data_3NMD
#
_model_server_result.job_id            OM0sdDif2L6lwCaC7r-YwQ 
_model_server_result.datetime_utc      '2025-03-04 14:15:03' 
_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          3nmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":56}' 
#
_entry.id    3NMD 
#
_exptl.entry_id    3NMD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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            3NMD 
_cell.length_a            62.774 
_cell.length_b            77.312 
_cell.length_c            148.616 
_cell.Z_PDB               40 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NMD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,F,N,O 1 1 
C,D,G,H,I,J,K,P,Q 2 1 
E,L,M,R 3 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 74.308 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             L 
_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
covale ? covale1 A C GLN 57 A GLN 40 1_555 A N MSE 58 A MSE 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C MSE 58 A MSE 41 1_555 A N LEU 59 A LEU 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale3 B C GLN 57 B GLN 40 1_555 B N MSE 58 B MSE 41 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.332 ? 
covale ? covale4 B C GLN 57 B GLN 40 1_555 B N MSE 58 B MSE 41 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.329 ? 
covale ? covale5 B C MSE 58 B MSE 41 1_555 B N LEU 59 B LEU 42 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale6 B C MSE 58 B MSE 41 1_555 B N LEU 59 B LEU 42 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale7 C C GLN 57 C GLN 40 1_555 C N MSE 58 C MSE 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 C C MSE 58 C MSE 41 1_555 C N LEU 59 C LEU 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale9 D C GLN 57 D GLN 40 1_555 D N MSE 58 D MSE 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale10 D C MSE 58 D MSE 41 1_555 D N LEU 59 D LEU 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale11 E C GLN 57 E GLN 40 1_555 E N MSE 58 E MSE 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale12 E C MSE 58 E MSE 41 1_555 E N LEU 59 E LEU 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
#
_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 116 n n 
C1 C2 GOL sing 117 n n 
C1 H11 GOL sing 118 n n 
C1 H12 GOL sing 119 n n 
O1 HO1 GOL sing 120 n n 
C2 O2 GOL sing 121 n n 
C2 C3 GOL sing 122 n n 
C2 H2 GOL sing 123 n n 
O2 HO2 GOL sing 124 n n 
C3 O3 GOL sing 125 n n 
C3 H31 GOL sing 126 n n 
C3 H32 GOL sing 127 n n 
O3 HO3 GOL sing 128 n n 
#
_atom_sites.entry_id                     3NMD 
_atom_sites.fract_transf_matrix[1][1]    0.01593 
_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]    0.012935 
_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]    0.006729 
_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
F 2 HEZ A 1 56 56 HEZ HEZ . 
G 2 HEZ C 1 56 56 HEZ HEZ . 
H 2 HEZ C 1 57 57 HEZ HEZ . 
I 2 HEZ C 1 58 58 HEZ HEZ . 
J 2 HEZ D 1 56 56 HEZ HEZ . 
K 2 HEZ D 1 57 57 HEZ HEZ . 
L 3 GOL E 1 56 56 GOL GOL . 
M 2 HEZ E 1 57 57 HEZ HEZ . 
N 4 HOH A 1 57 57 HOH HOH . 
N 4 HOH A 2 58 58 HOH HOH . 
N 4 HOH A 3 59 59 HOH HOH . 
N 4 HOH A 4 60 60 HOH HOH . 
N 4 HOH A 5 61 61 HOH HOH . 
N 4 HOH A 6 62 62 HOH HOH . 
N 4 HOH A 7 63 63 HOH HOH . 
N 4 HOH A 8 66 66 HOH HOH . 
N 4 HOH A 9 78 78 HOH HOH . 
N 4 HOH A 10 79 79 HOH HOH . 
N 4 HOH A 11 81 81 HOH HOH . 
N 4 HOH A 12 83 83 HOH HOH . 
N 4 HOH A 13 93 93 HOH HOH . 
N 4 HOH A 14 95 95 HOH HOH . 
N 4 HOH A 15 99 99 HOH HOH . 
O 4 HOH B 1 56 56 HOH HOH . 
O 4 HOH B 2 57 57 HOH HOH . 
O 4 HOH B 3 58 58 HOH HOH . 
O 4 HOH B 4 59 59 HOH HOH . 
O 4 HOH B 5 60 60 HOH HOH . 
O 4 HOH B 6 61 61 HOH HOH . 
O 4 HOH B 7 62 62 HOH HOH . 
O 4 HOH B 8 75 75 HOH HOH . 
O 4 HOH B 9 80 80 HOH HOH . 
O 4 HOH B 10 82 82 HOH HOH . 
O 4 HOH B 11 85 85 HOH HOH . 
O 4 HOH B 12 89 89 HOH HOH . 
O 4 HOH B 13 92 92 HOH HOH . 
O 4 HOH B 14 98 98 HOH HOH . 
P 4 HOH C 1 59 59 HOH HOH . 
P 4 HOH C 2 60 60 HOH HOH . 
