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 "beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-galactopyranose" 586.542 1 ? ? ? ?
2 non-polymer syn ? ? 1 ? ? ? ?
#
_pdbx_nonpoly_scheme.asym_id B
_pdbx_nonpoly_scheme.entity_id 2
_pdbx_nonpoly_scheme.mon_id ROH
_pdbx_nonpoly_scheme.ndb_seq_num 1
_pdbx_nonpoly_scheme.pdb_seq_num 1
_pdbx_nonpoly_scheme.auth_seq_num 1
_pdbx_nonpoly_scheme.pdb_mon_id ROH
_pdbx_nonpoly_scheme.auth_mon_id ROH
_pdbx_nonpoly_scheme.pdb_strand_id ?
_pdbx_nonpoly_scheme.pdb_ins_code .
#
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
NAG "D-saccharide, beta linking" . 2-acetamido-2-deoxy-beta-D-glucopyranose "N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE"
"C8 H15 N O6" 221.208
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" ? ? ?
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_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
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_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
_struct_conn.ptnr1_auth_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_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
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
covale1 covale both ? A NGA . O6 ? ? ? 1_555 A NAG . C1 ? ? ? NGA 1 ? NAG 2 1_555 ? ? ? ? ? ? ? 1.502 sing ?
covale2 covale both ? A NAG . O3 ? ? ? 1_555 A GAL . C1 ? ? ? NAG 2 ? GAL 3 1_555 ? ? ? ? ? ? ? 1.531 sing ?
#
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 ?
#
_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
#
_pdbx_validate_close_contact.id 1
_pdbx_validate_close_contact.PDB_model_num 1
_pdbx_validate_close_contact.auth_atom_id_1 O1
_pdbx_validate_close_contact.auth_asym_id_1 .
_pdbx_validate_close_contact.auth_comp_id_1 ROH
_pdbx_validate_close_contact.auth_seq_id_1 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 C1
_pdbx_validate_close_contact.auth_asym_id_2 .
_pdbx_validate_close_contact.auth_comp_id_2 NGA
_pdbx_validate_close_contact.auth_seq_id_2 1
_pdbx_validate_close_contact.PDB_ins_code_2 ?
_pdbx_validate_close_contact.label_alt_id_2 ?
_pdbx_validate_close_contact.dist 1.42
#
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 . NGA 1 ? C7 ? A NGA 1 C7
2 1 N 1 . NGA 1 ? C8 ? A NGA 1 C8
3 1 N 1 . NGA 1 ? O1 ? A NGA 1 O1
4 1 N 1 . NGA 1 ? O7 ? A NGA 1 O7
5 1 N 1 . NAG 2 ? C7 ? A NAG 2 C7
6 1 N 1 . NAG 2 ? C8 ? A NAG 2 C8
7 1 N 1 . NAG 2 ? O7 ? A NAG 2 O7
#
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 NGA 1 . NGA 1 ? NGA 2 n
A 1 NAG 2 . NAG 2 ? NAG 3 n
A 1 GAL 3 . GAL 3 ? GAL 4 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
NAG "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGlcpNAcb
NAG "COMMON NAME" GMML 1.0 N-acetyl-b-D-glucopyranosamine
NAG "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-GlcpNAc
NAG "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 GlcNAc
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 DGalpb1-3DGlcpNAcb1-6DGalpNAcb1-ROH
_pdbx_entity_branch_descriptor.type "Glycam Condensed Sequence"
_pdbx_entity_branch_descriptor.program GMML
_pdbx_entity_branch_descriptor.program_version 1.0
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.value_order
_pdbx_entity_branch_link.details
1 1 2 NAG C1 O1 1 NGA O6 HO6 sing ?
2 1 3 GAL C1 O1 2 NAG O3 HO3 sing ?
#
loop_
_pdbx_entity_branch_list.entity_id
_pdbx_entity_branch_list.comp_id
_pdbx_entity_branch_list.num
_pdbx_entity_branch_list.hetero
1 NGA 1 n
1 NAG 2 n
1 GAL 3 n
#
_pdbx_entity_nonpoly.entity_id 2
_pdbx_entity_nonpoly.name ?
