data_MD_SNFG
#
_pdbx_database_status.entry_id MD_SNFG
_pdbx_database_status.status_code .
_pdbx_database_status.status_code_sf ?
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.recvd_initial_deposition_date ?
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.deposit_site ?
_pdbx_database_status.process_site ?
_pdbx_database_status.SG_entry ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.methods_development_category ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 branched man "2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose" 383.349 1 ? ? ? ?
2 non-polymer syn ? ? 1 ? ? ? ?
3 non-polymer syn "1-(2,4-dihydroxyphenyl)-1,3-dihydro-2H-benzimidazol-2-one" 242.230 1 ? ? ? ?
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_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_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 ROH 1 1 1 ROH ROH ? .
C 3 MEX 1 4 4 MEX MEX ? .
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
GAL "D-saccharide, beta linking" . beta-D-galactopyranose "beta-D-galactose; D-galactose; galactose" "C6 H12 O6" 180.156
MEX non-polymer . "1-(2,4-dihydroxyphenyl)-1,3-dihydro-2H-benzimidazol-2-one" ? "C13 H10 N2 O3" 242.230
NGA "D-saccharide, beta linking" . 2-acetamido-2-deoxy-beta-D-galactopyranose
"N-acetyl-beta-D-galactosamine; 2-acetamido-2-deoxy-beta-D-galactose; 2-acetamido-2-deoxy-D-galactose; 2-acetamido-2-deoxy-galactose; N-ACETYL-D-GALACTOSAMINE" "C8 H15 N O6" 221.208
ROH non-polymer . "UNKNOWN LIGAND" ? ? ?
#
_struct_conn.id covale1
_struct_conn.conn_type_id covale
_struct_conn.pdbx_leaving_atom_flag both
_struct_conn.pdbx_PDB_id ?
_struct_conn.ptnr1_label_asym_id A
_struct_conn.ptnr1_label_comp_id GAL
_struct_conn.ptnr1_label_seq_id .
_struct_conn.ptnr1_label_atom_id O4
_struct_conn.pdbx_ptnr1_label_alt_id ?
_struct_conn.pdbx_ptnr1_PDB_ins_code ?
_struct_conn.pdbx_ptnr1_standard_comp_id ?
_struct_conn.ptnr1_symmetry 1_555
_struct_conn.ptnr2_label_asym_id A
_struct_conn.ptnr2_label_comp_id NGA
_struct_conn.ptnr2_label_seq_id .
_struct_conn.ptnr2_label_atom_id C1
_struct_conn.pdbx_ptnr2_label_alt_id ?
_struct_conn.pdbx_ptnr2_PDB_ins_code ?
_struct_conn.ptnr1_auth_asym_id ?
_struct_conn.ptnr1_auth_comp_id GAL
_struct_conn.ptnr1_auth_seq_id 1
_struct_conn.ptnr2_auth_asym_id ?
_struct_conn.ptnr2_auth_comp_id NGA
_struct_conn.ptnr2_auth_seq_id 2
_struct_conn.ptnr2_symmetry 1_555
_struct_conn.pdbx_ptnr3_label_atom_id ?
_struct_conn.pdbx_ptnr3_label_seq_id ?
_struct_conn.pdbx_ptnr3_label_comp_id ?
_struct_conn.pdbx_ptnr3_label_asym_id ?
_struct_conn.pdbx_ptnr3_label_alt_id ?
_struct_conn.pdbx_ptnr3_PDB_ins_code ?
_struct_conn.details ?
_struct_conn.pdbx_dist_value 1.482
_struct_conn.pdbx_value_order sing
_struct_conn.pdbx_role ?
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
C N N 3 ?
