 4 HOH A 106 606 106 HOH HOH . D 4 HOH A 107 607 107 HOH HOH . D 4 HOH A 108 608 108 HOH HOH . D 4 HOH A 109 609 109 HOH HOH . D 4 HOH A 110 610 110 HOH HOH . D 4 HOH A 111 611 111 HOH HOH . D 4 HOH A 112 612 112 HOH HOH . D 4 HOH A 113 613 113 HOH HOH . D 4 HOH A 114 614 114 HOH HOH . D 4 HOH A 115 615 115 HOH HOH . D 4 HOH A 116 616 116 HOH HOH . D 4 HOH A 117 617 117 HOH HOH . D 4 HOH A 118 618 118 HOH HOH . D 4 HOH A 119 619 119 HOH HOH . D 4 HOH A 120 620 120 HOH HOH . D 4 HOH A 121 621 121 HOH HOH . D 4 HOH A 122 622 122 HOH HOH . D 4 HOH A 123 623 123 HOH HOH . D 4 HOH A 124 624 124 HOH HOH . D 4 HOH A 125 625 125 HOH HOH . D 4 HOH A 126 626 126 HOH HOH . D 4 HOH A 127 627 127 HOH HOH . D 4 HOH A 128 628 128 HOH HOH . D 4 HOH A 129 629 129 HOH HOH . D 4 HOH A 130 630 130 HOH HOH . D 4 HOH A 131 631 131 HOH HOH . D 4 HOH A 132 632 132 HOH HOH . D 4 HOH A 133 633 133 HOH HOH . D 4 HOH A 134 634 134 HOH HOH . D 4 HOH A 135 635 135 HOH HOH . D 4 HOH A 136 636 136 HOH HOH . D 4 HOH A 137 637 137 HOH HOH . D 4 HOH A 138 638 138 HOH HOH . D 4 HOH A 139 639 139 HOH HOH . D 4 HOH A 140 640 140 HOH HOH . D 4 HOH A 141 641 141 HOH HOH . D 4 HOH A 142 642 142 HOH HOH . D 4 HOH A 143 643 143 HOH HOH . D 4 HOH A 144 644 144 HOH HOH . D 4 HOH A 145 645 145 HOH HOH . D 4 HOH A 146 646 146 HOH HOH . D 4 HOH A 147 647 147 HOH HOH . D 4 HOH A 148 648 148 HOH HOH . D 4 HOH A 149 649 149 HOH HOH . D 4 HOH A 150 650 150 HOH HOH . D 4 HOH A 151 651 151 HOH HOH . D 4 HOH A 152 652 152 HOH HOH . D 4 HOH A 153 653 153 HOH HOH . D 4 HOH A 154 654 154 HOH HOH . D 4 HOH A 155 655 155 HOH HOH . D 4 HOH A 156 656 156 HOH HOH . D 4 HOH A 157 657 157 HOH HOH . D 4 HOH A 158 658 158 HOH HOH . D 4 HOH A 159 659 159 HOH HOH . D 4 HOH A 160 660 160 HOH HOH . D 4 HOH A 161 661 161 HOH HOH . D 4 HOH A 162 662 162 HOH HOH . D 4 HOH A 163 663 163 HOH HOH . D 4 HOH A 164 664 164 HOH HOH . D 4 HOH A 165 665 165 HOH HOH . D 4 HOH A 166 666 166 HOH HOH . D 4 HOH A 167 667 167 HOH HOH . D 4 HOH A 168 668 168 HOH HOH . D 4 HOH A 169 669 169 HOH HOH . D 4 HOH A 170 670 170 HOH HOH . D 4 HOH A 171 671 171 HOH HOH . D 4 HOH A 172 672 172 HOH HOH . D 4 HOH A 173 673 173 HOH HOH . D 4 HOH A 174 674 174 HOH HOH . D 4 HOH A 175 675 175 HOH HOH . D 4 HOH A 176 676 176 HOH HOH . D 4 HOH A 177 677 177 HOH HOH . D 4 HOH A 178 678 178 HOH HOH . D 4 HOH A 179 679 179 HOH HOH . D 4 HOH A 180 680 180 HOH HOH . D 4 HOH A 181 681 181 HOH HOH . D 4 HOH A 182 682 182 HOH HOH . D 4 HOH A 183 683 183 HOH HOH . D 4 HOH A 184 684 184 HOH HOH . D 4 HOH A 185 685 185 HOH HOH . D 4 HOH A 186 686 186 HOH HOH . D 4 HOH A 187 687 187 HOH HOH . D 4 HOH A 188 688 188 HOH HOH . D 4 HOH A 189 689 189 HOH HOH . D 4 HOH A 190 690 190 HOH HOH . D 4 HOH A 191 691 191 HOH HOH . D 4 HOH A 192 692 192 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 O3P C5P . . . B 2 18.957 3.806 56.857 1 17.08 ? O3P C5P 400 A 1 HETATM 2 P P C5P . . . B 2 20.274 3.089 56.846 1 17.05 ? P C5P 400 A 1 HETATM 3 O O1P C5P . . . B 2 20.994 3.284 58.205 1 15.47 ? O1P C5P 400 A 1 HETATM 4 O O2P C5P . . . B 2 20.071 1.592 56.591 1 17.28 ? O2P C5P 400 A 1 HETATM 5 O O5' C5P . . . B 2 21.33 3.647 55.758 1 17.09 ? O5' C5P 400 A 1 HETATM 6 C C5' C5P . . . B 2 21.584 5.035 55.644 1 16.01 ? C5' C5P 400 A 1 HETATM 7 C C4' C5P . . . B 2 22.255 5.408 54.306 1 14.21 ? C4' C5P 400 A 1 HETATM 8 O O4' C5P . . . B 2 23.511 4.773 54.252 1 15.07 ? O4' C5P 400 A 1 HETATM 9 C C3' C5P . . . B 2 21.436 4.873 53.121 1 14.26 ? C3' C5P 400 A 1 HETATM 10 O O3' C5P . . . B 2 21.56 5.77 52.036 1 15.03 ? O3' C5P 400 A 1 HETATM 11 C C2' C5P . . . B 2 22.098 3.539 52.803 1 17.14 ? C2' C5P 400 A 1 HETATM 12 O O2' C5P . . . B 2 21.904 3.137 51.437 1 15.55 ? O2' C5P 400 A 1 HETATM 13 C C1' C5P . . . B 2 23.545 3.934 53.043 1 16.24 ? C1' C5P 400 A 1 HETATM 14 N N1 C5P . . . B 2 24.346 2.74 53.312 1 18.21 ? N1 C5P 400 A 1 HETATM 15 C C2 C5P . . . B 2 25.279 2.313 52.322 1 17.76 ? C2 C5P 400 A 1 HETATM 16 N N3 C5P . . . B 2 26.045 1.197 52.534 1 18.56 ? N3 C5P 400 A 1 HETATM 17 C C4 C5P . . . B 2 25.908 0.466 53.71 1 18.19 ? C4 C5P 400 A 1 HETATM 18 C C5 C5P . . . B 2 25 0.866 54.692 1 17.25 ? C5 C5P 400 A 1 HETATM 19 C C6 C5P . . . B 2 24.206 1.985 54.489 1 17.25 ? C6 C5P 400 A 1 HETATM 20 O O2 C5P . . . B 2 25.407 2.938 51.282 1 18.93 ? O2 C5P 400 A 1 HETATM 21 N N4 C5P . . . B 2 26.681 -0.596 53.9 1 18.26 ? N4 C5P 400 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #