data_4MDB
#
_model_server_result.job_id            tjQMlKvmFcUpG7843-q9Vw 
_model_server_result.datetime_utc      '2024-11-29 19:59:13' 
_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          4mdb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    4MDB 
#
_exptl.entry_id    4MDB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              444.416 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide' 
_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            4MDB 
_cell.length_a            44.24 
_cell.length_b            44.24 
_cell.length_c            206.28 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4MDB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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 
#
_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
metalc ? metalc1 A OD2 ASP 36 A ASP 156 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? 
metalc ? metalc2 A OD1 ASP 36 A ASP 156 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc3 A OD2 ASP 129 A ASP 249 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc4 A OD1 ASP 164 A ASP 284 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc5 A OD2 ASP 164 A ASP 284 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc6 B OAH RLT . A RLT 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc7 B OAG RLT . A RLT 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc8 B OAE RLT . A RLT 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc9 B OAH RLT . A RLT 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc10 C MG MG . A MG 402 1_555 E O HOH . A HOH 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc11 D MG MG . A MG 403 1_555 E O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc12 D MG MG . A MG 403 1_555 E O HOH . A HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
#
_chem_comp.formula           'C20 H21 F N6 O5' 
_chem_comp.formula_weight    444.416 
_chem_comp.id                RLT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'RALTEGRAVIR, MK0518' 
#
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
CAA CAW RLT sing 277 n n 
CAB NBE RLT sing 278 n n 
CAC CBF RLT sing 279 n n 
CAD CBF RLT sing 280 n n 
OAE CAU RLT doub 281 n n 
OAF CAV RLT doub 282 n n 
OAG CBD RLT doub 283 n n 
OAH CAZ RLT sing 284 n n 
FAI CAX RLT sing 285 n n 
CAJ CAL RLT doub 286 n y 
CAJ CAX RLT sing 287 n y 
CAK CAM RLT sing 288 n y 
CAK CAX RLT doub 289 n y 
CAL CAY RLT sing 290 n y 
CAM CAY RLT doub 291 n y 
CAN NAR RLT sing 292 n n 
CAN CAY RLT sing 293 n n 
NAO NAP RLT sing 294 n y 
NAO CAW RLT doub 295 n y 
NAP CBA RLT doub 296 n y 
NAQ CBB RLT sing 297 n n 
NAQ CBC RLT doub 298 n n 
NAR CAU RLT sing 299 n n 
NAS CAV RLT sing 300 n n 
NAS CBF RLT sing 301 n n 
OAT CAW RLT sing 302 n y 
OAT CBA RLT sing 303 n y 
CAU CBB RLT sing 304 n n 
CAV CBA RLT sing 305 n n 
CAZ CBB RLT doub 306 n n 
CAZ CBD RLT sing 307 n n 
CBC NBE RLT sing 308 n n 
CBC CBF RLT sing 309 n n 
CBD NBE RLT sing 310 n n 
CAA HAA RLT sing 311 n n 
CAA HAAA RLT sing 312 n n 
CAA HAAB RLT sing 313 n n 
CAB HAB RLT sing 314 n n 
CAB HABA RLT sing 315 n n 
CAB HABB RLT sing 316 n n 
CAC HAC RLT sing 317 n n 
CAC HACA RLT sing 318 n n 
CAC HACB RLT sing 319 n n 
CAD HAD RLT sing 320 n n 
CAD HADA RLT sing 321 n n 
CAD HADB RLT sing 322 n n 
OAH HOAH RLT sing 323 n n 
CAJ HAJ RLT sing 324 n n 
CAK HAK RLT sing 325 n n 
CAL HAL RLT sing 326 n n 
CAM HAM RLT sing 327 n n 
CAN HAN RLT sing 328 n n 
CAN HANA RLT sing 329 n n 
NAR HNAR RLT sing 330 n n 
NAS HNAS RLT sing 331 n n 
#
_atom_sites.entry_id                     4MDB 
_atom_sites.fract_transf_matrix[1][1]    0.022604 
_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]    0.022604 
_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]    0.004848 
_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 RLT A 1 401 1 RLT RLT . 
C 3 MG A 1 402 1 MG MG . 
D 3 MG A 1 403 1 MG MG . 
E 4 HOH A 1 501 1 HOH HOH . 
E 4 HOH A 2 502 2 HOH HOH . 
E 4 HOH A 3 503 3 HOH HOH . 
E 4 HOH A 4 504 4 HOH HOH . 
E 4 HOH A 5 505 5 HOH HOH . 
E 4 HOH A 6 506 6 HOH HOH . 
E 4 HOH A 7 507 7 HOH HOH . 
E 4 HOH A 8 508 8 HOH HOH . 
E 4 HOH A 9 509 9 HOH HOH . 
E 4 HOH A 10 510 10 HOH HOH . 
E 4 HOH A 11 511 11 HOH HOH . 
E 4 HOH A 12 512 12 HOH HOH . 
E 4 HOH A 13 513 13 HOH HOH . 
E 4 HOH A 14 514 14 HOH HOH . 