#
_atom_sites.entry_id MD_SNFG
_atom_sites.fract_transf_matrix[1][1] 1.000000
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 1.000000
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 1.000000
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
#
loop_
_pdbx_validate_close_contact.id
_pdbx_validate_close_contact.PDB_model_num
_pdbx_validate_close_contact.auth_atom_id_1
_pdbx_validate_close_contact.auth_asym_id_1
_pdbx_validate_close_contact.auth_comp_id_1
_pdbx_validate_close_contact.auth_seq_id_1
_pdbx_validate_close_contact.PDB_ins_code_1
_pdbx_validate_close_contact.label_alt_id_1
_pdbx_validate_close_contact.auth_atom_id_2
_pdbx_validate_close_contact.auth_asym_id_2
_pdbx_validate_close_contact.auth_comp_id_2
_pdbx_validate_close_contact.auth_seq_id_2
_pdbx_validate_close_contact.PDB_ins_code_2
_pdbx_validate_close_contact.label_alt_id_2
_pdbx_validate_close_contact.dist
1 1 O1 . ROH 1 ? ? C1 . GAL 1 ? ? 1.41
2 1 O6 . NGA 2 ? ? CH3 . MEX 4 ? ? 1.47
#
loop_
_pdbx_unobs_or_zero_occ_atoms.id
_pdbx_unobs_or_zero_occ_atoms.PDB_model_num
_pdbx_unobs_or_zero_occ_atoms.polymer_flag
_pdbx_unobs_or_zero_occ_atoms.occupancy_flag
_pdbx_unobs_or_zero_occ_atoms.auth_asym_id
_pdbx_unobs_or_zero_occ_atoms.auth_comp_id
_pdbx_unobs_or_zero_occ_atoms.auth_seq_id
_pdbx_unobs_or_zero_occ_atoms.PDB_ins_code
_pdbx_unobs_or_zero_occ_atoms.auth_atom_id
_pdbx_unobs_or_zero_occ_atoms.label_alt_id
_pdbx_unobs_or_zero_occ_atoms.label_asym_id
_pdbx_unobs_or_zero_occ_atoms.label_comp_id
_pdbx_unobs_or_zero_occ_atoms.label_seq_id
_pdbx_unobs_or_zero_occ_atoms.label_atom_id
1 1 N 1 . GAL 1 ? O1 ? A GAL 1 O1
2 1 N 1 . NGA 2 ? C7 ? A NGA 2 C7
3 1 N 1 . NGA 2 ? C8 ? A NGA 2 C8
4 1 N 1 . NGA 2 ? O7 ? A NGA 2 O7
5 1 N 1 . MEX 4 ? C1 ? C MEX 1 C1
6 1 N 1 . MEX 4 ? C2 ? C MEX 1 C2
7 1 N 1 . MEX 4 ? C3 ? C MEX 1 C3
8 1 N 1 . MEX 4 ? C4 ? C MEX 1 C4
9 1 N 1 . MEX 4 ? C5 ? C MEX 1 C5
10 1 N 1 . MEX 4 ? C6 ? C MEX 1 C6
11 1 N 1 . MEX 4 ? O7 ? C MEX 1 O7
12 1 N 1 . MEX 4 ? O8 ? C MEX 1 O8
13 1 N 1 . MEX 4 ? N9 ? C MEX 1 N9
14 1 N 1 . MEX 4 ? C10 ? C MEX 1 C10
15 1 N 1 . MEX 4 ? C11 ? C MEX 1 C11
16 1 N 1 . MEX 4 ? N12 ? C MEX 1 N12
17 1 N 1 . MEX 4 ? C13 ? C MEX 1 C13
18 1 N 1 . MEX 4 ? C14 ? C MEX 1 C14
19 1 N 1 . MEX 4 ? C15 ? C MEX 1 C15
20 1 N 1 . MEX 4 ? C16 ? C MEX 1 C16
21 1 N 1 . MEX 4 ? C17 ? C MEX 1 C17
22 1 N 1 . MEX 4 ? O18 ? C MEX 1 O18
#
loop_
_atom_type.symbol
C
H
N
O
#
_entry.id MD_SNFG
#
loop_
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_mon_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.hetero
A 1 GAL 1 . GAL 1 ? GAL 2 n
A 1 NGA 2 . NGA 2 ? NGA 3 n
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
GAL "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGalpb
GAL "COMMON NAME" GMML 1.0 b-D-galactopyranose
GAL "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-Galp
GAL "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Gal
NGA "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGalpNAcb
NGA "COMMON NAME" GMML 1.0 N-acetyl-b-D-galactopyranosamine
NGA "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-GalpNAc
NGA "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 GalNAc
#
_pdbx_entity_branch.entity_id 1
_pdbx_entity_branch.type oligosaccharide
#
_pdbx_entity_branch_descriptor.ordinal 1
_pdbx_entity_branch_descriptor.entity_id 1
_pdbx_entity_branch_descriptor.descriptor DGalpNAcb1-4DGalpb1-ROH
_pdbx_entity_branch_descriptor.type "Glycam Condensed Sequence"
_pdbx_entity_branch_descriptor.program GMML
_pdbx_entity_branch_descriptor.program_version 1.0
#
_pdbx_entity_branch_link.link_id 1
_pdbx_entity_branch_link.entity_id 1
_pdbx_entity_branch_link.entity_branch_list_num_1 2
_pdbx_entity_branch_link.comp_id_1 NGA
_pdbx_entity_branch_link.atom_id_1 C1
_pdbx_entity_branch_link.leaving_atom_id_1 O1
_pdbx_entity_branch_link.entity_branch_list_num_2 1
_pdbx_entity_branch_link.comp_id_2 GAL
_pdbx_entity_branch_link.atom_id_2 O4
_pdbx_entity_branch_link.leaving_atom_id_2 HO4
_pdbx_entity_branch_link.value_order sing
_pdbx_entity_branch_link.details ?