P 4 HOH C 3 61 61 HOH HOH . 
P 4 HOH C 4 62 62 HOH HOH . 
P 4 HOH C 5 63 63 HOH HOH . 
P 4 HOH C 6 64 64 HOH HOH . 
P 4 HOH C 7 65 65 HOH HOH . 
P 4 HOH C 8 66 66 HOH HOH . 
P 4 HOH C 9 67 67 HOH HOH . 
P 4 HOH C 10 68 68 HOH HOH . 
P 4 HOH C 11 69 69 HOH HOH . 
P 4 HOH C 12 70 70 HOH HOH . 
P 4 HOH C 13 71 71 HOH HOH . 
P 4 HOH C 14 73 73 HOH HOH . 
P 4 HOH C 15 77 77 HOH HOH . 
P 4 HOH C 16 87 87 HOH HOH . 
P 4 HOH C 17 88 88 HOH HOH . 
P 4 HOH C 18 97 97 HOH HOH . 
Q 4 HOH D 1 58 58 HOH HOH . 
Q 4 HOH D 2 59 59 HOH HOH . 
Q 4 HOH D 3 60 60 HOH HOH . 
Q 4 HOH D 4 61 61 HOH HOH . 
Q 4 HOH D 5 62 62 HOH HOH . 
Q 4 HOH D 6 63 63 HOH HOH . 
Q 4 HOH D 7 64 64 HOH HOH . 
Q 4 HOH D 8 65 65 HOH HOH . 
Q 4 HOH D 9 66 66 HOH HOH . 
Q 4 HOH D 10 67 67 HOH HOH . 
Q 4 HOH D 11 68 68 HOH HOH . 
Q 4 HOH D 12 69 69 HOH HOH . 
Q 4 HOH D 13 70 70 HOH HOH . 
Q 4 HOH D 14 71 71 HOH HOH . 
Q 4 HOH D 15 72 72 HOH HOH . 
Q 4 HOH D 16 73 73 HOH HOH . 
Q 4 HOH D 17 74 74 HOH HOH . 
Q 4 HOH D 18 75 75 HOH HOH . 
Q 4 HOH D 19 76 76 HOH HOH . 
Q 4 HOH D 20 77 77 HOH HOH . 
Q 4 HOH D 21 78 78 HOH HOH . 
Q 4 HOH D 22 79 79 HOH HOH . 
R 4 HOH E 1 58 58 HOH HOH . 
R 4 HOH E 2 59 59 HOH HOH . 
R 4 HOH E 3 60 60 HOH HOH . 
R 4 HOH E 4 61 61 HOH HOH . 
R 4 HOH E 5 62 62 HOH HOH . 
R 4 HOH E 6 63 63 HOH HOH . 
R 4 HOH E 7 64 64 HOH HOH . 
R 4 HOH E 8 65 65 HOH HOH . 
R 4 HOH E 9 66 66 HOH HOH . 
R 4 HOH E 10 67 67 HOH HOH . 
R 4 HOH E 11 68 68 HOH HOH . 
R 4 HOH E 12 69 69 HOH HOH . 
R 4 HOH E 13 70 70 HOH HOH . 
R 4 HOH E 14 71 71 HOH HOH . 
R 4 HOH E 15 72 72 HOH HOH . 
R 4 HOH E 16 73 73 HOH HOH . 
R 4 HOH E 17 74 74 HOH HOH . 
R 4 HOH E 18 75 75 HOH HOH . 
R 4 HOH E 19 76 76 HOH HOH . 
R 4 HOH E 20 77 77 HOH HOH . 
R 4 HOH E 21 78 78 HOH HOH . 
R 4 HOH E 22 79 79 HOH HOH . 
R 4 HOH E 23 80 80 HOH HOH . 
R 4 HOH E 24 84 84 HOH HOH . 
R 4 HOH E 25 86 86 HOH HOH . 
R 4 HOH E 26 90 90 HOH HOH . 
R 4 HOH E 27 91 91 HOH HOH . 
R 4 HOH E 28 94 94 HOH HOH . 
R 4 HOH E 29 96 96 HOH HOH . 
R 4 HOH E 30 100 100 HOH HOH . 
R 4 HOH E 31 101 101 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 3 -4.208 32.137 29.191 1 57 ? C1 GOL 56 E 1 
HETATM 2 O O1 GOL . . . L 3 -4.591 30.797 29.469 1 62.4 ? O1 GOL 56 E 1 
HETATM 3 C C2 GOL . . . L 3 -3.16 32.141 28.065 1 53.74 ? C2 GOL 56 E 1 
HETATM 4 O O2 GOL . . . L 3 -1.971 31.524 28.513 1 64.01 ? O2 GOL 56 E 1 
HETATM 5 C C3 GOL . . . L 3 -2.859 33.565 27.581 1 46.33 ? C3 GOL 56 E 1 
HETATM 6 O O3 GOL . . . L 3 -4.003 34.384 27.745 1 67.36 ? O3 GOL 56 E 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           6 
#