data_2XQS
#
_model_server_result.job_id            kOcMo0bn_hrPdPUvrGa8IA 
_model_server_result.datetime_utc      '2024-11-25 04:24:18' 
_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          2xqs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"LA","auth_seq_id":102}' 
#
_entry.id    2XQS 
#
_exptl.entry_id    2XQS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              480.546 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            CYMAL-4 
_entity.pdbx_number_of_molecules    40 
_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            2XQS 
_cell.length_a            92.93 
_cell.length_b            92.93 
_cell.length_c            258.54 
_cell.Z_PDB               60 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2XQS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    pentadecameric 
_pdbx_struct_assembly.oligomeric_count      15 
_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,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -46.465 80.479741 0 
3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -92.93 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
? 2 AA N N 
? 2 BA N N 
? 2 CA N N 
? 2 DA N N 
? 2 EA N N 
? 2 FA N N 
? 2 GA N N 
? 2 HA N N 
? 2 IA N N 
? 2 JA N N 
? 2 KA N N 
? 2 LA N N 
? 2 MA N N 
? 2 NA N N 
? 2 OA N N 
? 2 PA N N 
? 2 QA N N 
? 2 RA N N 
? 2 SA 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
covale ? covale1 A C FME 1 A FME 1 1_555 A N GLU 2 A GLU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale2 B C FME 1 B FME 1 1_555 B N GLU 2 B GLU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 C C FME 1 C FME 1 1_555 C N GLU 2 C GLU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 D C FME 1 D FME 1 1_555 D N GLU 2 D GLU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale5 E C FME 1 E FME 1 1_555 E N GLU 2 E GLU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
#
_chem_comp.formula           'C22 H40 O11' 
_chem_comp.formula_weight    480.546 
_chem_comp.id                CVM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              CYMAL-4 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE' 
#
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 C2 CVM sing 55 n n 
C1 O12 CVM sing 56 n n 
C2 C3 CVM sing 57 n n 
C3 C4 CVM sing 58 n n 
C4 C6 CVM sing 59 n n 
C6 C7 CVM sing 60 n n 
C6 C11 CVM sing 61 n n 
C7 C8 CVM sing 62 n n 
C8 C9 CVM sing 63 n n 
C9 C10 CVM sing 64 n n 
C10 C11 CVM sing 65 n n 
O12 C13 CVM sing 66 n n 
C13 O14 CVM sing 67 n n 
C13 C18 CVM sing 68 n n 
O14 C15 CVM sing 69 n n 
C15 C16 CVM sing 70 n n 
C15 C19 CVM sing 71 n n 
C16 C17 CVM sing 72 n n 
C16 O23 CVM sing 73 n n 
C17 C18 CVM sing 74 n n 
C17 O21 CVM sing 75 n n 
C18 O22 CVM sing 76 n n 
C19 O20 CVM sing 77 n n 
O23 C24 CVM sing 78 n n 
C24 O25 CVM sing 79 n n 
C24 C29 CVM sing 80 n n 
O25 C26 CVM sing 81 n n 
C26 C27 CVM sing 82 n n 
C26 C30 CVM sing 83 n n 
C27 C28 CVM sing 84 n n 
C27 O32 CVM sing 85 n n 
C28 C29 CVM sing 86 n n 
C28 O33 CVM sing 87 n n 
C29 O34 CVM sing 88 n n 
C30 O31 CVM sing 89 n n 
C1 H11C CVM sing 90 n n 
C1 H12C CVM sing 91 n n 
C2 H21C CVM sing 92 n n 
C2 H22C CVM sing 93 n n 
C3 H31C CVM sing 94 n n 
C3 H32C CVM sing 95 n n 
C4 H41C CVM sing 96 n n 
C4 H42C CVM sing 97 n n 
C6 H6 CVM sing 98 n n 
C7 H71C CVM sing 99 n n 
C7 H72C CVM sing 100 n n 
C11 H111 CVM sing 101 n n 
C11 H112 CVM sing 102 n n 
C8 H81C CVM sing 103 n n 
C8 H82C CVM sing 104 n n 
C9 H91C CVM sing 105 n n 
C9 H92C CVM sing 106 n n 
C10 H101 CVM sing 107 n n 
C10 H102 CVM sing 108 n n 
C13 H13 CVM sing 109 n n 
C18 H18 CVM sing 110 n n 
C15 H15 CVM sing 111 n n 
C16 H16 CVM sing 112 n n 
C19 H191 CVM sing 113 n n 
C19 H192 CVM sing 114 n n 
C17 H17 CVM sing 115 n n 
O21 H21 CVM sing 116 n n 
O22 H22 CVM sing 117 n n 
O20 H20 CVM sing 118 n n 
C24 H24 CVM sing 119 n n 
C29 H29 CVM sing 120 n n 
C26 H26 CVM sing 121 n n 
C27 H27 CVM sing 122 n n 
C30 H301 CVM sing 123 n n 
C30 H302 CVM sing 124 n n 
C28 H28 CVM sing 125 n n 
O32 H32 CVM sing 126 n n 
O33 H33 CVM sing 127 n n 
O34 H34 CVM sing 128 n n 
O31 H31 CVM sing 129 n n 
#
_atom_sites.entry_id                     2XQS 
_atom_sites.fract_transf_matrix[1][1]    0.010761 
_atom_sites.fract_transf_matrix[1][2]    0.006213 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012425 
_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]    0.003868 
_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 CVM A 1 102 102 CVM CVM . 
