data_2X72 # _model_server_result.job_id uGXB6W2_hhPe4RmskERJ_Q _model_server_result.datetime_utc '2024-11-23 02:49:51' _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 2x72 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 2X72 # _exptl.entry_id 2X72 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 691.959 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE _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 120 _cell.entry_id 2X72 _cell.length_a 243.986 _cell.length_b 243.986 _cell.length_c 109.156 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2X72 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 109.156 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG A 1333 NAG 3 n C NAG 2 C 2 NAG A 1334 NAG 3 n C BMA 3 C 3 BMA A 1335 BMA 3 n C MAN 4 C 4 MAN A 1336 MAN 3 n C MAN 5 C 5 MAN A 1337 MAN # 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 disulf ? disulf1 A SG CYS 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 A SG CYS 323 A CYS 322 1_555 G C1 PLM . A PLM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.674 ? covale ? covale4 A SG CYS 324 A CYS 323 1_555 F C1 PLM . A PLM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.692 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _chem_comp.formula 'C37 H74 N O8 P' _chem_comp.formula_weight 691.959 _chem_comp.id PEF _chem_comp.mon_nstd_flag . _chem_comp.name DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL # 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 C2 C1 PEF sing 487 n n C2 C3 PEF sing 488 n n C2 O2 PEF sing 489 n n C2 H21 PEF sing 490 n n C1 O3P PEF sing 491 n n C1 H11 PEF sing 492 n n C1 H12 PEF sing 493 n n N C5 PEF sing 494 n n N HN1 PEF sing 495 n n N HN2 PEF sing 496 n n C3 O3 PEF sing 497 n n C3 H31 PEF sing 498 n n C3 H32 PEF sing 499 n n C4 C5 PEF sing 500 n n C4 O4P PEF sing 501 n n C4 H41 PEF sing 502 n n C4 H42 PEF sing 503 n n C5 H51 PEF sing 504 n n C5 H52 PEF sing 505 n n C10 C11 PEF sing 506 n n C10 O4 PEF doub 507 n n C10 O2 PEF sing 508 n n C11 C12 PEF sing 509 n n C11 H112 PEF sing 510 n n C11 H111 PEF sing 511 n n C12 C13 PEF sing 512 n n C12 H122 PEF sing 513 n n C12 H121 PEF sing 514 n n C13 C14 PEF sing 515 n n C13 H132 PEF sing 516 n n C13 H131 PEF sing 517 n n C14 C15 PEF sing 518 n n C14 H142 PEF sing 519 n n C14 H141 PEF sing 520 n n C15 C16 PEF sing 521 n n C15 H152 PEF sing 522 n n C15 H151 PEF sing 523 n n C16 C17 PEF sing 524 n n C16 H162 PEF sing 525 n n C16 H161 PEF sing 526 n n C17 C18 PEF sing 527 n n C17 H172 PEF sing 528 n n C17 H171 PEF sing 529 n n C18 C19 PEF sing 530 n n C18 H182 PEF sing 531 n n C18 H181 PEF sing 532 n n C19 C20 PEF sing 533 n n C19 H192 PEF sing 534 n n C19 H191 PEF sing 535 n n C20 C21 PEF sing 536 n n C20 H202 PEF sing 537 n n C20 H201 PEF sing 538 n n C21 C22 PEF sing 539 n n C21 H212 PEF sing 540 n n C21 H211 PEF sing 541 n n C22 C23 PEF sing 542 n n C22 H222 PEF sing 543 n n C22 H221 PEF sing 544 n n C23 C24 PEF sing 545 n n C23 H232 PEF sing 546 n n C23 H231 PEF sing 547 n n C24 C25 PEF sing 548 n n C24 H242 PEF sing 549 n n C24 H241 PEF sing 550 n n C25 H252 PEF sing 551 