E 4 HOH A 15 515 15 HOH HOH . 
E 4 HOH A 16 516 16 HOH HOH . 
E 4 HOH A 17 517 17 HOH HOH . 
E 4 HOH A 18 518 18 HOH HOH . 
E 4 HOH A 19 519 19 HOH HOH . 
E 4 HOH A 20 520 20 HOH HOH . 
E 4 HOH A 21 521 21 HOH HOH . 
E 4 HOH A 22 522 22 HOH HOH . 
E 4 HOH A 23 523 23 HOH HOH . 
E 4 HOH A 24 524 24 HOH HOH . 
E 4 HOH A 25 525 25 HOH HOH . 
E 4 HOH A 26 526 26 HOH HOH . 
E 4 HOH A 27 527 27 HOH HOH . 
E 4 HOH A 28 528 28 HOH HOH . 
E 4 HOH A 29 529 29 HOH HOH . 
E 4 HOH A 30 530 30 HOH HOH . 
E 4 HOH A 31 531 31 HOH HOH . 
E 4 HOH A 32 532 32 HOH HOH . 
E 4 HOH A 33 533 33 HOH HOH . 
E 4 HOH A 34 534 34 HOH HOH . 
E 4 HOH A 35 535 35 HOH HOH . 
E 4 HOH A 36 536 36 HOH HOH . 
E 4 HOH A 37 537 37 HOH HOH . 
E 4 HOH A 38 538 38 HOH HOH . 
E 4 HOH A 39 539 39 HOH HOH . 
E 4 HOH A 40 540 40 HOH HOH . 
E 4 HOH A 41 541 41 HOH HOH . 
E 4 HOH A 42 542 42 HOH HOH . 
E 4 HOH A 43 543 43 HOH HOH . 
E 4 HOH A 44 544 44 HOH HOH . 
E 4 HOH A 45 545 45 HOH HOH . 
E 4 HOH A 46 546 46 HOH HOH . 
E 4 HOH A 47 547 47 HOH HOH . 
E 4 HOH A 48 548 48 HOH HOH . 
E 4 HOH A 49 549 49 HOH HOH . 
E 4 HOH A 50 550 50 HOH HOH . 
E 4 HOH A 51 551 51 HOH HOH . 
E 4 HOH A 52 552 52 HOH HOH . 
E 4 HOH A 53 553 53 HOH HOH . 
E 4 HOH A 54 554 54 HOH HOH . 
E 4 HOH A 55 555 55 HOH HOH . 
E 4 HOH A 56 556 56 HOH HOH . 
E 4 HOH A 57 557 57 HOH HOH . 
E 4 HOH A 58 558 58 HOH HOH . 
E 4 HOH A 59 559 59 HOH HOH . 
E 4 HOH A 60 560 60 HOH HOH . 
E 4 HOH A 61 561 61 HOH HOH . 
E 4 HOH A 62 562 62 HOH HOH . 
E 4 HOH A 63 563 63 HOH HOH . 
E 4 HOH A 64 564 64 HOH HOH . 
E 4 HOH A 65 565 65 HOH HOH . 
E 4 HOH A 66 566 66 HOH HOH . 
E 4 HOH A 67 567 67 HOH HOH . 
E 4 HOH A 68 568 68 HOH HOH . 
E 4 HOH A 69 569 69 HOH HOH . 
E 4 HOH A 70 570 70 HOH HOH . 
E 4 HOH A 71 571 71 HOH HOH . 
E 4 HOH A 72 572 73 HOH HOH . 
E 4 HOH A 73 573 74 HOH HOH . 
E 4 HOH A 74 574 75 HOH HOH . 
E 4 HOH A 75 575 76 HOH HOH . 
E 4 HOH A 76 576 77 HOH HOH . 
E 4 HOH A 77 577 78 HOH HOH . 
E 4 HOH A 78 578 79 HOH HOH . 
E 4 HOH A 79 579 80 HOH HOH . 
E 4 HOH A 80 580 81 HOH HOH . 
E 4 HOH A 81 581 82 HOH HOH . 
E 4 HOH A 82 582 83 HOH HOH . 
E 4 HOH A 83 583 84 HOH HOH . 
E 4 HOH A 84 584 85 HOH HOH . 
E 4 HOH A 85 585 86 HOH HOH . 
E 4 HOH A 86 586 87 HOH HOH . 
E 4 HOH A 87 587 88 HOH HOH . 
E 4 HOH A 88 588 89 HOH HOH . 
E 4 HOH A 89 589 90 HOH HOH . 
E 4 HOH A 90 590 91 HOH HOH . 
E 4 HOH A 91 591 92 HOH HOH . 
E 4 HOH A 92 592 93 HOH HOH . 
E 4 HOH A 93 593 94 HOH HOH . 
E 4 HOH A 94 594 95 HOH HOH . 
E 4 HOH A 95 595 96 HOH HOH . 
E 4 HOH A 96 596 97 HOH HOH . 
E 4 HOH A 97 597 98 HOH HOH . 
E 4 HOH A 98 598 99 HOH HOH . 