G 2 CVM A 1 103 103 CVM CVM . 
H 2 CVM A 1 104 104 CVM CVM . 
I 2 CVM A 1 106 106 CVM CVM . 
J 2 CVM A 1 107 107 CVM CVM . 
K 2 CVM A 1 108 108 CVM CVM . 
L 2 CVM A 1 109 109 CVM CVM . 
M 2 CVM A 1 110 110 CVM CVM . 
N 2 CVM B 1 102 102 CVM CVM . 
O 2 CVM B 1 103 103 CVM CVM . 
P 2 CVM B 1 104 104 CVM CVM . 
Q 2 CVM B 1 106 106 CVM CVM . 
R 2 CVM B 1 107 107 CVM CVM . 
S 2 CVM B 1 108 108 CVM CVM . 
T 2 CVM B 1 109 109 CVM CVM . 
U 2 CVM B 1 110 110 CVM CVM . 
V 2 CVM C 1 102 102 CVM CVM . 
W 2 CVM C 1 103 103 CVM CVM . 
X 2 CVM C 1 104 104 CVM CVM . 
Y 2 CVM C 1 106 106 CVM CVM . 
Z 2 CVM C 1 107 107 CVM CVM . 
AA 2 CVM C 1 108 108 CVM CVM . 
BA 2 CVM C 1 109 109 CVM CVM . 
CA 2 CVM C 1 110 110 CVM CVM . 
DA 2 CVM D 1 102 102 CVM CVM . 
EA 2 CVM D 1 103 103 CVM CVM . 
FA 2 CVM D 1 104 104 CVM CVM . 
GA 2 CVM D 1 106 106 CVM CVM . 
HA 2 CVM D 1 107 107 CVM CVM . 
IA 2 CVM D 1 108 108 CVM CVM . 
JA 2 CVM D 1 109 109 CVM CVM . 
KA 2 CVM D 1 110 110 CVM CVM . 
LA 2 CVM E 1 102 102 CVM CVM . 
MA 2 CVM E 1 103 103 CVM CVM . 
NA 2 CVM E 1 104 104 CVM CVM . 
OA 2 CVM E 1 106 106 CVM CVM . 
PA 2 CVM E 1 107 107 CVM CVM . 
QA 2 CVM E 1 108 108 CVM CVM . 
RA 2 CVM E 1 109 109 CVM CVM . 
SA 2 CVM E 1 110 110 CVM CVM . 
TA 3 HOH A 1 2001 2001 HOH HOH . 
TA 3 HOH A 2 2002 2002 HOH HOH . 
UA 3 HOH C 1 2001 2001 HOH HOH . 
UA 3 HOH C 2 2002 2002 HOH HOH . 