n n C25 H251 PEF sing 552 n n C25 H253 PEF sing 553 n n C30 C31 PEF sing 554 n n C30 O5 PEF doub 555 n n C30 O3 PEF sing 556 n n C31 C32 PEF sing 557 n n C31 H312 PEF sing 558 n n C31 H311 PEF sing 559 n n C32 C33 PEF sing 560 n n C32 H322 PEF sing 561 n n C32 H321 PEF sing 562 n n C33 C34 PEF sing 563 n n C33 H332 PEF sing 564 n n C33 H331 PEF sing 565 n n C34 C35 PEF sing 566 n n C34 H342 PEF sing 567 n n C34 H341 PEF sing 568 n n C35 C36 PEF sing 569 n n C35 H352 PEF sing 570 n n C35 H351 PEF sing 571 n n C36 C37 PEF sing 572 n n C36 H362 PEF sing 573 n n C36 H361 PEF sing 574 n n C37 C38 PEF sing 575 n n C37 H372 PEF sing 576 n n C37 H371 PEF sing 577 n n C38 C39 PEF sing 578 n n C38 H382 PEF sing 579 n n C38 H381 PEF sing 580 n n C39 C40 PEF sing 581 n n C39 H392 PEF sing 582 n n C39 H391 PEF sing 583 n n C40 C41 PEF sing 584 n n C40 H402 PEF sing 585 n n C40 H401 PEF sing 586 n n C41 C42 PEF sing 587 n n C41 H412 PEF sing 588 n n C41 H411 PEF sing 589 n n C42 C43 PEF sing 590 n n C42 H422 PEF sing 591 n n C42 H421 PEF sing 592 n n C43 C44 PEF sing 593 n n C43 H432 PEF sing 594 n n C43 H431 PEF sing 595 n n C44 C45 PEF sing 596 n n C44 H442 PEF sing 597 n n C44 H441 PEF sing 598 n n C45 H452 PEF sing 599 n n C45 H451 PEF sing 600 n n C45 H453 PEF sing 601 n n O1P P PEF doub 602 n n O2P P PEF sing 603 n n O2P HOP2 PEF sing 604 n n O3P P PEF sing 605 n n O4P P PEF sing 606 n n # _atom_sites.entry_id 2X72 _atom_sites.fract_transf_matrix[1][1] 0.004099 _atom_sites.fract_transf_matrix[1][2] 0.002366 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004733 _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] 0.009161 _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 D 4 PEF A 1 401 1329 PEF PEF . E 5 BOG A 1 402 1330 BOG BOG . F 6 PLM A 1 403 1331 PLM PLM . G 6 PLM A 1 404 1332 PLM PLM . H 7 RET A 1 410 1338 RET RET . I 8 LPP A 1 411 1340 LPP LPP . J 9 ACT A 1 412 1351 ACT ACT . K 10 HOH A 1 501 2014 HOH HOH . K 10 HOH A 2 502 2011 HOH HOH . K 10 HOH A 3 503 2009 HOH HOH . K 10 HOH A 4 504 2018 HOH HOH . K 10 HOH A 5 505 2007 HOH HOH . K 10 HOH A 6 506 2013 HOH HOH . K 10 HOH A 7 507 2003 HOH HOH . K 10 HOH A 8 508 2004 HOH HOH . K 10 HOH A 9 509 2001 HOH HOH . K 10 HOH A 10 510 2002 HOH HOH . K 10 HOH A 11 511 2010 HOH HOH . K 10 HOH A 12 512 2016 HOH HOH . K 10 HOH A 13 513 2012 HOH HOH . K 10 HOH A 14 514 2006 HOH HOH . K 10 HOH A 15 515 2017 HOH HOH . K 10 HOH A 16 516 2015 HOH HOH . L 10 HOH B 1 401 2005 HOH HOH . L 10 HOH B 2 402 2008 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 C2 PEF . . . D 4 25.341 -59.4 47.326 1 119.4 ? C2 PEF 401 A 1 HETATM 2 C C1 PEF . . . D 4 26.539 -59.485 48.269 1 116.03 ? C1 PEF 401 A 1 HETATM 3 N N PEF . . . D 4 31.274 -57.312 49.13 1 92.81 ? N PEF 401 A 1 HETATM 4 C C3 PEF . . . D 4 24.171 -60.35 47.672 1 117.87 ? C3 PEF 401 A 1 HETATM 5 C C4 PEF . . . D 4 29.59 -57.972 47.301 1 104.08 ? C4 PEF 401 A 1 HETATM 6 C C5 PEF . . . D 4 30.869 -57.187 47.715 1 93.51 ? C5 PEF 401 A 1 HETATM 7 C C10 PEF . . . D 4 25.51 -57.035 47.285 1 108.97 ? C10 PEF 401 A 1 HETATM 8 C C11 PEF . . . D 4 24.659 -55.875 46.761 1 