data_5VDI
#
_model_server_result.job_id            EnHwQEulGCyFl7tI-SNdFA 
_model_server_result.datetime_utc      '2024-11-16 19:04:02' 
_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          5vdi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":402}' 
#
_entry.id    5VDI 
#
_exptl.entry_id    5VDI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              75.067 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCINE 
_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            5VDI 
_cell.length_a            136.006 
_cell.length_b            136 
_cell.length_c            191.635 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VDI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_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
? 3 G N N 
? 3 K N N 
? 3 O N N 
? 3 S N N 
? 3 W 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 138 A CYS 138 1_555 A SG CYS 152 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf2 A SG CYS 198 A CYS 198 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf3 B SG CYS 138 B CYS 138 1_555 B SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf4 B SG CYS 198 B CYS 198 1_555 B SG CYS 209 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf5 C SG CYS 138 C CYS 138 1_555 C SG CYS 152 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf6 C SG CYS 198 C CYS 198 1_555 C SG CYS 209 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf7 D SG CYS 138 D CYS 138 1_555 D SG CYS 152 D CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf8 D SG CYS 198 D CYS 198 1_555 D SG CYS 209 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf9 E SG CYS 138 E CYS 138 1_555 E SG CYS 152 E CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf10 E SG CYS 198 E CYS 198 1_555 E SG CYS 209 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc1 C OE2 GLU 192 C GLU 192 1_555 Q ZN ZN . C ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc2 C NE2 HIS 215 C HIS 215 1_555 Q ZN ZN . C ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? 
metalc ? metalc3 E OE2 GLU 192 E GLU 192 1_555 Y ZN ZN . E ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc4 E OD1 ASP 194 E ASP 194 1_555 Y ZN ZN . E ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
#
_chem_comp.formula           'C2 H5 N O2' 
_chem_comp.formula_weight    75.067 
_chem_comp.id                GLY 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              GLYCINE 
_chem_comp.type              'peptide linking' 
_chem_comp.pdbx_synonyms     ? 
#
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
N CA GLY sing 171 n n 
N H GLY sing 172 n n 
N H2 GLY sing 173 n n 
CA C GLY sing 174 n n 
CA HA2 GLY sing 175 n n 
CA HA3 GLY sing 176 n n 
C O GLY doub 177 n n 
C OXT GLY sing 178 n n 
OXT HXT GLY sing 179 n n 
#
_atom_sites.entry_id                     5VDI 
_atom_sites.fract_transf_matrix[1][1]    0.007353 
_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]    0.007353 
_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]    0.005218 
_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 7C6 A 1 401 401 7C6 7C6 . 
G 3 GLY A 1 402 402 GLY GLY . 
H 4 IVM A 1 403 403 IVM IVM . 
I 5 ZN A 1 404 404 ZN ZN . 
J 2 7C6 B 1 401 401 7C6 7C6 . 
K 3 GLY B 1 402 402 GLY GLY . 
L 4 IVM B 1 403 403 IVM IVM . 
M 5 ZN B 1 404 404 ZN ZN . 
N 2 7C6 C 1 401 401 7C6 7C6 . 
O 3 GLY C 1 402 402 GLY GLY . 
P 4 IVM C 1 403 403 IVM IVM . 
Q 5 ZN C 1 404 404 ZN ZN . 
R 2 7C6 D 1 401 401 7C6 7C6 . 
S 3 GLY D 1 402 402 GLY GLY . 
T 4 IVM D 1 403 403 IVM IVM . 
U 5 ZN D 1 404 404 ZN ZN . 
V 2 7C6 E 1 401 401 7C6 7C6 . 
W 3 GLY E 1 402 402 GLY GLY . 
X 4 IVM E 1 403 403 IVM IVM . 
Y 5 ZN E 1 404 404 ZN ZN . 
Z 6 HOH A 1 501 501 HOH HOH . 
Z 6 HOH A 2 502 502 HOH HOH . 
Z 6 HOH A 3 503 503 HOH HOH . 
Z 6 HOH A 4 504 504 HOH HOH . 
Z 6 HOH A 5 505 505 HOH HOH . 
Z 6 HOH A 6 506 506 HOH HOH . 
Z 6 HOH A 7 507 507 HOH HOH . 
Z 6 HOH A 8 508 508 HOH HOH . 
Z 6 HOH A 9 509 509 HOH HOH . 
Z 6 HOH A 10 510 510 HOH HOH . 
Z 6 HOH A 11 511 511 HOH HOH . 
Z 6 HOH A 12 512 512 HOH HOH . 
Z 6 HOH A 13 513 513 HOH HOH . 
Z 6 HOH A 14 514 514 HOH HOH . 
Z 6 HOH A 15 515 515 HOH HOH . 
Z 6 HOH A 16 516 516 HOH HOH . 
Z 6 HOH A 17 517 517 HOH HOH . 
Z 6 HOH A 18 518 518 HOH HOH . 
Z 6 HOH A 19 519 519 HOH HOH . 
Z 6 HOH A 20 520 520 HOH HOH . 
Z 6 HOH A 21 521 521 HOH HOH . 
Z 6 HOH A 22 522 522 HOH HOH . 
Z 6 HOH A 23 523 523 HOH HOH . 
Z 6 HOH A 24 524 524 HOH HOH . 
Z 6 HOH A 25 525 525 HOH HOH . 
AA 6 HOH B 1 501 501 HOH HOH . 
AA 6 HOH B 2 502 502 HOH HOH . 
AA 6 HOH B 3 503 503 HOH HOH . 
AA 6 HOH B 4 504 504 HOH HOH . 
AA 6 HOH B 5 505 505 HOH HOH . 
AA 6 HOH B 6 506 506 HOH HOH . 
AA 6 HOH B 7 507 507 HOH HOH . 
AA 6 HOH B 8 508 508 HOH HOH . 
AA 6 HOH B 9 509 509 HOH HOH . 
AA 6 HOH B 10 510 510 HOH HOH . 
AA 6 HOH B 11 511 511 HOH HOH . 
AA 6 HOH B 12 512 512 HOH HOH . 
AA 6 HOH B 13 513 513 HOH HOH . 
AA 6 HOH B 14 514 514 HOH HOH . 
AA 6 HOH B 15 515 515 HOH HOH . 
AA 6 HOH B 16 516 516 HOH HOH . 
AA 6 HOH B 17 517 517 HOH HOH . 
AA 6 HOH B 18 518 518 HOH HOH . 
AA 6 HOH B 19 519 519 HOH HOH . 
AA 6 HOH B 20 520 520 HOH HOH . 
AA 6 HOH B 21 521 521 HOH HOH . 
AA 6 HOH B 22 522 522 HOH HOH . 
AA 6 HOH B 23 523 523 HOH HOH . 
BA 6 HOH C 1 601 601 HOH HOH . 
BA 6 HOH C 2 602 602 HOH HOH . 
BA 6 HOH C 3 603 603 HOH HOH . 
BA 6 HOH C 4 604 604 HOH HOH . 
BA 6 HOH C 5 605 605 HOH HOH . 
BA 6 HOH C 6 606 606 HOH HOH . 
BA 6 HOH C 7 607 607 HOH HOH . 
BA 6 HOH C 8 608 608 HOH HOH . 
BA 6 HOH C 9 609 609 HOH HOH . 
BA 6 HOH C 10 610 610 HOH HOH . 
BA 6 HOH C 11 611 611 HOH HOH . 
BA 6 HOH C 12 612 612 HOH HOH . 
BA 6 HOH C 13 613 613 HOH HOH . 
BA 6 HOH C 14 614 614 HOH HOH . 
BA 6 HOH C 15 615 615 HOH HOH . 
BA 6 HOH C 16 616 616 HOH HOH . 