_pdbx_entity_nonpoly.comp_id ROH
#
_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 . NGA A 1 . ? 7.910 8.660 13.070 1.00 0.00 ? 1 NGA ? C1 1
HETATM 2 C C2 . NGA A 1 . ? 6.370 8.720 13.130 1.00 0.00 ? 1 NGA ? C2 1
HETATM 3 C C3 . NGA A 1 . ? 5.910 9.500 14.390 1.00 0.00 ? 1 NGA ? C3 1
HETATM 4 C C4 . NGA A 1 . ? 6.490 8.880 15.670 1.00 0.00 ? 1 NGA ? C4 1
HETATM 5 C C5 . NGA A 1 . ? 8.050 8.780 15.520 1.00 0.00 ? 1 NGA ? C5 1
HETATM 6 C C6 . NGA A 1 . ? 8.920 8.290 16.720 1.00 0.00 ? 1 NGA ? C6 1
HETATM 7 N N2 . NGA A 1 . ? 5.770 9.290 11.880 1.00 0.00 ? 1 NGA ? N2 1
HETATM 8 O O3 . NGA A 1 . ? 4.490 9.640 14.530 1.00 0.00 ? 1 NGA ? O3 1
HETATM 9 O O4 . NGA A 1 . ? 5.890 7.570 15.850 1.00 0.00 ? 1 NGA ? O4 1
HETATM 10 O O5 . NGA A 1 . ? 8.350 7.960 14.280 1.00 0.00 ? 1 NGA ? O5 1
HETATM 11 O O6 . NGA A 1 . ? 10.180 8.970 16.720 1.00 0.00 ? 1 NGA ? O6 1
HETATM 12 H H1 . NGA A 1 . ? 8.460 9.600 13.050 1.00 0.00 ? 1 NGA ? H1 1
HETATM 13 H H2 . NGA A 1 . ? 6.050 7.680 13.200 1.00 0.00 ? 1 NGA ? H2 1
HETATM 14 H H3 . NGA A 1 . ? 6.370 10.490 14.290 1.00 0.00 ? 1 NGA ? H3 1
HETATM 15 H H4 . NGA A 1 . ? 6.320 9.530 16.530 1.00 0.00 ? 1 NGA ? H4 1
HETATM 16 H H5 . NGA A 1 . ? 8.350 9.800 15.310 1.00 0.00 ? 1 NGA ? H5 1
HETATM 17 H H61 . NGA A 1 . ? 8.380 8.540 17.630 1.00 0.00 ? 1 NGA ? H61 1
HETATM 18 H H62 . NGA A 1 . ? 8.980 7.210 16.660 1.00 0.00 ? 1 NGA ? H62 1
HETATM 19 H H4O . NGA A 1 . ? 5.260 7.430 15.140 1.00 0.00 ? 1 NGA ? H4O 1
HETATM 20 H H3O . NGA A 1 . ? 4.080 8.880 14.100 1.00 0.00 ? 1 NGA ? H3O 1
HETATM 21 H H2N . NGA A 1 . ? 6.210 10.100 11.450 1.00 0.00 ? 1 NGA ? H2N 1
HETATM 22 C C2N . NGA A 1 . ? 4.590 9.050 11.430 1.00 0.00 ? 1 NGA ? C2N 1
HETATM 23 O O2N . NGA A 1 . ? 3.800 8.380 12.070 1.00 0.00 ? 1 NGA ? O2N 1
HETATM 24 C CME . NGA A 1 . ? 4.200 9.570 10.080 1.00 0.00 ? 1 NGA ? CME 1
HETATM 25 H H3M . NGA A 1 . ? 4.710 10.520 9.900 1.00 0.00 ? 1 NGA ? H3M 1
HETATM 26 H H2M . NGA A 1 . ? 4.470 8.870 9.290 1.00 0.00 ? 1 NGA ? H2M 1
HETATM 27 H H1M . NGA A 1 . ? 3.120 9.610 9.990 1.00 0.00 ? 1 NGA ? H1M 1
HETATM 28 C C1 . NAG A 1 . ? 11.340 8.220 17.310 1.00 0.00 ? 2 NAG ? C1 1
HETATM 29 C C2 . NAG A 1 . ? 12.700 9.010 17.050 1.00 0.00 ? 2 NAG ? C2 1
HETATM 30 C C3 . NAG A 1 . ? 13.890 8.030 17.610 1.00 0.00 ? 2 NAG ? C3 1
HETATM 31 C C4 . NAG A 1 . ? 13.650 7.760 19.120 1.00 0.00 ? 2 NAG ? C4 1
HETATM 32 C C5 . NAG A 1 . ? 12.170 7.360 19.530 1.00 0.00 ? 2 NAG ? C5 1
HETATM 33 C C6 . NAG A 1 . ? 11.940 7.840 20.940 1.00 0.00 ? 2 NAG ? C6 1
HETATM 34 N N2 . NAG A 1 . ? 12.900 9.330 15.600 1.00 0.00 ? 2 NAG ? N2 1
HETATM 35 O O3 . NAG A 1 . ? 15.140 8.840 17.460 1.00 0.00 ? 2 NAG ? O3 1
HETATM 36 O O4 . NAG A 1 . ? 14.530 6.720 19.440 1.00 0.00 ? 2 NAG ? O4 1