100.54 ? C11 PEF 401 A 1 HETATM 9 C C12 PEF . . . D 4 23.922 -55.074 47.821 1 96.84 ? C12 PEF 401 A 1 HETATM 10 C C13 PEF . . . D 4 23.093 -54.033 47.054 1 90.43 ? C13 PEF 401 A 1 HETATM 11 C C14 PEF . . . D 4 22.359 -53.148 48.05 1 87.57 ? C14 PEF 401 A 1 HETATM 12 C C15 PEF . . . D 4 21.463 -52.122 47.362 1 83.46 ? C15 PEF 401 A 1 HETATM 13 C C16 PEF . . . D 4 20.864 -51.295 48.493 1 88.4 ? C16 PEF 401 A 1 HETATM 14 C C17 PEF . . . D 4 19.862 -50.239 48.012 1 94.75 ? C17 PEF 401 A 1 HETATM 15 C C18 PEF . . . D 4 19.359 -49.493 49.262 1 92.95 ? C18 PEF 401 A 1 HETATM 16 C C19 PEF . . . D 4 18.238 -48.49 48.944 1 100.27 ? C19 PEF 401 A 1 HETATM 17 C C20 PEF . . . D 4 17.852 -47.78 50.251 1 106.87 ? C20 PEF 401 A 1 HETATM 18 C C21 PEF . . . D 4 17.34 -48.671 51.426 1 105.6 ? C21 PEF 401 A 1 HETATM 19 C C22 PEF . . . D 4 17.197 -47.607 52.544 1 106.16 ? C22 PEF 401 A 1 HETATM 20 C C23 PEF . . . D 4 16.803 -48.021 53.972 1 96.7 ? C23 PEF 401 A 1 HETATM 21 C C24 PEF . . . D 4 16.861 -46.682 54.764 1 80.48 ? C24 PEF 401 A 1 HETATM 22 C C25 PEF . . . D 4 16.584 -46.835 56.267 1 63.72 ? C25 PEF 401 A 1 HETATM 23 C C30 PEF . . . D 4 21.969 -59.421 47.451 1 118.47 ? C30 PEF 401 A 1 HETATM 24 C C31 PEF . . . D 4 21.103 -58.506 46.53 1 117.35 ? C31 PEF 401 A 1 HETATM 25 C C32 PEF . . . D 4 19.57 -58.338 46.735 1 113.77 ? C32 PEF 401 A 1 HETATM 26 C C33 PEF . . . D 4 19.135 -57.795 48.111 1 105.4 ? C33 PEF 401 A 1 HETATM 27 C C34 PEF . . . D 4 17.607 -57.516 48.102 1 108.6 ? C34 PEF 401 A 1 HETATM 28 C C35 PEF . . . D 4 17.135 -56.968 49.464 1 110.68 ? C35 PEF 401 A 1 HETATM 29 C C36 PEF . . . D 4 15.657 -56.495 49.41 1 110.28 ? C36 PEF 401 A 1 HETATM 30 C C37 PEF . . . D 4 15.157 -55.91 50.761 1 103.95 ? C37 PEF 401 A 1 HETATM 31 C C38 PEF . . . D 4 14.986 -56.9 51.937 1 110.79 ? C38 PEF 401 A 1 HETATM 32 C C39 PEF . . . D 4 16.215 -57.733 52.331 1 105.39 ? C39 PEF 401 A 1 HETATM 33 C C40 PEF . . . D 4 15.819 -58.577 53.548 1 104.04 ? C40 PEF 401 A 1 HETATM 34 C C41 PEF . . . D 4 16.969 -59.505 53.904 1 103.82 ? C41 PEF 401 A 1 HETATM 35 C C42 PEF . . . D 4 16.625 -60.329 55.147 1 106.93 ? C42 PEF 401 A 1 HETATM 36 C C43 PEF . . . D 4 17.771 -61.324 55.376 1 114.07 ? C43 PEF 401 A 1 HETATM 37 C C44 PEF . . . D 4 19.138 -60.627 55.54 1 101.59 ? C44 PEF 401 A 1 HETATM 38 C C45 PEF . . . D 4 20.232 -61.696 55.757 1 83.79 ? C45 PEF 401 A 1 HETATM 39 O O4 PEF . . . D 4 26.72 -56.911 47.509 1 101.87 ? O4 PEF 401 A 1 HETATM 40 O O5 PEF . . . D 4 21.635 -59.721 48.606 1 108.97 ? O5 PEF 401 A 1 HETATM 41 O O2 PEF . . . D 4 24.726 -58.135 47.537 1 119.52 ? O2 PEF 401 A 1 HETATM 42 O O3 PEF . . . D 4 23.1 -59.894 46.807 1 115.45 ? O3 PEF 401 A 1 HETATM 43 O O1P PEF . . . D 4 28.915 -59.806 49.983 1 132.69 ? O1P PEF 401 A 1 HETATM 44 O O2P PEF . . . D 4 29.705 -61.805 48.504 1 116.64 ? O2P PEF 401 A 1 HETATM 45 O O3P PEF . . . D 4 27.371 -60.624 48.054 1 124.69 ? O3P PEF 401 A 1 HETATM 46 O O4P PEF . . . D 4 29.675 -59.422 47.435 1 133.86 ? O4P PEF 401 A 1 HETATM 47 P P PEF . . . D 4 28.914 -60.357 48.598 1 147.98 ? P PEF 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 47 #