data_2VAQ
#
_model_server_result.job_id            Sv596nZ542frumUTwFJMLQ 
_model_server_result.datetime_utc      '2024-11-15 12:38:24' 
_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          2vaq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1334}' 
#
_entry.id    2VAQ 
#
_exptl.entry_id    2VAQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              532.583 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2S,3R,4S)-methyl 4-(2-(2-(1H-indol-3-yl)ethylamino)ethyl)-2-((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylate' 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            2VAQ 
_cell.length_a            149.993 
_cell.length_b            149.993 
_cell.length_c            121.688 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VAQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 2 C N N 
? 2 D 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
disulf ? disulf1 A SG CYS 67 A CYS 89 1_555 A SG CYS 79 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf2 B SG CYS 67 B CYS 89 1_555 B SG CYS 79 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
#
_chem_comp.formula           'C27 H36 N2 O9' 
_chem_comp.formula_weight    532.583 
_chem_comp.id                VAW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2S,3R,4S)-methyl 4-(2-(2-(1H-indol-3-yl)ethylamino)ethyl)-2-((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'methyl (2S,3R,4S)-3-ethenyl-2-(beta-D-glucopyranosyloxy)-4-(2-{[2-(1H-indol-3-yl)ethyl]amino}ethyl)-3,4-dihydro-2H-pyran-5-carboxylate' 
#
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
CBD CAM VAW sing 376 n y 
CBD CBC VAW doub 377 n y 
CBD CBB VAW sing 378 n y 
CAM CAK VAW doub 379 n y 
CAK CAJ VAW sing 380 n y 
CAJ CAL VAW doub 381 n y 
CAL CBC VAW sing 382 n y 
CBC NAU VAW sing 383 n y 
NAU CAN VAW sing 384 n y 
CAN CBB VAW doub 385 n y 
CBB CAR VAW sing 386 n n 
CAR CAP VAW sing 387 n n 
CAP NAT VAW sing 388 n n 
NAT CAQ VAW sing 389 n n 
CAQ CAS VAW sing 390 n n 
CAS CBJ VAW sing 391 n n 
CBJ CBH VAW sing 392 n n 
CBJ CBA VAW sing 393 n n 
CBH CAH VAW sing 394 n n 
CBH CBK VAW sing 395 n n 
CAH CAA VAW doub 396 n n 
CBA CAZ VAW sing 397 n n 
CBA CAI VAW doub 398 n n 
CAZ OAC VAW doub 399 n n 
CAZ OAV VAW sing 400 n n 
OAV CAB VAW sing 401 n n 
CAI OAW VAW sing 402 n n 
OAW CBK VAW sing 403 n n 
CBK O1 VAW sing 404 n n 
O1 C1 VAW sing 405 n n 
C1 O5 VAW sing 406 n n 
C1 C2 VAW sing 407 n n 
O5 C5 VAW sing 408 n n 
C5 C6 VAW sing 409 n n 
C5 C4 VAW sing 410 n n 
C6 O6 VAW sing 411 n n 
C4 O4 VAW sing 412 n n 
C4 C3 VAW sing 413 n n 
C3 O3 VAW sing 414 n n 
C3 C2 VAW sing 415 n n 
C2 O2 VAW sing 416 n n 
CAM HAM VAW sing 417 n n 
CAK HAK VAW sing 418 n n 
CAJ HAJ VAW sing 419 n n 
CAL HAL VAW sing 420 n n 
NAU HAU VAW sing 421 n n 
CAN HAN VAW sing 422 n n 
CAR HAR1 VAW sing 423 n n 
CAR HAR2 VAW sing 424 n n 
CAP HAP1 VAW sing 425 n n 
CAP HAP2 VAW sing 426 n n 
NAT HAT VAW sing 427 n n 
CAQ HAQ1 VAW sing 428 n n 
CAQ HAQ2 VAW sing 429 n n 
CAS HAS1 VAW sing 430 n n 
CAS HAS2 VAW sing 431 n n 
CBJ HBJ VAW sing 432 n n 
CBH HBH VAW sing 433 n n 
CAH HAH VAW sing 434 n n 
CBK HBK VAW sing 435 n n 
CAA HAA1 VAW sing 436 n n 
CAA HAA2 VAW sing 437 n n 
CAI HAI VAW sing 438 n n 
CAB HAB1 VAW sing 439 n n 
CAB HAB2 VAW sing 440 n n 
CAB HAB3 VAW sing 441 n n 
C1 H1 VAW sing 442 n n 
C2 H2 VAW sing 443 n n 
C5 H5 VAW sing 444 n n 
C6 H6C1 VAW sing 445 n n 
C6 H6C2 VAW sing 446 n n 
C4 H4 VAW sing 447 n n 
O6 H6 VAW sing 448 n n 
O4 HA VAW sing 449 n n 
C3 H3 VAW sing 450 n n 
O3 HB VAW sing 451 n n 
O2 HC VAW sing 452 n n 
#
_atom_sites.entry_id                     2VAQ 
_atom_sites.fract_transf_matrix[1][1]    0.006667 
_atom_sites.fract_transf_matrix[1][2]    0.003849 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007698 
_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]    0.008218 
_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
C 2 VAW A 1 1334 1334 VAW VAW . 
D 2 VAW B 1 1334 1334 VAW VAW . 
E 3 HOH A 1 2001 2001 HOH HOH . 
E 3 HOH A 2 2002 2002 HOH HOH . 
E 3 HOH A 3 2003 2003 HOH HOH . 
E 3 HOH A 4 2004 2004 HOH HOH . 
E 3 HOH A 5 2005 2005 HOH HOH . 
E 3 HOH A 6 2006 2006 HOH HOH . 
E 3 HOH A 7 2007 2007 HOH HOH . 
