data_7WI8
#
_model_server_result.job_id            bqfdAypJDx22wCPSm-dnpw 
_model_server_result.datetime_utc      '2024-11-23 10:05:25' 
_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          7wi8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":902}' 
#
_entry.id    7WI8 
#
_exptl.entry_id    7WI8 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              353.369 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine 
_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         90 
_cell.entry_id            7WI8 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7WI8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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    ? 
_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 D N N 
? 3 F 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 248 A CYS 240 1_555 A SG CYS 535 A CYS 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 A SG CYS 420 A CYS 412 1_555 A SG CYS 427 A CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf3 A SG CYS 517 A CYS 509 1_555 A SG CYS 536 A CYS 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 A SG CYS 521 A CYS 513 1_555 A SG CYS 539 A CYS 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf5 A SG CYS 542 A CYS 534 1_555 A SG CYS 554 A CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 A SG CYS 557 A CYS 549 1_555 A SG CYS 570 A CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 A SG CYS 649 A CYS 641 1_555 A SG CYS 738 A CYS 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf8 B SG CYS 248 B CYS 240 1_555 B SG CYS 535 B CYS 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf9 B SG CYS 420 B CYS 412 1_555 B SG CYS 427 B CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf10 B SG CYS 517 B CYS 509 1_555 B SG CYS 536 B CYS 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf11 B SG CYS 521 B CYS 513 1_555 B SG CYS 539 B CYS 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf12 B SG CYS 542 B CYS 534 1_555 B SG CYS 554 B CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf13 B SG CYS 557 B CYS 549 1_555 B SG CYS 570 B CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf14 B SG CYS 649 B CYS 641 1_555 B SG CYS 738 B CYS 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A ND2 ASN 217 A ASN 209 1_555 C C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale2 B ND2 ASN 217 B ASN 209 1_555 E C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
#
_chem_comp.formula           'C20 H19 N O5' 
_chem_comp.formula_weight    353.369 
_chem_comp.id                Z99 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(1S,2S)-2-[(2S)-2-amino-1-hydroxy-1-oxo-3-(9H-xanthen-9-yl)propan-2-yl]cyclopropane-1-carboxylic acid' 
#
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
NAA CAY Z99 sing 404 n n 
NAA HNAA Z99 sing 405 n n 
NAA HNAB Z99 sing 406 n n 
OAB CAQ Z99 doub 407 n n 
CAR OAC Z99 sing 408 n n 
OAC HOAC Z99 sing 409 n n 
CAQ OAD Z99 sing 410 n n 
OAD HOAD Z99 sing 411 n n 
OAE CAR Z99 doub 412 n n 
CAH CAF Z99 doub 413 n y 
CAF CAJ Z99 sing 414 n y 
CAF HAF Z99 sing 415 n n 
CAI CAG Z99 doub 416 n y 
CAG CAK Z99 sing 417 n y 
CAG HAG Z99 sing 418 n n 
CAL CAH Z99 sing 419 n y 
CAH HAH Z99 sing 420 n n 
CAM CAI Z99 sing 421 n y 
CAI HAI Z99 sing 422 n n 
CAS CAJ Z99 doub 423 n y 
CAJ HAJ Z99 sing 424 n n 
CAT CAK Z99 doub 425 n y 
CAK HAK Z99 sing 426 n n 
CAL CAU Z99 doub 427 n y 
CAL HAL Z99 sing 428 n n 
CAM CAV Z99 doub 429 n y 
CAM HAM Z99 sing 430 n n 
CAY CAN Z99 sing 431 n n 
CAN CAW Z99 sing 432 n n 
CAN HAN Z99 sing 433 n n 
CAN HANA Z99 sing 434 n n 
CAZ CAO Z99 sing 435 n n 
CAO CAX Z99 sing 436 n n 
CAO HAO Z99 sing 437 n n 
CAO HAOA Z99 sing 438 n n 
CAS OAP Z99 sing 439 n n 
CAT OAP Z99 sing 440 n n 
CAQ CAX Z99 sing 441 n n 
CAY CAR Z99 sing 442 n n 
CAU CAS Z99 sing 443 n y 
CAV CAT Z99 sing 444 n y 
CAW CAU Z99 sing 445 n n 
CAW CAV Z99 sing 446 n n 
CAW HAW Z99 sing 447 n n 
CAZ CAX Z99 sing 448 n n 
CAX HAX Z99 sing 449 n n 
CAZ CAY Z99 sing 450 n n 
CAZ HAZ Z99 sing 451 n n 
#
_atom_sites.entry_id                     7WI8 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 NAG A 1 901 901 NAG NAG . 
D 3 Z99 A 1 902 487 Z99 Z99 . 
E 2 NAG B 1 901 901 NAG NAG . 
F 3 Z99 B 1 902 488 Z99 Z99 . 
#
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 N NAA Z99 . . . D 3 182.977 162.477 91.727 1 57.1 ? NAA Z99 902 A 1 
HETATM 2 O OAB Z99 . . . D 3 186.439 164.811 89.05 1 57.1 ? OAB Z99 902 A 1 
HETATM 3 O OAC Z99 . . . D 3 182.703 165.77 90.525 1 57.1 ? OAC Z99 902 A 1 
HETATM 4 O OAD Z99 . . . D 3 185.597 163.406 87.609 1 57.1 ? OAD Z99 902 A 1 
HETATM 5 O OAE Z99 . . . D 3 181.122 164.405 91.1 1 57.1 ? OAE Z99 902 A 1 
HETATM 6 C CAF Z99 . . . D 3 186.448 167.021 96.312 1 57.1 ? CAF Z99 902 A 1 
HETATM 7 C CAG Z99 . . . D 3 179.381 166.251 95.655 1 57.1 ? CAG Z99 902 A 1 
HETATM 8 C CAH Z99 . . . D 3 186.667 165.986 95.412 1 57.1 ? CAH Z99 902 A 1 
HETATM 9 C CAI Z99 . . . D 3 179.575 165.21 94.764 1 57.1 ? CAI Z99 902 A 1 
HETATM 10 C CAJ Z99 . . . D 3 185.205 167.623 96.377 1 57.1 ? CAJ Z99 902 A 1 
HETATM 11 C CAK Z99 . . . D 3 180.435 167.105 95.92 1 57.1 ? CAK Z99 902 A 1 
HETATM 12 C CAL Z99 . . . D 3 185.641 165.551 94.582 1 57.1 ? CAL Z99 902 A 1 
HETATM 13 C CAM Z99 . . . D 3 180.799 165.016 94.142 1 57.1 ? CAM Z99 902 A 1 
HETATM 14 C CAN Z99 . . . D 3 183.445 164.185 93.369 1 57.1 ? CAN Z99 902 A 1 
HETATM 15 C CAO Z99 . . . D 3 185.557 162.838 91.125 1 57.1 ? CAO Z99 902 A 1 
HETATM 16 O OAP Z99 . . . D 3 182.822 167.801 95.573 1 57.1 ? OAP Z99 902 A 1 
HETATM 17 C CAQ Z99 . . . D 3 185.655 163.863 88.779 1 57.1 ? CAQ Z99 902 A 1 
HETATM 18 C CAR Z99 . . . D 3 182.333 164.735 91.135 1 57.1 ? CAR Z99 902 A 1 
HETATM 19 C CAS Z99 . . . D 3 184.172 167.185 95.537 1 57.1 ? CAS Z99 902 A 1 
HETATM 20 C CAT Z99 . . . D 3 181.672 166.909 95.288 1 57.1 ? CAT Z99 902 A 1 
HETATM 21 C CAU Z99 . . . D 3 184.382 166.16 94.652 1 57.1 ? CAU Z99 902 A 1 
HETATM 22 C CAV Z99 . . . D 3 181.855 165.879 94.409 1 57.1 ? CAV Z99 902 A 1 
HETATM 23 C CAW Z99 . . . D 3 183.219 165.729 93.771 1 57.1 ? CAW Z99 902 A 1 
HETATM 24 C CAX Z99 . . . D 3 184.784 163.255 89.876 1 57.1 ? CAX Z99 902 A 1 
HETATM 25 C CAY Z99 . . . D 3 183.341 163.877 91.865 1 57.1 ? CAY Z99 902 A 1 
HETATM 26 C CAZ Z99 . . . D 3 184.671 164.078 91.159 1 57.1 ? CAZ Z99 902 A 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           354 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           26 
#