data_2Z0P # _model_server_result.job_id YR2e53Gl5Oa3GXWOng72NA _model_server_result.datetime_utc '2024-10-18 08:52:51' _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 2z0p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":504}' # _entry.id 2Z0P # _exptl.entry_id 2Z0P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 716.35 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE' _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 94.33 _cell.angle_gamma 90 _cell.entry_id 2Z0P _cell.length_a 59.417 _cell.length_b 62.499 _cell.length_c 117.064 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Z0P _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 PISA dimeric 2 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,M 1 1 B,G,H,N 2 1 C,I,J,O 3 1 D,K,L,P 4 1 A,B,E,F,G,H,M,N 5 1 C,D,I,J,K,L,O,P 6 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 ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L 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 ND1 HIS 142 A HIS 143 1_555 E ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc2 A SG CYS 153 A CYS 154 1_555 E ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc3 A SG CYS 154 A CYS 155 1_555 E ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc4 A SG CYS 164 A CYS 165 1_555 E ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc5 B ND1 HIS 142 B HIS 143 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc6 B SG CYS 153 B CYS 154 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 B SG CYS 154 B CYS 155 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc8 B SG CYS 164 B CYS 165 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc9 C ND1 HIS 142 C HIS 143 1_555 I ZN ZN . C ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc10 C SG CYS 153 C CYS 154 1_555 I ZN ZN . C ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc11 C SG CYS 154 C CYS 155 1_555 I ZN ZN . C ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc12 C SG CYS 164 C CYS 165 1_555 I ZN ZN . C ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc13 D ND1 HIS 142 D HIS 143 1_555 K ZN ZN . D ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc14 D SG CYS 153 D CYS 154 1_555 K ZN ZN . D ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc15 D SG CYS 154 D CYS 155 1_555 K ZN ZN . D ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc16 D SG CYS 164 D CYS 165 1_555 K ZN ZN . D ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? # _chem_comp.formula 'C17 H36 O22 P4' _chem_comp.formula_weight 716.35 _chem_comp.id 4PT _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DIC4-PHOSPHATIDYLINOSITOL(3,4,5)TRISPHOSPHATE # 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 O0F C0E 4PT sing 1 n n O0F C0L 4PT sing 2 n n C0E C0C 4PT sing 3 n n C0E H0E1 4PT sing 4 n n C0E H0E2 4PT sing 5 n n C0C O0D 4PT sing 6 n n C0C C0B 4PT sing 7 n n C0C H0C 4PT sing 8 n n O0D C0G 4PT sing 9 n n C0B OP1 4PT sing 10 n n C0B H0B1 4PT sing 11 n n C0B H0B2 4PT sing 12 n n OP1 P1 4PT sing 13 n n P1 OP3 4PT sing 14 n n P1 OP2 4PT doub 15 n n P1 O1 4PT sing 16 n n OP3 HP3 4PT sing 17 n n O1 C1 4PT sing 18 n n C1 C2 4PT sing 19 n n C1 C6 4PT sing 20 n n C1 H1 4PT sing 21 n n C2 O2 4PT sing 22 n n C2 C3 4PT sing 23 n n C2 H2 4PT sing 24 n n O2 HA 4PT sing 25 n n C3 O3 4PT sing 26 n n C3 C4 4PT sing 27 n n C3 H3 4PT sing 28 n n O3 P3 4PT sing 29 n n P3 O11 4PT sing 30 n n P3 O10 4PT sing 31 n n P3 O12 4PT doub 32 n n O11 H11 4PT sing 33 n n O10 H10 4PT sing 34 n n C4 O4 4PT sing 35 n n C4 C5 4PT sing 36 n n C4 H4 4PT sing 37 n n O4 P4 4PT sing 38 n n P4 OP5 4PT sing 39 n n P4 OP6 4PT sing 40 n n P4 OP4 4PT doub 41 n n OP5 HP5 4PT sing 42 n n OP6 HP6 4PT sing 43 n n C5 O5 4PT sing 44 n n C5 C6 4PT sing 45 n n C5 H5 4PT sing 46 n n O5 P5 4PT sing 47 n n P5 OP8 4PT sing 48 n n P5 OP7 4PT sing 49 n n P5 OP9 4PT doub 50 n n OP8 HP8 4PT sing 51 n n OP7 HP7 4PT sing 52 n n C6 O6 4PT sing 53 n n C6 H6 4PT sing 54 n n O6 HB 4PT sing 55 n n C0L O0M 4PT doub 56 n n C0L C0N 4PT sing 57 n n C0N C0P 4PT sing 58 n n C0N H0N1 4PT sing 59 n n C0N H0N2 4PT sing 60 n n C0P C0Q 4PT sing 61 n n C0P H0P1 4PT sing 62 n n C0P H0P2 4PT sing 63 n n C0Q H0Q1 4PT sing 64 n n C0Q H0Q2 4PT sing 65 n n C0Q H0Q3 4PT sing 66 n n C0G O0H 4PT sing 67 n n C0G C0I 4PT sing 68 n n C0G H0G 4PT sing 69 n n O0H H0H 4PT sing 70 n n C0I C0J 4PT sing 71 n n C0I H0I1 4PT sing 72 n n C0I H0I2 4PT sing 73 n n C0J C0K 4PT sing 74 n n C0J H0J1 4PT sing 75 n n C0J H0J2 4PT sing 76 n n C0K H0K1 4PT sing 77 n n C0K H0K2 4PT sing 78 n n C0K H0K3 4PT sing 79 n n # _atom_sites.entry_id 2Z0P _atom_sites.fract_transf_matrix[1][1] 0.01683 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001274 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016 _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] 0.008567 _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 ZN A 1 301 301 ZN ZN2 . F 3 4PT A 1 501 501 4PT 4PT . G 2 ZN B 1 302 302 ZN ZN2 . H 3 4PT B 1 502 502 4PT 4PT . I 2 ZN C 1 303 303 ZN ZN2 . J 3 4PT C 1 503 503 4PT 4PT . K 2 ZN D 1 304 304 ZN ZN2 . L 3 4PT D 1 504 504 4PT 4PT . M 4 HOH A 1 502 14 HOH TIP . M 4 HOH A 2 503 15 HOH TIP . M 4 HOH A 3 504 18 HOH TIP . M 4 HOH A 4 505 19 HOH TIP . M 4 