data_4ELM # _model_server_result.job_id C-3GUK3QaNMX9cmngt07LQ _model_server_result.datetime_utc '2024-11-01 15:34:56' _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 4elm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":507}' # _entry.id 4ELM # _exptl.entry_id 4ELM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 541.696 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside' _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 110.53 _cell.angle_gamma 90 _cell.entry_id 4ELM _cell.length_a 98.514 _cell.length_b 126.996 _cell.length_c 104.349 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ELM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,C,G,H,I,K,L,M,N 1 1 B,D,E,F,J,O,P,Q,R 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 ? 8 M N N ? 8 Q N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 1 FUC NAG 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 5 n I NAG 1 I 1 NAG A 521 NAG 5 n I NAG 2 I 2 NAG A 522 NAG 6 n J NAG 1 J 1 NAG C 521 NAG 6 n J NAG 2 J 2 NAG C 522 NAG 6 n J BMA 3 J 3 BMA C 523 BMA 6 n J FUC 4 J 4 FUC C 525 FUC # 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 104 C CYS 104 1_555 B SG CYS 168 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 B SG CYS 208 C CYS 208 1_555 B SG CYS 263 C CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 C SG CYS 25 B CYS 25 1_555 C SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 D SG CYS 25 D CYS 25 1_555 D SG CYS 80 D CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 E SG CYS 24 E CYS 24 1_555 E SG CYS 90 E CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 E SG CYS 162 E CYS 162 1_555 F SG CYS 172 F CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 F SG CYS 24 F CYS 23 1_555 F SG CYS 93 F CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 F SG CYS 146 F CYS 145 1_555 F SG CYS 211 F CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 G SG CYS 24 G CYS 24 1_555 G SG CYS 90 G CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf12 G SG CYS 137 G CYS 137 1_555 G SG CYS 187 G CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf13 G SG CYS 162 G CYS 162 1_555 H SG CYS 172 H CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf14 H SG CYS 24 H CYS 23 1_555 H SG CYS 93 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 H SG CYS 146 H CYS 145 1_555 H SG CYS 211 H CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 K C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 L C1 NAG . A NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 B ND2 ASN 20 C ASN 20 1_555 O C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale5 B ND2 ASN 42 C ASN 42 1_555 P C1 NAG . C NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 B ND2 ASN 165 C ASN 165 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 J O6 NAG . J NAG 1 1_555 J C1 FUC . J FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale10 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _chem_comp.formula 'C24 H47 N O10 S' _chem_comp.formula_weight 541.696 _chem_comp.id SGF _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Sphingosine-1-galactoside-3-sulfate # 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 O10 S SGF doub 414 n n O9 S SGF doub 415 n n S O4 SGF sing 416 n n S O8 SGF sing 417 n n O4 C45 SGF sing 418 n n O5 C46 SGF sing 419 n n C46 C45 SGF sing 420 n n C46 C47 SGF sing 421 n n C48 C47 SGF sing 422 n n C48 O7 SGF sing 423 n n C45 C44 SGF sing 424 n n C47 O6 SGF sing 425 n n C44 O3 SGF sing 426 n n C44 C43 SGF sing 427 n n O6 C43 SGF sing 428 n n C43 O SGF sing 429 n n O C SGF sing 430 n n C C1 SGF sing 431 n n C1 N SGF sing 432 n n C1 C2 SGF sing 433 n n O1 C2 SGF sing 434 n n C2 C3 SGF sing 435 n n C3 C4 SGF doub 436 e n C4 C5 SGF sing 437 n n C5 C6 SGF sing 438 n n C6 C7 SGF sing 439 n n C17 C16 SGF sing 440 n n C16 C15 SGF sing 441 n n C7 C8 SGF sing 442 n n C8 C9 SGF sing 443 n n C10 C9 SGF sing 444 n n C10 C11 SGF sing 445 n n C15 C14 SGF sing 446 n n C11 C12 SGF sing 447 n n C14 C13 SGF sing 448 n n C12 C13 SGF sing 449 n n C17 H1 SGF sing 450 n n C17 H2 SGF sing 451 n n C17 H3 SGF sing 452 n n C16 H4 SGF sing 453 n n C16 H5 SGF sing 454 n n C15 H6 SGF sing 455 n n C15 H7 SGF sing 456 n n C14 H8 SGF sing 457 n n C14 H9 SGF sing 458 n n C13 H10 SGF sing 459 n n C13 H11 SGF sing 460 