data_2PM8
#
_model_server_result.job_id            AHrYkULOTIb0WfcYT9I96g 
_model_server_result.datetime_utc      '2024-11-04 22:50:02' 
_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          2pm8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":609}' 
#
_entry.id    2PM8 
#
_exptl.entry_id    2PM8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    5 
_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            2PM8 
_cell.length_a            150.803 
_cell.length_b            150.803 
_cell.length_c            142.12 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PM8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        90 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 4 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,M,N,O,P,Q,R,S,T,U,V 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -150.803 0 
3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -75.4015 -75.4015 0 
4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 75.4015 -75.4015 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 L N N 
? 5 M N N 
? 5 N N N 
? 5 S N N 
? 5 T N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   NAG 
_pdbx_entity_branch_link.comp_id_2                   NAG 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 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
2 n C NAG 1 C 1 NAG A 781 NAG 
2 n C NAG 2 C 2 NAG A 782 NAG 
#
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 65 A CYS 65 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
disulf ? disulf4 B SG CYS 65 B CYS 65 1_555 B SG CYS 92 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf5 B SG CYS 252 B CYS 252 1_555 B SG CYS 263 B CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf6 B SG CYS 400 B CYS 400 1_555 B SG CYS 519 B CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
covale ? covale1 A ND2 ASN 57 A ASN 57 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale3 A ND2 ASN 341 A ASN 341 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale4 A ND2 ASN 485 A ASN 485 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale5 B ND2 ASN 106 B ASN 106 1_555 P C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? 
covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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
C1 O1 GOL sing 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     2PM8 
_atom_sites.fract_transf_matrix[1][1]    0.006631 
_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]    0.006631 
_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]    0.007036 
_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 3 NAG A 1 601 791 NAG NAG . 
E 3 NAG A 1 602 678 NAG NAG . 
F 3 NAG A 1 603 798 NAG NAG . 
G 4 SO4 A 1 604 601 SO4 SO4 . 
H 4 SO4 A 1 605 602 SO4 SO4 . 
I 4 SO4 A 1 606 603 SO4 SO4 . 
J 4 SO4 A 1 607 604 SO4 SO4 . 
K 4 SO4 A 1 608 606 SO4 SO4 . 
L 5 GOL A 1 609 999 GOL GOL . 
M 5 GOL A 1 610 774 GOL GOL . 
N 5 GOL A 1 611 777 GOL GOL . 
O 3 NAG B 1 601 781 NAG NAG . 
P 3 NAG B 1 602 791 NAG NAG . 
Q 4 SO4 B 1 603 601 SO4 SO4 . 
R 4 SO4 B 1 604 602 SO4 SO4 . 
S 5 GOL B 1 605 774 GOL GOL . 
T 5 GOL B 1 606 777 GOL GOL . 
U 6 HOH A 1 701 8 HOH HOH . 
U 6 HOH A 2 702 43 HOH HOH . 
U 6 HOH A 3 703 36 HOH HOH . 
U 6 HOH A 4 704 25 HOH HOH . 
U 6 HOH A 5 705 10 HOH HOH . 
U 6 HOH A 6 706 19 HOH HOH . 
U 6 HOH A 7 707 11 HOH HOH . 
U 6 HOH A 8 708 5 HOH HOH . 
U 6 HOH A 9 709 85 HOH HOH . 
U 6 HOH A 10 710 44 HOH HOH . 
U 6 HOH A 11 711 34 HOH HOH . 
U 6 HOH A 12 712 47 HOH HOH . 
U 6 HOH A 13 713 84 HOH HOH . 
U 6 HOH A 14 714 30 HOH HOH . 
U 6 HOH A 15 715 40 HOH HOH . 
U 6 HOH A 16 716 35 HOH HOH . 
U 6 HOH A 17 717 41 HOH HOH . 
U 6 HOH A 18 718 12 HOH HOH . 
U 6 HOH A 19 719 97 HOH HOH . 
U 6 HOH A 20 720 50 HOH HOH . 
U 6 HOH A 21 721 6 HOH HOH . 
U 6 HOH A 22 722 21 HOH HOH . 
U 6 HOH A 23 723 2 HOH HOH . 
U 6 HOH A 24 724 58 HOH HOH . 
U 6 HOH A 25 725 9 HOH HOH . 
U 6 HOH A 26 726 23 HOH HOH . 
U 6 HOH A 27 727 46 HOH HOH . 
U 6 HOH A 28 728 11 HOH HOH . 
U 6 HOH A 29 729 51 HOH HOH . 
U 6 HOH A 30 730 45 HOH HOH . 
U 6 HOH A 31 731 83 HOH HOH . 