HOH A 5 506 20 HOH TIP . M 4 HOH A 6 507 24 HOH TIP . M 4 HOH A 7 508 31 HOH TIP . M 4 HOH A 8 509 32 HOH TIP . M 4 HOH A 9 510 33 HOH TIP . M 4 HOH A 10 511 36 HOH TIP . M 4 HOH A 11 512 47 HOH TIP . M 4 HOH A 12 513 50 HOH TIP . M 4 HOH A 13 514 56 HOH TIP . N 4 HOH B 1 503 3 HOH TIP . N 4 HOH B 2 504 5 HOH TIP . N 4 HOH B 3 505 6 HOH TIP . N 4 HOH B 4 506 8 HOH TIP . N 4 HOH B 5 507 9 HOH TIP . N 4 HOH B 6 508 10 HOH TIP . N 4 HOH B 7 509 12 HOH TIP . N 4 HOH B 8 510 13 HOH TIP . N 4 HOH B 9 511 16 HOH TIP . N 4 HOH B 10 512 17 HOH TIP . N 4 HOH B 11 513 21 HOH TIP . N 4 HOH B 12 514 23 HOH TIP . N 4 HOH B 13 515 26 HOH TIP . N 4 HOH B 14 516 30 HOH TIP . N 4 HOH B 15 517 37 HOH TIP . N 4 HOH B 16 518 38 HOH TIP . N 4 HOH B 17 519 39 HOH TIP . N 4 HOH B 18 520 45 HOH TIP . N 4 HOH B 19 521 49 HOH TIP . N 4 HOH B 20 522 51 HOH TIP . N 4 HOH B 21 523 52 HOH TIP . N 4 HOH B 22 524 53 HOH TIP . N 4 HOH B 23 525 61 HOH TIP . N 4 HOH B 24 526 63 HOH TIP . N 4 HOH B 25 527 65 HOH TIP . O 4 HOH C 1 504 7 HOH TIP . O 4 HOH C 2 505 22 HOH TIP . O 4 HOH C 3 506 55 HOH TIP . O 4 HOH C 4 507 57 HOH TIP . O 4 HOH C 5 508 59 HOH TIP . O 4 HOH C 6 509 67 HOH TIP . P 4 HOH D 1 505 1 HOH TIP . P 4 HOH D 2 506 2 HOH TIP . P 4 HOH D 3 507 4 HOH TIP . P 4 HOH D 4 508 11 HOH TIP . P 4 HOH D 5 509 25 HOH TIP . P 4 HOH D 6 510 27 HOH TIP . P 4 HOH D 7 511 28 HOH TIP . P 4 HOH D 8 512 29 HOH TIP . P 4 HOH D 9 513 34 HOH TIP . P 4 HOH D 10 514 35 HOH TIP . P 4 HOH D 11 515 40 HOH TIP . P 4 HOH D 12 516 41 HOH TIP . P 4 HOH D 13 517 42 HOH TIP . P 4 HOH D 14 518 43 HOH TIP . P 4 HOH D 15 519 44 HOH TIP . P 4 HOH D 16 520 46 HOH TIP . P 4 HOH D 17 521 48 HOH TIP . P 4 HOH D 18 522 54 HOH TIP . P 4 HOH D 19 523 58 HOH TIP . P 4 HOH D 20 524 60 HOH TIP . P 4 HOH D 21 525 62 HOH TIP . P 4 HOH D 22 526 64 HOH TIP . P 4 HOH D 23 527 66 HOH TIP . P 4 HOH D 24 528 68 HOH TIP . # 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 O0F 4PT . . . L 3 2.65 9.17 50.23 1 83.19 ? O0F 4PT 504 D 1 HETATM 2 C C0E 4PT . . . L 3 2.764 10.59 50.046 1 78.82 ? C0E 4PT 504 D 1 HETATM 3 C C0C 4PT . . . L 3 1.396 11.15 49.688 1 75.39 ? C0C 4PT 504 D 1 HETATM 4 O O0D 4PT . . . L 3 0.875 10.611 48.461 1 76.99 ? O0D 4PT 504 D 1 HETATM 5 C C0B 4PT . . . L 3 1.385 12.681 49.637 1 69.38 ? C0B 4PT 504 D 1 HETATM 6 O OP1 4PT . . . L 3 2.171 13.202 48.561 1 61.41 ? OP1 4PT 504 D 1 HETATM 7 P P1 4PT . . . L 3 1.864 14.682 48.006 1 52.91 ? P1 4PT 504 D 1 HETATM 8 O OP3 4PT . . . L 3 0.403 14.913 48.063 1 50.63 ? OP3 4PT 504 D 1 HETATM 9 O OP2 4PT . . . L 3 2.556 14.825 46.705 1 52.73 ? OP2 4PT 504 D 1 