#
loop_
_pdbx_entity_branch_list.entity_id
_pdbx_entity_branch_list.comp_id
_pdbx_entity_branch_list.num
_pdbx_entity_branch_list.hetero
1 GAL 1 n
1 NGA 2 n
#
loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2 ? ROH
3 "1-(2,4-dihydroxyphenyl)-1,3-dihydro-2H-benzimidazol-2-one" MEX
#
_struct_conn_type.id covale
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_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_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C1 . GAL A 1 . ? 12.960 10.310 22.660 1.00 0.00 ? 1 GAL ? C1 1
HETATM 2 C C2 . GAL A 1 . ? 12.520 11.080 21.450 1.00 0.00 ? 1 GAL ? C2 1
HETATM 3 C C3 . GAL A 1 . ? 13.070 12.520 21.500 1.00 0.00 ? 1 GAL ? C3 1
HETATM 4 C C4 . GAL A 1 . ? 12.860 13.200 22.820 1.00 0.00 ? 1 GAL ? C4 1
HETATM 5 C C5 . GAL A 1 . ? 13.330 12.290 24.040 1.00 0.00 ? 1 GAL ? C5 1
HETATM 6 C C6 . GAL A 1 . ? 12.990 12.900 25.430 1.00 0.00 ? 1 GAL ? C6 1
HETATM 7 O O2 . GAL A 1 . ? 12.970 10.390 20.220 1.00 0.00 ? 1 GAL ? O2 1
HETATM 8 O O3 . GAL A 1 . ? 12.510 13.240 20.390 1.00 0.00 ? 1 GAL ? O3 1
HETATM 9 O O4 . GAL A 1 . ? 11.400 13.510 22.920 1.00 0.00 ? 1 GAL ? O4 1
HETATM 10 O O5 . GAL A 1 . ? 12.620 10.920 23.880 1.00 0.00 ? 1 GAL ? O5 1
HETATM 11 O O6 . GAL A 1 . ? 12.940 11.850 26.400 1.00 0.00 ? 1 GAL ? O6 1
HETATM 12 H H1 . GAL A 1 . ? 14.040 10.170 22.620 1.00 0.00 ? 1 GAL ? H1 1
HETATM 13 H H2 . GAL A 1 . ? 11.440 11.140 21.570 1.00 0.00 ? 1 GAL ? H2 1
HETATM 14 H H3 . GAL A 1 . ? 14.130 12.490 21.250 1.00 0.00 ? 1 GAL ? H3 1
HETATM 15 H H4 . GAL A 1 . ? 13.380 14.150 22.930 1.00 0.00 ? 1 GAL ? H4 1
HETATM 16 H H5 . GAL A 1 . ? 14.390 12.040 24.030 1.00 0.00 ? 1 GAL ? H5 1
HETATM 17 H H61 . GAL A 1 . ? 13.650 13.710 25.750 1.00 0.00 ? 1 GAL ? H61 1
HETATM 18 H H62 . GAL A 1 . ? 11.970 13.280 25.540 1.00 0.00 ? 1 GAL ? H62 1
HETATM 19 H H6O . GAL A 1 . ? 12.550 11.040 26.080 1.00 0.00 ? 1 GAL ? H6O 1
HETATM 20 H H3O . GAL A 1 . ? 12.600 12.580 19.700 1.00 0.00 ? 1 GAL ? H3O 1
HETATM 21 H H2O . GAL A 1 . ? 12.570 9.520 20.180 1.00 0.00 ? 1 GAL ? H2O 1
HETATM 22 C C1 . NGA A 1 . ? 11.010 14.920 22.680 1.00 0.00 ? 2 NGA ? C1 1
HETATM 23 C C2 . NGA A 1 . ? 9.500 15.040 22.900 1.00 0.00 ? 2 NGA ? C2 1
HETATM 24 C C3 . NGA A 1 . ? 8.990 16.480 22.780 1.00 0.00 ? 2 NGA ? C3 1