n n C12 H12 SGF sing 461 n n C12 H13 SGF sing 462 n n C11 H14 SGF sing 463 n n C11 H15 SGF sing 464 n n C10 H16 SGF sing 465 n n C10 H17 SGF sing 466 n n C9 H18 SGF sing 467 n n C9 H19 SGF sing 468 n n C8 H20 SGF sing 469 n n C8 H21 SGF sing 470 n n C7 H22 SGF sing 471 n n C7 H23 SGF sing 472 n n C6 H24 SGF sing 473 n n C6 H25 SGF sing 474 n n C5 H26 SGF sing 475 n n C5 H27 SGF sing 476 n n C4 H28 SGF sing 477 n n C3 H29 SGF sing 478 n n C2 H30 SGF sing 479 n n O1 H31 SGF sing 480 n n C1 H32 SGF sing 481 n n C H33 SGF sing 482 n n C H34 SGF sing 483 n n C43 H35 SGF sing 484 n n C44 H36 SGF sing 485 n n O3 H37 SGF sing 486 n n C47 H38 SGF sing 487 n n C48 H39 SGF sing 488 n n C48 H40 SGF sing 489 n n O7 H41 SGF sing 490 n n C46 H42 SGF sing 491 n n O5 H43 SGF sing 492 n n C45 H44 SGF sing 493 n n N H45 SGF sing 494 n n N H46 SGF sing 495 n n O8 H48 SGF sing 496 n n # _atom_sites.entry_id 4ELM _atom_sites.fract_transf_matrix[1][1] 0.010151 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003801 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007874 _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] 0.010233 _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 K 7 NAG A 1 303 501 NAG NAG . L 7 NAG A 1 304 511 NAG NAG . M 8 SGF A 1 305 2 SGF CIS . N 9 PLM A 1 306 3 PLM PLM . O 7 NAG C 1 501 501 NAG NAG . P 7 NAG C 1 502 511 NAG NAG . Q 8 SGF C 1 507 1 SGF CIS . R 9 PLM C 1 508 4 PLM PLM . # 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 C17 SGF . . . Q 8 45.784 -16.279 59.367 1 133.58 ? C17 SGF 507 C 1 HETATM 2 C C16 SGF . . . Q 8 45.097 -17.146 58.308 1 130.94 ? C16 SGF 507 C 1 HETATM 3 C C15 SGF . . . Q 8 45.926 -18.389 57.973 1 130.83 ? C15 SGF 507 C 1 HETATM 4 C C14 SGF . . . Q 8 45.485 -19.008 56.644 1 126.87 ? C14 SGF 507 C 1 HETATM 5 C C13 SGF . . . Q 8 46.17 -20.352 56.405 1 127.14 ? C13 SGF 507 C 1 HETATM 6 C C12 SGF . . . Q 8 45.167 -21.432 56.003 1 126.99 ? C12 SGF 507 C 1 HETATM 7 C C11 SGF . . . Q 8 44.913 -22.4 57.161 1 132.21 ? C11 SGF 507 C 1 HETATM 8 C C10 SGF . . . Q 8 45.043 -23.856 56.71 1 132.55 ? C10 SGF 507 C 1 HETATM 9 C C9 SGF . . . Q 8 44.866 -24.812 57.889 1 138.28 ? C9 SGF 507 C 1 HETATM 10 C C8 SGF . . . Q 8 43.605 -25.662 57.736 1 139.55 ? C8 SGF 507 C 1 HETATM 11 C C7 SGF . . . Q 8 42.906 -25.831 59.085 1 145.45 ? C7 SGF 507 C 1 HETATM 12 C C6 SGF . . . Q 8 42.49 -27.283 59.326 1 149 ? C6 SGF 507 C 1 HETATM 13 C C5 SGF . . . Q 8 41.482 -27.368 60.474 1 154.35 ? C5 SGF 507 C 1 HETATM 14 C C4 SGF . . . Q 8 41.966 -28.129 61.53 1 159.6 ? C4 SGF 507 C 1 HETATM 15 C C3 SGF . . . Q 8 41.834 -27.662 62.833 1 164.11 ? C3 SGF 507 C 1 HETATM 16 C C2 SGF . . . Q 8 42.36 -28.499 64.006 1 170.51 ? C2 SGF 507 C 1 HETATM 17 O O1 SGF . . . Q 8 43.077 -27.664 64.922 1 172.32 ? O1 SGF 507 C 1 HETATM 18 C C1 SGF . . . Q 8 41.202 -29.163 64.758 1 175.78 ? C1 SGF 507 C 1 HETATM 19 C C SGF . . . Q 8 41.688 -30.352 65.59 1 181.81 ? C SGF 507 C 1 HETATM 20 O O SGF . . . Q 8 42.812 -30.081 66.433 1 184.16 ? O SGF 507 C 1 HETATM 21 C C43 SGF . . . Q 8 42.386 -30.31 67.771 1 190.96 ? C43 SGF 507 C 1 HETATM 22 C C44 SGF . . . Q 8 43.272 -31.358 68.473 1 196.43 ? C44 SGF 507 C 1 HETATM 23 O O3 SGF . . . Q 8 43.027 -32.648 67.917 1 197.21 ? O3 SGF 507 C 1 HETATM 24 O O6 SGF . . . Q 8 42.4 -29.024 68.43 1 190.83 ? O6 SGF 507 C 1 HETATM 25 C C47 SGF . . . Q 8 41.898 -29.139 69.777 1 197.59 ? C47 SGF 507 C 1 HETATM 26 C C48 SGF . . . Q 8 41.642 -27.753 70.372 1 197.2 ? C48 SGF 507 C 1 HETATM 27 O O7 SGF . . . Q 8 40.409 -27.248 69.852 1 194.38 ? O7 SGF 507 C 1 HETATM 28 C C46 SGF . . . Q 8 42.915 -29.976 70.564 1 202.83 ? C46 SGF 507 C 1 HETATM 29 O O5 SGF . . . Q 8 44.206 -29.365 70.493 1 200.46 ? O5 SGF 507 C 1 HETATM 30 C C45 SGF . . . Q 8 42.982 -31.394 69.978 1 203.69 ? C45 SGF 507 C 1 HETATM 31 O O4 SGF . . . Q 8 43.989 -32.165 70.65 1 208.71 ? O4 SGF 507 C 1 HETATM 32 S S SGF . . . Q 8 43.459 -33.15 71.562 1 216.22 ? S SGF 507 C 1 HETATM 33 O O10 SGF . . . Q 8 42.745 -34.22 70.78 1 215.73 ? O10 SGF 507 C 1 HETATM 34 O O9 SGF . . . Q 8 44.586 -33.769 72.331 1 221.48 ? O9 SGF 507 C 1 HETATM 35 O O8 SGF . . . Q 8 42.526 -32.523 72.56 1 219.62 ? O8 SGF 507 C 1 HETATM 36 N N SGF . . . Q 8 40.173 -29.632 63.816 1 173.36 ? N SGF 507 C 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #