data_2VGB
#
_model_server_result.job_id            IiggwPgbJONQ_dHwJazd4A 
_model_server_result.datetime_utc      '2024-11-08 08:37:37' 
_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          2vgb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":581}' 
#
_entry.id    2VGB 
#
_exptl.entry_id    2VGB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              156.031 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            '2-PHOSPHOGLYCOLIC ACID' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          92.46 
_cell.angle_gamma         90 
_cell.entry_id            2VGB 
_cell.length_a            74.413 
_cell.length_b            172.058 
_cell.length_c            85.512 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VGB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 F N N 
? 3 J N N 
? 3 N N N 
? 3 R 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
metalc ? metalc1 A OD1 ASN 72 A ASN 118 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? 
metalc ? metalc2 A OG SER 74 A SER 120 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.442 ? 
metalc ? metalc3 A OD1 ASP 110 A ASP 156 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? 
metalc ? metalc4 A O THR 111 A THR 157 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? 
metalc ? metalc5 A OE2 GLU 269 A GLU 315 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? 
metalc ? metalc6 A OD2 ASP 293 A ASP 339 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? 
metalc ? metalc7 F O2P PGA . A PGA 581 1_555 G K K . A K 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? 
metalc ? metalc8 F O1P PGA . A PGA 581 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc9 F O2 PGA . A PGA 581 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc10 F O4P PGA . A PGA 581 1_555 H MN MN . A MN 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc11 B OD1 ASN 72 B ASN 118 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.208 ? 
metalc ? metalc12 B OD1 ASP 110 B ASP 156 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc13 B O THR 111 B THR 157 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc14 B OE2 GLU 269 B GLU 315 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? 
metalc ? metalc15 B OD2 ASP 293 B ASP 339 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? 
metalc ? metalc16 J O2P PGA . B PGA 581 1_555 K K K . B K 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? 
metalc ? metalc17 J O1 PGA . B PGA 581 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc18 J O4P PGA . B PGA 581 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? 
metalc ? metalc19 J O1P PGA . B PGA 581 1_555 L MN MN . B MN 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc20 C OD1 ASN 72 C ASN 118 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? 
metalc ? metalc21 C OD1 ASP 110 C ASP 156 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? 
metalc ? metalc22 C O THR 111 C THR 157 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc23 C OE2 GLU 269 C GLU 315 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.567 ? 
metalc ? metalc24 C OD2 ASP 293 C ASP 339 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.72 ? 
metalc ? metalc25 N O2P PGA . C PGA 581 1_555 O K K . C K 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.968 ? 
metalc ? metalc26 N O1 PGA . C PGA 581 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc27 N O4P PGA . C PGA 581 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc28 N O1P PGA . C PGA 581 1_555 P MN MN . C MN 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc29 D OD1 ASN 72 D ASN 118 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
metalc ? metalc30 D OD1 ASP 110 D ASP 156 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc31 D O THR 111 D THR 157 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.036 ? 
metalc ? metalc32 D OE2 GLU 269 D GLU 315 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? 
metalc ? metalc33 D OD2 ASP 293 D ASP 339 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? 
metalc ? metalc34 R O2P PGA . D PGA 581 1_555 S K K . D K 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? 
metalc ? metalc35 R O2 PGA . D PGA 581 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? 
metalc ? metalc36 R O1P PGA . D PGA 581 1_555 T MN MN . D MN 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
#
_chem_comp.formula           'C2 H5 O6 P' 
_chem_comp.formula_weight    156.031 
_chem_comp.id                PGA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '2-PHOSPHOGLYCOLIC ACID' 
_chem_comp.type              non-polymer 
_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
P O1P PGA sing 271 n n 
P O2P PGA doub 272 n n 
P O3P PGA sing 273 n n 
P O4P PGA sing 274 n n 
O1P C2 PGA sing 275 n n 
O3P HOP3 PGA sing 276 n n 
O4P HOP4 PGA sing 277 n n 
C2 C1 PGA sing 278 n n 
C2 H21 PGA sing 279 n n 
C2 H22 PGA sing 280 n n 
C1 O1 PGA doub 281 n n 
C1 O2 PGA sing 282 n n 
O2 HO2 PGA sing 283 n n 
#
_atom_sites.entry_id                     2VGB 
_atom_sites.fract_transf_matrix[1][1]    0.013439 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000577 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005812 
_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]    0.011705 
_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
E 2 FBP A 1 580 580 FBP FBP . 
F 3 PGA A 1 581 581 PGA PGA . 
G 4 K A 1 582 582 K K . 
H 5 MN A 1 583 583 MN MN . 
I 2 FBP B 1 580 580 FBP FBP . 
J 3 PGA B 1 581 581 PGA PGA . 
K 4 K B 1 586 586 K K . 
L 5 MN B 1 587 587 MN MN . 
M 2 FBP C 1 580 580 FBP FBP . 
N 3 PGA C 1 581 581 PGA PGA . 
O 4 K C 1 590 590 K K . 
P 5 MN C 1 591 591 MN MN . 
Q 2 FBP D 1 580 580 FBP FBP . 
R 3 PGA D 1 581 581 PGA PGA . 
S 4 K D 1 594 594 K K . 
T 5 MN D 1 595 595 MN MN . 
U 6 HOH A 1 2001 2001 HOH HOH . 