HETATM 25 C C4 . NGA A 1 . ? 9.910 17.420 23.600 1.00 0.00 ? 2 NGA ? C4 1
HETATM 26 C C5 . NGA A 1 . ? 11.400 17.160 23.380 1.00 0.00 ? 2 NGA ? C5 1
HETATM 27 C C6 . NGA A 1 . ? 12.200 17.970 24.410 1.00 0.00 ? 2 NGA ? C6 1
HETATM 28 N N2 . NGA A 1 . ? 8.730 14.240 21.930 1.00 0.00 ? 2 NGA ? N2 1
HETATM 29 O O3 . NGA A 1 . ? 7.590 16.520 23.200 1.00 0.00 ? 2 NGA ? O3 1
HETATM 30 O O4 . NGA A 1 . ? 9.610 17.270 25.020 1.00 0.00 ? 2 NGA ? O4 1
HETATM 31 O O5 . NGA A 1 . ? 11.640 15.740 23.680 1.00 0.00 ? 2 NGA ? O5 1
HETATM 32 O O6 . NGA A 1 . ? 13.560 18.220 23.890 1.00 0.00 ? 2 NGA ? O6 1
HETATM 33 H H1 . NGA A 1 . ? 11.310 15.170 21.660 1.00 0.00 ? 2 NGA ? H1 1
HETATM 34 H H2 . NGA A 1 . ? 9.250 14.520 23.820 1.00 0.00 ? 2 NGA ? H2 1
HETATM 35 H H3 . NGA A 1 . ? 9.090 16.750 21.730 1.00 0.00 ? 2 NGA ? H3 1
HETATM 36 H H4 . NGA A 1 . ? 9.680 18.470 23.390 1.00 0.00 ? 2 NGA ? H4 1
HETATM 37 H H5 . NGA A 1 . ? 11.700 17.460 22.370 1.00 0.00 ? 2 NGA ? H5 1
HETATM 38 H H61 . NGA A 1 . ? 11.870 19.010 24.510 1.00 0.00 ? 2 NGA ? H61 1
HETATM 39 H H62 . NGA A 1 . ? 12.190 17.560 25.420 1.00 0.00 ? 2 NGA ? H62 1
HETATM 40 H H4O . NGA A 1 . ? 8.770 16.800 25.110 1.00 0.00 ? 2 NGA ? H4O 1
HETATM 41 H H3O . NGA A 1 . ? 7.290 17.430 23.240 1.00 0.00 ? 2 NGA ? H3O 1
HETATM 42 H H2N . NGA A 1 . ? 8.290 14.750 21.190 1.00 0.00 ? 2 NGA ? H2N 1
HETATM 43 C C2N . NGA A 1 . ? 8.890 12.910 21.730 1.00 0.00 ? 2 NGA ? C2N 1
HETATM 44 O O2N . NGA A 1 . ? 8.810 12.150 22.660 1.00 0.00 ? 2 NGA ? O2N 1
HETATM 45 C CME . NGA A 1 . ? 9.020 12.350 20.270 1.00 0.00 ? 2 NGA ? CME 1
HETATM 46 H H3M . NGA A 1 . ? 9.310 13.130 19.570 1.00 0.00 ? 2 NGA ? H3M 1
HETATM 47 H H2M . NGA A 1 . ? 9.790 11.590 20.220 1.00 0.00 ? 2 NGA ? H2M 1
HETATM 48 H H1M . NGA A 1 . ? 8.070 11.960 19.900 1.00 0.00 ? 2 NGA ? H1M 1
HETATM 49 H HO1 . ROH B 2 . ? 12.350 8.720 21.820 1.00 0.00 ? 1 ROH ? HO1 1
HETATM 50 O O1 . ROH B 2 . ? 12.330 9.050 22.720 1.00 0.00 ? 1 ROH ? O1 1
HETATM 51 H H2 . MEX C 3 . ? 15.450 17.440 23.870 1.00 0.00 ? 4 MEX ? H2 1
HETATM 52 H H1 . MEX C 3 . ? 14.690 17.350 25.540 1.00 0.00 ? 4 MEX ? H1 1
HETATM 53 H H3 . MEX C 3 . ? 14.160 16.320 24.180 1.00 0.00 ? 4 MEX ? H3 1
HETATM 54 C CH3 . MEX C 3 . ? 14.550 17.300 24.460 1.00 0.00 ? 4 MEX ? CH3 1
#