U 6 HOH A 32 732 18 HOH HOH . 
U 6 HOH A 33 733 25 HOH HOH . 
U 6 HOH A 34 734 32 HOH HOH . 
U 6 HOH A 35 735 42 HOH HOH . 
U 6 HOH A 36 736 23 HOH HOH . 
U 6 HOH A 37 737 73 HOH HOH . 
U 6 HOH A 38 738 31 HOH HOH . 
U 6 HOH A 39 739 26 HOH HOH . 
U 6 HOH A 40 740 66 HOH HOH . 
U 6 HOH A 41 741 18 HOH HOH . 
U 6 HOH A 42 742 76 HOH HOH . 
U 6 HOH A 43 743 37 HOH HOH . 
U 6 HOH A 44 744 24 HOH HOH . 
U 6 HOH A 45 745 13 HOH HOH . 
U 6 HOH A 46 746 13 HOH HOH . 
U 6 HOH A 47 747 90 HOH HOH . 
U 6 HOH A 48 748 48 HOH HOH . 
U 6 HOH A 49 749 1 HOH HOH . 
U 6 HOH A 50 750 28 HOH HOH . 
U 6 HOH A 51 751 70 HOH HOH . 
U 6 HOH A 52 752 7 HOH HOH . 
V 6 HOH B 1 701 17 HOH HOH . 
V 6 HOH B 2 702 6 HOH HOH . 
V 6 HOH B 3 703 29 HOH HOH . 
V 6 HOH B 4 704 63 HOH HOH . 
V 6 HOH B 5 705 33 HOH HOH . 
V 6 HOH B 6 706 94 HOH HOH . 
V 6 HOH B 7 707 15 HOH HOH . 
V 6 HOH B 8 708 32 HOH HOH . 
V 6 HOH B 9 709 95 HOH HOH . 
V 6 HOH B 10 710 31 HOH HOH . 
V 6 HOH B 11 711 27 HOH HOH . 
V 6 HOH B 12 712 53 HOH HOH . 
V 6 HOH B 13 713 39 HOH HOH . 
V 6 HOH B 14 714 12 HOH HOH . 
V 6 HOH B 15 715 54 HOH HOH . 
V 6 HOH B 16 716 24 HOH HOH . 
V 6 HOH B 17 717 14 HOH HOH . 
V 6 HOH B 18 718 22 HOH HOH . 
V 6 HOH B 19 719 9 HOH HOH . 
V 6 HOH B 20 720 52 HOH HOH . 
V 6 HOH B 21 721 14 HOH HOH . 
V 6 HOH B 22 722 29 HOH HOH . 
V 6 HOH B 23 723 71 HOH HOH . 
V 6 HOH B 24 724 30 HOH HOH . 
V 6 HOH B 25 725 60 HOH HOH . 
V 6 HOH B 26 726 49 HOH HOH . 
V 6 HOH B 27 727 21 HOH HOH . 
V 6 HOH B 28 728 38 HOH HOH . 
V 6 HOH B 29 729 22 HOH HOH . 
V 6 HOH B 30 730 15 HOH HOH . 
V 6 HOH B 31 731 69 HOH HOH . 
V 6 HOH B 32 732 100 HOH HOH . 
V 6 HOH B 33 733 3 HOH HOH . 
V 6 HOH B 34 734 7 HOH HOH . 
V 6 HOH B 35 735 16 HOH HOH . 
V 6 HOH B 36 736 99 HOH HOH . 
V 6 HOH B 37 737 16 HOH HOH . 
V 6 HOH B 38 738 4 HOH HOH . 
V 6 HOH B 39 739 27 HOH HOH . 
V 6 HOH B 40 740 80 HOH HOH . 
V 6 HOH B 41 741 5 HOH HOH . 
V 6 HOH B 42 742 20 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 C1 GOL . . . L 5 -8.142 -38.611 10.126 1 63.09 ? C1 GOL 609 A 1 
HETATM 2 O O1 GOL . . . L 5 -7.339 -38.129 11.191 1 62.42 ? O1 GOL 609 A 1 
HETATM 3 C C2 GOL . . . L 5 -7.263 -38.749 8.879 1 62.47 ? C2 GOL 609 A 1 
HETATM 4 O O2 GOL . . . L 5 -7.997 -39.094 7.716 1 62.12 ? O2 GOL 609 A 1 
HETATM 5 C C3 GOL . . . L 5 -6.13 -39.731 9.135 1 61.71 ? C3 GOL 609 A 1 
HETATM 6 O O3 GOL . . . L 5 -5.129 -39.065 9.859 1 61.6 ? O3 GOL 609 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#