BA 6 HOH C 17 617 617 HOH HOH . 
BA 6 HOH C 18 618 618 HOH HOH . 
BA 6 HOH C 19 619 619 HOH HOH . 
BA 6 HOH C 20 620 620 HOH HOH . 
BA 6 HOH C 21 621 621 HOH HOH . 
BA 6 HOH C 22 622 622 HOH HOH . 
BA 6 HOH C 23 623 623 HOH HOH . 
BA 6 HOH C 24 624 624 HOH HOH . 
BA 6 HOH C 25 625 625 HOH HOH . 
BA 6 HOH C 26 626 626 HOH HOH . 
BA 6 HOH C 27 627 627 HOH HOH . 
BA 6 HOH C 28 628 628 HOH HOH . 
BA 6 HOH C 29 629 629 HOH HOH . 
BA 6 HOH C 30 630 630 HOH HOH . 
BA 6 HOH C 31 631 631 HOH HOH . 
CA 6 HOH D 1 501 501 HOH HOH . 
CA 6 HOH D 2 502 502 HOH HOH . 
CA 6 HOH D 3 503 503 HOH HOH . 
CA 6 HOH D 4 504 504 HOH HOH . 
CA 6 HOH D 5 505 505 HOH HOH . 
CA 6 HOH D 6 506 506 HOH HOH . 
CA 6 HOH D 7 507 507 HOH HOH . 
CA 6 HOH D 8 508 508 HOH HOH . 
CA 6 HOH D 9 509 509 HOH HOH . 
CA 6 HOH D 10 510 510 HOH HOH . 
CA 6 HOH D 11 511 511 HOH HOH . 
CA 6 HOH D 12 512 512 HOH HOH . 
CA 6 HOH D 13 513 513 HOH HOH . 
CA 6 HOH D 14 514 514 HOH HOH . 
CA 6 HOH D 15 515 515 HOH HOH . 
CA 6 HOH D 16 516 516 HOH HOH . 
CA 6 HOH D 17 517 517 HOH HOH . 
CA 6 HOH D 18 518 518 HOH HOH . 
CA 6 HOH D 19 519 519 HOH HOH . 
CA 6 HOH D 20 520 520 HOH HOH . 
DA 6 HOH E 1 501 501 HOH HOH . 
DA 6 HOH E 2 502 502 HOH HOH . 
DA 6 HOH E 3 503 503 HOH HOH . 
DA 6 HOH E 4 504 504 HOH HOH . 
DA 6 HOH E 5 505 505 HOH HOH . 
DA 6 HOH E 6 506 506 HOH HOH . 
DA 6 HOH E 7 507 507 HOH HOH . 
DA 6 HOH E 8 508 508 HOH HOH . 
DA 6 HOH E 9 509 509 HOH HOH . 
DA 6 HOH E 10 510 510 HOH HOH . 
DA 6 HOH E 11 511 511 HOH HOH . 
DA 6 HOH E 12 512 512 HOH HOH . 
DA 6 HOH E 13 513 513 HOH HOH . 
DA 6 HOH E 14 514 514 HOH HOH . 
DA 6 HOH E 15 515 515 HOH HOH . 
DA 6 HOH E 16 516 516 HOH HOH . 
DA 6 HOH E 17 517 517 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 N N GLY . . . O 3 -22.734 -52.908 28.471 1 52.78 ? N GLY 402 C 1 
HETATM 2 C CA GLY . . . O 3 -23.948 -53.612 27.94 1 52.69 ? CA GLY 402 C 1 
HETATM 3 C C GLY . . . O 3 -25.019 -53.889 28.977 1 53.12 ? C GLY 402 C 1 
HETATM 4 O O GLY . . . O 3 -26.096 -53.313 28.905 1 52.76 ? O GLY 402 C 1 
HETATM 5 O OXT GLY . . . O 3 -24.852 -54.691 29.897 1 53.89 ? OXT GLY 402 C 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           244 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           5 
#