HETATM 10 O O1 4PT . . . L 3 2.601 15.617 49.087 1 51.14 ? O1 4PT 504 D 1 HETATM 11 C C1 4PT . . . L 3 1.94 15.968 50.305 1 46.31 ? C1 4PT 504 D 1 HETATM 12 C C2 4PT . . . L 3 1.28 17.34 50.155 1 45.26 ? C2 4PT 504 D 1 HETATM 13 O O2 4PT . . . L 3 2.274 18.312 49.819 1 40.51 ? O2 4PT 504 D 1 HETATM 14 C C3 4PT . . . L 3 0.589 17.741 51.46 1 42.31 ? C3 4PT 504 D 1 HETATM 15 O O3 4PT . . . L 3 0.033 19.048 51.302 1 42.02 ? O3 4PT 504 D 1 HETATM 16 P P3 4PT . . . L 3 -1.542 19.288 51.523 1 43.97 ? P3 4PT 504 D 1 HETATM 17 O O11 4PT . . . L 3 -2.356 18.519 50.555 1 45.64 ? O11 4PT 504 D 1 HETATM 18 O O10 4PT . . . L 3 -1.758 20.876 51.375 1 45.38 ? O10 4PT 504 D 1 HETATM 19 O O12 4PT . . . L 3 -1.878 18.917 53.052 1 39.79 ? O12 4PT 504 D 1 HETATM 20 C C4 4PT . . . L 3 1.586 17.763 52.619 1 41.55 ? C4 4PT 504 D 1 HETATM 21 O O4 4PT . . . L 3 0.872 17.998 53.835 1 38.95 ? O4 4PT 504 D 1 HETATM 22 P P4 4PT . . . L 3 0.927 19.422 54.581 1 33.7 ? P4 4PT 504 D 1 HETATM 23 O OP5 4PT . . . L 3 -0.421 20.013 54.735 1 37.03 ? OP5 4PT 504 D 1 HETATM 24 O OP6 4PT . . . L 3 1.636 19.19 56.007 1 37.04 ? OP6 4PT 504 D 1 HETATM 25 O OP4 4PT . . . L 3 1.931 20.335 53.714 1 35.82 ? OP4 4PT 504 D 1 HETATM 26 C C5 4PT . . . L 3 2.311 16.423 52.754 1 43.73 ? C5 4PT 504 D 1 HETATM 27 O O5 4PT . . . L 3 3.33 16.561 53.746 1 44.78 ? O5 4PT 504 D 1 HETATM 28 P P5 4PT . . . L 3 3.1 15.995 55.235 1 46.9 ? P5 4PT 504 D 1 HETATM 29 O OP8 4PT . . . L 3 2.9 17.065 56.238 1 47.38 ? OP8 4PT 504 D 1 HETATM 30 O OP7 4PT . . . L 3 4.416 15.118 55.533 1 48.41 ? OP7 4PT 504 D 1 HETATM 31 O OP9 4PT . . . L 3 1.854 14.979 55.171 1 47.92 ? OP9 4PT 504 D 1 HETATM 32 C C6 4PT . . . L 3 2.967 16.003 51.437 1 46.17 ? C6 4PT 504 D 1 HETATM 33 O O6 4PT . . . L 3 3.564 14.712 51.585 1 46.34 ? O6 4PT 504 D 1 HETATM 34 C C0L 4PT . . . L 3 2.121 8.84 51.441 1 84.27 ? C0L 4PT 504 D 1 HETATM 35 O O0M 4PT . . . L 3 1.933 7.653 51.702 1 84.91 ? O0M 4PT 504 D 1 HETATM 36 C C0N 4PT . . . L 3 1.749 9.921 52.459 1 85.45 ? C0N 4PT 504 D 1 HETATM 37 C C0P 4PT . . . L 3 2.93 10.256 53.372 1 85.77 ? C0P 4PT 504 D 1 HETATM 38 C C0Q 4PT . . . L 3 2.559 11.351 54.375 1 86.22 ? C0Q 4PT 504 D 1 HETATM 39 C C0G 4PT . . . L 3 1.711 10.732 47.392 1 77.24 ? C0G 4PT 504 D 1 HETATM 40 O O0H 4PT . . . L 3 2.969 11.232 47.526 1 76.38 ? O0H 4PT 504 D 1 HETATM 41 C C0I 4PT . . . L 3 1.274 10.314 46.14 1 76.95 ? C0I 4PT 504 D 1 HETATM 42 C C0J 4PT . . . L 3 -0.043 9.905 45.971 1 77.62 ? C0J 4PT 504 D 1 HETATM 43 C C0K 4PT . . . L 3 -0.49 9.486 44.722 1 78.18 ? C0K 4PT 504 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 43 #