U 6 HOH A 2 2002 2002 HOH HOH . 
U 6 HOH A 3 2003 2003 HOH HOH . 
U 6 HOH A 4 2004 2004 HOH HOH . 
U 6 HOH A 5 2005 2005 HOH HOH . 
U 6 HOH A 6 2006 2006 HOH HOH . 
U 6 HOH A 7 2007 2007 HOH HOH . 
U 6 HOH A 8 2008 2008 HOH HOH . 
U 6 HOH A 9 2009 2009 HOH HOH . 
U 6 HOH A 10 2010 2010 HOH HOH . 
U 6 HOH A 11 2011 2011 HOH HOH . 
U 6 HOH A 12 2012 2012 HOH HOH . 
V 6 HOH B 1 2001 2001 HOH HOH . 
V 6 HOH B 2 2002 2002 HOH HOH . 
V 6 HOH B 3 2003 2003 HOH HOH . 
V 6 HOH B 4 2004 2004 HOH HOH . 
V 6 HOH B 5 2005 2005 HOH HOH . 
V 6 HOH B 6 2006 2006 HOH HOH . 
V 6 HOH B 7 2007 2007 HOH HOH . 
V 6 HOH B 8 2008 2008 HOH HOH . 
V 6 HOH B 9 2009 2009 HOH HOH . 
V 6 HOH B 10 2010 2010 HOH HOH . 
V 6 HOH B 11 2011 2011 HOH HOH . 
V 6 HOH B 12 2012 2012 HOH HOH . 
V 6 HOH B 13 2013 2013 HOH HOH . 
V 6 HOH B 14 2014 2014 HOH HOH . 
V 6 HOH B 15 2015 2015 HOH HOH . 
V 6 HOH B 16 2016 2016 HOH HOH . 
W 6 HOH C 1 2001 2001 HOH HOH . 
W 6 HOH C 2 2002 2002 HOH HOH . 
W 6 HOH C 3 2003 2003 HOH HOH . 
W 6 HOH C 4 2004 2004 HOH HOH . 
W 6 HOH C 5 2005 2005 HOH HOH . 
W 6 HOH C 6 2006 2006 HOH HOH . 
W 6 HOH C 7 2007 2007 HOH HOH . 
W 6 HOH C 8 2008 2008 HOH HOH . 
W 6 HOH C 9 2009 2009 HOH HOH . 
W 6 HOH C 10 2010 2010 HOH HOH . 
W 6 HOH C 11 2011 2011 HOH HOH . 
W 6 HOH C 12 2012 2012 HOH HOH . 
W 6 HOH C 13 2013 2013 HOH HOH . 
W 6 HOH C 14 2014 2014 HOH HOH . 
W 6 HOH C 15 2015 2015 HOH HOH . 
W 6 HOH C 16 2016 2016 HOH HOH . 
W 6 HOH C 17 2017 2017 HOH HOH . 
W 6 HOH C 18 2018 2018 HOH HOH . 
W 6 HOH C 19 2019 2019 HOH HOH . 
W 6 HOH C 20 2020 2020 HOH HOH . 
X 6 HOH D 1 2001 2001 HOH HOH . 
X 6 HOH D 2 2002 2002 HOH HOH . 
X 6 HOH D 3 2003 2003 HOH HOH . 
X 6 HOH D 4 2004 2004 HOH HOH . 
X 6 HOH D 5 2005 2005 HOH HOH . 
X 6 HOH D 6 2006 2006 HOH HOH . 
X 6 HOH D 7 2007 2007 HOH HOH . 
X 6 HOH D 8 2008 2008 HOH HOH . 
X 6 HOH D 9 2009 2009 HOH HOH . 
X 6 HOH D 10 2010 2010 HOH HOH . 
X 6 HOH D 11 2011 2011 HOH HOH . 
X 6 HOH D 12 2012 2012 HOH HOH . 
X 6 HOH D 13 2013 2013 HOH HOH . 
X 6 HOH D 14 2014 2014 HOH HOH . 
X 6 HOH D 15 2015 2015 HOH HOH . 
X 6 HOH D 16 2016 2016 HOH HOH . 
X 6 HOH D 17 2017 2017 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 P P PGA . . . F 3 39.702 7.601 36.815 1 104.89 ? P PGA 581 A 1 
HETATM 2 O O1P PGA . . . F 3 39.047 7.015 35.478 1 107.06 ? O1P PGA 581 A 1 
HETATM 3 O O2P PGA . . . F 3 40.715 6.619 37.326 1 106.3 ? O2P PGA 581 A 1 
HETATM 4 O O3P PGA . . . F 3 38.633 7.77 37.85 1 106.94 ? O3P PGA 581 A 1 
HETATM 5 O O4P PGA . . . F 3 40.373 8.918 36.532 1 106.47 ? O4P PGA 581 A 1 
HETATM 6 C C2 PGA . . . F 3 37.657 6.872 35.379 1 107.65 ? C2 PGA 581 A 1 
HETATM 7 C C1 PGA . . . F 3 37.123 8.221 35.018 1 107.78 ? C1 PGA 581 A 1 
HETATM 8 O O1 PGA . . . F 3 35.979 8.555 35.348 1 107.74 ? O1 PGA 581 A 1 
HETATM 9 O O2 PGA . . . F 3 37.828 9.019 34.383 1 108.38 ? O2 PGA 581 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           9 
#