VA 3 HOH E 1 2001 2001 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 CVM . . . LA 2 -36.685 20.366 3.079 1 107.68 ? C1 CVM 102 E 1 
HETATM 2 C C2 CVM . . . LA 2 -36.478 20.988 4.46 1 100.59 ? C2 CVM 102 E 1 
HETATM 3 C C3 CVM . . . LA 2 -36.08 19.924 5.486 1 97.25 ? C3 CVM 102 E 1 
HETATM 4 C C4 CVM . . . LA 2 -36.276 20.373 6.935 1 90.43 ? C4 CVM 102 E 1 
HETATM 5 C C6 CVM . . . LA 2 -35.758 19.341 7.946 1 89.34 ? C6 CVM 102 E 1 
HETATM 6 C C7 CVM . . . LA 2 -36.409 19.581 9.308 1 87 ? C7 CVM 102 E 1 
HETATM 7 C C8 CVM . . . LA 2 -35.805 18.728 10.421 1 79.95 ? C8 CVM 102 E 1 
HETATM 8 C C9 CVM . . . LA 2 -34.729 17.787 9.895 1 79.26 ? C9 CVM 102 E 1 
HETATM 9 C C10 CVM . . . LA 2 -33.647 18.569 9.169 1 80.69 ? C10 CVM 102 E 1 
HETATM 10 C C11 CVM . . . LA 2 -34.238 19.449 8.068 1 87.92 ? C11 CVM 102 E 1 
HETATM 11 O O12 CVM . . . LA 2 -35.479 20.335 2.305 1 115.35 ? O12 CVM 102 E 1 
HETATM 12 C C13 CVM . . . LA 2 -35.032 19.01 1.955 1 123.13 ? C13 CVM 102 E 1 
HETATM 13 O O14 CVM . . . LA 2 -33.776 19.073 1.26 1 125.63 ? O14 CVM 102 E 1 
HETATM 14 C C15 CVM . . . LA 2 -33.171 17.808 0.934 1 124.58 ? C15 CVM 102 E 1 
HETATM 15 C C16 CVM . . . LA 2 -34.122 16.797 0.285 1 125.87 ? C16 CVM 102 E 1 
HETATM 16 C C17 CVM . . . LA 2 -35.541 16.838 0.857 1 123.85 ? C17 CVM 102 E 1 
HETATM 17 C C18 CVM . . . LA 2 -36.028 18.268 1.066 1 124.61 ? C18 CVM 102 E 1 
HETATM 18 C C19 CVM . . . LA 2 -31.949 18.033 0.038 1 120.54 ? C19 CVM 102 E 1 
HETATM 19 O O20 CVM . . . LA 2 -31.352 16.78 -0.324 1 116.16 ? O20 CVM 102 E 1 
HETATM 20 O O21 CVM . . . LA 2 -36.45 16.186 -0.037 1 120.56 ? O21 CVM 102 E 1 
HETATM 21 O O22 CVM . . . LA 2 -37.342 18.231 1.641 1 125.01 ? O22 CVM 102 E 1 
HETATM 22 O O23 CVM . . . LA 2 -33.514 15.51 0.451 0 125.25 ? O23 CVM 102 E 1 
HETATM 23 C C24 CVM . . . LA 2 -34.055 14.449 -0.34 0 124.79 ? C24 CVM 102 E 1 
HETATM 24 O O25 CVM . . . LA 2 -34.76 14.982 -1.461 0 124.54 ? O25 CVM 102 E 1 
HETATM 25 C C26 CVM . . . LA 2 -33.943 15.254 -2.597 0 124.48 ? C26 CVM 102 E 1 
HETATM 26 C C27 CVM . . . LA 2 -33.424 13.96 -3.209 0 124.87 ? C27 CVM 102 E 1 
HETATM 27 C C28 CVM . . . LA 2 -33.132 12.906 -2.145 0 124.95 ? C28 CVM 102 E 1 
HETATM 28 C C29 CVM . . . LA 2 -32.912 13.525 -0.766 0 124.76 ? C29 CVM 102 E 1 
HETATM 29 C C30 CVM . . . LA 2 -34.783 16.037 -3.598 0 124.35 ? C30 CVM 102 E 1 
HETATM 30 O O31 CVM . . . LA 2 -36.171 15.79 -3.343 0 124.18 ? O31 CVM 102 E 1 
HETATM 31 O O32 CVM . . . LA 2 -32.223 14.241 -3.937 0 125.02 ? O32 CVM 102 E 1 
HETATM 32 O O33 CVM . . . LA 2 -34.205 11.958 -2.082 0 125 ? O33 CVM 102 E 1 
HETATM 33 O O34 CVM . . . LA 2 -31.668 14.238 -0.736 0 124.65 ? O34 CVM 102 E 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           256 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           33 
#