E 3 HOH A 8 2008 2008 HOH HOH . 
E 3 HOH A 9 2009 2009 HOH HOH . 
E 3 HOH A 10 2010 2010 HOH HOH . 
F 3 HOH B 1 2001 2001 HOH HOH . 
F 3 HOH B 2 2002 2002 HOH HOH . 
F 3 HOH B 3 2003 2003 HOH HOH . 
F 3 HOH B 4 2004 2004 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 CBD VAW . . . D 2 127.932 44.301 8.486 1 81.05 ? CBD VAW 1334 B 1 
HETATM 2 C CAM VAW . . . D 2 127.191 45.386 8.006 1 82.07 ? CAM VAW 1334 B 1 
HETATM 3 C CAK VAW . . . D 2 126.84 46.419 8.887 1 80.54 ? CAK VAW 1334 B 1 
HETATM 4 C CAJ VAW . . . D 2 127.214 46.379 10.239 1 79.15 ? CAJ VAW 1334 B 1 
HETATM 5 C CAL VAW . . . D 2 127.941 45.292 10.723 1 77.41 ? CAL VAW 1334 B 1 
HETATM 6 C CBC VAW . . . D 2 128.292 44.267 9.836 1 80.81 ? CBC VAW 1334 B 1 
HETATM 7 N NAU VAW . . . D 2 128.978 43.142 10.011 1 84.55 ? NAU VAW 1334 B 1 
HETATM 8 C CAN VAW . . . D 2 129.072 42.465 8.859 1 82.48 ? CAN VAW 1334 B 1 
HETATM 9 C CBB VAW . . . D 2 128.454 43.141 7.906 1 79.11 ? CBB VAW 1334 B 1 
HETATM 10 C CAR VAW . . . D 2 128.348 42.653 6.478 1 75.86 ? CAR VAW 1334 B 1 
HETATM 11 C CAP VAW . . . D 2 127.146 41.704 6.366 1 66.81 ? CAP VAW 1334 B 1 
HETATM 12 N NAT VAW . . . D 2 125.971 42.309 6.991 1 54.61 ? NAT VAW 1334 B 1 
HETATM 13 C CAQ VAW . . . D 2 125.136 42.76 5.9 1 55.03 ? CAQ VAW 1334 B 1 
HETATM 14 C CAS VAW . . . D 2 123.72 42.973 6.42 1 62.29 ? CAS VAW 1334 B 1 
HETATM 15 C CBJ VAW . . . D 2 123.528 44.277 7.221 1 63.25 ? CBJ VAW 1334 B 1 
HETATM 16 C CBH VAW . . . D 2 122.746 45.397 6.48 1 64.34 ? CBH VAW 1334 B 1 
HETATM 17 C CAH VAW . . . D 2 123.53 46.009 5.294 1 64.05 ? CAH VAW 1334 B 1 
HETATM 18 C CAA VAW . . . D 2 124.846 46.427 5.49 1 62.88 ? CAA VAW 1334 B 1 
HETATM 19 C CBA VAW . . . D 2 122.678 43.957 8.433 1 63.05 ? CBA VAW 1334 B 1 
HETATM 20 C CAZ VAW . . . D 2 123.34 43.357 9.682 1 67.5 ? CAZ VAW 1334 B 1 
HETATM 21 O OAC VAW . . . D 2 122.696 43.098 10.707 1 66.97 ? OAC VAW 1334 B 1 
HETATM 22 O OAV VAW . . . D 2 124.685 43.128 9.636 1 68.76 ? OAV VAW 1334 B 1 
HETATM 23 C CAB VAW . . . D 2 125.012 41.74 9.548 1 68.31 ? CAB VAW 1334 B 1 
HETATM 24 C CAI VAW . . . D 2 121.31 44.212 8.386 1 63.19 ? CAI VAW 1334 B 1 
HETATM 25 O OAW VAW . . . D 2 120.649 44.747 7.302 1 63.85 ? OAW VAW 1334 B 1 
HETATM 26 C CBK VAW . . . D 2 121.354 44.869 6.069 1 60.51 ? CBK VAW 1334 B 1 
HETATM 27 O O1 VAW . . . D 2 120.607 45.7 5.155 1 56.82 ? O1 VAW 1334 B 1 
HETATM 28 C C1 VAW . . . D 2 119.219 45.352 5.157 1 54.78 ? C1 VAW 1334 B 1 
HETATM 29 O O5 VAW . . . D 2 119.168 44.511 3.997 1 47.54 ? O5 VAW 1334 B 1 
HETATM 30 C C5 VAW . . . D 2 117.894 44.382 3.337 1 54.32 ? C5 VAW 1334 B 1 
HETATM 31 C C6 VAW . . . D 2 118.002 43.291 2.135 1 52.61 ? C6 VAW 1334 B 1 
HETATM 32 O O6 VAW . . . D 2 118.733 43.713 0.934 1 44.71 ? O6 VAW 1334 B 1 
HETATM 33 C C4 VAW . . . D 2 117.365 45.812 3.023 1 57.12 ? C4 VAW 1334 B 1 
HETATM 34 O O4 VAW . . . D 2 116.1 45.783 2.35 1 60.45 ? O4 VAW 1334 B 1 
HETATM 35 C C3 VAW . . . D 2 117.21 46.671 4.282 1 59.62 ? C3 VAW 1334 B 1 
HETATM 36 O O3 VAW . . . D 2 116.868 48.004 3.866 1 61.11 ? O3 VAW 1334 B 1 
HETATM 37 C C2 VAW . . . D 2 118.507 46.725 5.111 1 61.29 ? C2 VAW 1334 B 1 
HETATM 38 O O2 VAW . . . D 2 118.28 47.277 6.447 1 61.48 ? O2 VAW 1334 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           38 
#