E 4 HOH A 99 599 100 HOH HOH . 
E 4 HOH A 100 600 101 HOH HOH . 
E 4 HOH A 101 601 102 HOH HOH . 
E 4 HOH A 102 602 103 HOH HOH . 
E 4 HOH A 103 603 105 HOH HOH . 
E 4 HOH A 104 604 106 HOH HOH . 
E 4 HOH A 105 605 108 HOH HOH . 
E 4 HOH A 106 606 109 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 C CAA RLT . . . B 2 -4.244 27.117 -5.483 1 50.49 ? CAA RLT 401 A 1 
HETATM 2 C CAB RLT . . . B 2 -12.698 23.028 -3.058 1 24.29 ? CAB RLT 401 A 1 
HETATM 3 C CAC RLT . . . B 2 -11.051 25.602 -2.924 1 27.77 ? CAC RLT 401 A 1 
HETATM 4 C CAD RLT . . . B 2 -10.541 24.091 -0.683 1 31.69 ? CAD RLT 401 A 1 
HETATM 5 O OAE RLT . . . B 2 -7.126 20.326 -4.391 1 16.88 ? OAE RLT 401 A 1 
HETATM 6 O OAF RLT . . . B 2 -8.492 25.373 -4.497 1 44.73 ? OAF RLT 401 A 1 
HETATM 7 O OAG RLT . . . B 2 -12.227 20.928 -4.301 1 18.36 ? OAG RLT 401 A 1 
HETATM 8 O OAH RLT . . . B 2 -9.853 19.895 -4.956 1 18.02 ? OAH RLT 401 A 1 
HETATM 9 F FAI RLT . . . B 2 -2.476 25.366 -6.53 1 42.41 ? FAI RLT 401 A 1 
HETATM 10 C CAJ RLT . . . B 2 -4.169 23.719 -6.145 1 36.53 ? CAJ RLT 401 A 1 
HETATM 11 C CAK RLT . . . B 2 -2.709 24.357 -4.365 1 35.2 ? CAK RLT 401 A 1 
HETATM 12 C CAL RLT . . . B 2 -4.832 22.828 -5.276 1 35.68 ? CAL RLT 401 A 1 
HETATM 13 C CAM RLT . . . B 2 -3.361 23.473 -3.494 1 35.15 ? CAM RLT 401 A 1 
HETATM 14 C CAN RLT . . . B 2 -5.115 21.772 -2.952 1 32.82 ? CAN RLT 401 A 1 
HETATM 15 N NAO RLT . . . B 2 -4.604 26.656 -2.892 1 56.22 ? NAO RLT 401 A 1 
HETATM 16 N NAP RLT . . . B 2 -5.76 26.157 -2.234 1 58.65 ? NAP RLT 401 A 1 
HETATM 17 N NAQ RLT . . . B 2 -8.856 22.984 -3.042 1 24.14 ? NAQ RLT 401 A 1 
HETATM 18 N NAR RLT . . . B 2 -6.546 22.092 -3.031 1 28.32 ? NAR RLT 401 A 1 
HETATM 19 N NAS RLT . . . B 2 -8.723 25.168 -2.179 1 34.5 ? NAS RLT 401 A 1 
HETATM 20 O OAT RLT . . . B 2 -6.172 26.275 -4.461 1 52.76 ? OAT RLT 401 A 1 
HETATM 21 C CAU RLT . . . B 2 -7.372 21.366 -3.842 1 25.6 ? CAU RLT 401 A 1 
HETATM 22 C CAV RLT . . . B 2 -8.057 25.444 -3.335 1 43.29 ? CAV RLT 401 A 1 
HETATM 23 C CAW RLT . . . B 2 -4.922 26.702 -4.212 1 49.86 ? CAW RLT 401 A 1 
HETATM 24 C CAX RLT . . . B 2 -3.099 24.494 -5.688 1 38.08 ? CAX RLT 401 A 1 
HETATM 25 C CAY RLT . . . B 2 -4.422 22.694 -3.929 1 32.73 ? CAY RLT 401 A 1 
HETATM 26 C CAZ RLT . . . B 2 -9.837 21 -4.197 1 19.9 ? CAZ RLT 401 A 1 
HETATM 27 C CBA RLT . . . B 2 -6.656 25.925 -3.23 1 49.4 ? CBA RLT 401 A 1 
HETATM 28 C CBB RLT . . . B 2 -8.711 21.804 -3.759 1 23.01 ? CBB RLT 401 A 1 
HETATM 29 C CBC RLT . . . B 2 -10.098 23.474 -2.791 1 23.27 ? CBC RLT 401 A 1 
HETATM 30 C CBD RLT . . . B 2 -11.159 21.529 -3.969 1 22.31 ? CBD RLT 401 A 1 
HETATM 31 N NBE RLT . . . B 2 -11.243 22.724 -3.234 1 28.46 ? NBE RLT 401 A 1 
HETATM 32 C CBF RLT . . . B 2 -10.12 24.861 -1.966 1 29.64 ? CBF RLT 401 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           497 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#