HETATM 37 O O5 . NAG A 1 . ? 11.140 8.000 18.750 1.00 0.00 ? 2 NAG ? O5 1
HETATM 38 O O6 . NAG A 1 . ? 12.190 9.230 20.990 1.00 0.00 ? 2 NAG ? O6 1
HETATM 39 H H1 . NAG A 1 . ? 11.340 7.290 16.730 1.00 0.00 ? 2 NAG ? H1 1
HETATM 40 H H2 . NAG A 1 . ? 12.820 9.890 17.680 1.00 0.00 ? 2 NAG ? H2 1
HETATM 41 H H3 . NAG A 1 . ? 13.950 7.090 17.070 1.00 0.00 ? 2 NAG ? H3 1
HETATM 42 H H4 . NAG A 1 . ? 13.950 8.660 19.660 1.00 0.00 ? 2 NAG ? H4 1
HETATM 43 H H5 . NAG A 1 . ? 12.080 6.280 19.450 1.00 0.00 ? 2 NAG ? H5 1
HETATM 44 H H61 . NAG A 1 . ? 10.890 7.640 21.160 1.00 0.00 ? 2 NAG ? H61 1
HETATM 45 H H62 . NAG A 1 . ? 12.680 7.380 21.600 1.00 0.00 ? 2 NAG ? H62 1
HETATM 46 H H6O . NAG A 1 . ? 11.410 9.630 20.620 1.00 0.00 ? 2 NAG ? H6O 1
HETATM 47 H H4O . NAG A 1 . ? 15.370 6.980 19.050 1.00 0.00 ? 2 NAG ? H4O 1
HETATM 48 H H2N . NAG A 1 . ? 12.750 8.640 14.880 1.00 0.00 ? 2 NAG ? H2N 1
HETATM 49 C C2N . NAG A 1 . ? 13.320 10.570 15.240 1.00 0.00 ? 2 NAG ? C2N 1
HETATM 50 O O2N . NAG A 1 . ? 13.400 11.520 16.020 1.00 0.00 ? 2 NAG ? O2N 1
HETATM 51 C CME . NAG A 1 . ? 13.740 10.700 13.800 1.00 0.00 ? 2 NAG ? CME 1
HETATM 52 H H3M . NAG A 1 . ? 14.340 11.590 13.590 1.00 0.00 ? 2 NAG ? H3M 1
HETATM 53 H H2M . NAG A 1 . ? 14.270 9.810 13.480 1.00 0.00 ? 2 NAG ? H2M 1
HETATM 54 H H1M . NAG A 1 . ? 12.770 10.720 13.290 1.00 0.00 ? 2 NAG ? H1M 1
HETATM 55 C C1 . GAL A 1 . ? 16.310 8.020 16.910 1.00 0.00 ? 3 GAL ? C1 1
HETATM 56 C C2 . GAL A 1 . ? 17.440 9.090 16.670 1.00 0.00 ? 3 GAL ? C2 1
HETATM 57 C C3 . GAL A 1 . ? 18.750 8.360 16.220 1.00 0.00 ? 3 GAL ? C3 1
HETATM 58 C C4 . GAL A 1 . ? 19.020 7.060 17.110 1.00 0.00 ? 3 GAL ? C4 1
HETATM 59 C C5 . GAL A 1 . ? 17.780 6.190 17.290 1.00 0.00 ? 3 GAL ? C5 1
HETATM 60 C C6 . GAL A 1 . ? 17.910 4.980 18.120 1.00 0.00 ? 3 GAL ? C6 1
HETATM 61 O O2 . GAL A 1 . ? 17.090 10.060 15.620 1.00 0.00 ? 3 GAL ? O2 1
HETATM 62 O O3 . GAL A 1 . ? 19.880 9.230 16.280 1.00 0.00 ? 3 GAL ? O3 1
HETATM 63 O O4 . GAL A 1 . ? 19.570 7.420 18.390 1.00 0.00 ? 3 GAL ? O4 1
HETATM 64 O O5 . GAL A 1 . ? 16.720 7.000 17.840 1.00 0.00 ? 3 GAL ? O5 1
HETATM 65 O O6 . GAL A 1 . ? 16.910 4.050 17.860 1.00 0.00 ? 3 GAL ? O6 1
HETATM 66 H H1 . GAL A 1 . ? 15.990 7.660 15.930 1.00 0.00 ? 3 GAL ? H1 1
HETATM 67 H H2 . GAL A 1 . ? 17.750 9.640 17.550 1.00 0.00 ? 3 GAL ? H2 1
HETATM 68 H H3 . GAL A 1 . ? 18.670 8.070 15.170 1.00 0.00 ? 3 GAL ? H3 1
HETATM 69 H H4 . GAL A 1 . ? 19.760 6.410 16.630 1.00 0.00 ? 3 GAL ? H4 1
HETATM 70 H H5 . GAL A 1 . ? 17.440 5.760 16.340 1.00 0.00 ? 3 GAL ? H5 1
HETATM 71 H H61 . GAL A 1 . ? 18.890 4.570 17.870 1.00 0.00 ? 3 GAL ? H61 1
HETATM 72 H H62 . GAL A 1 . ? 17.910 5.250 19.170 1.00 0.00 ? 3 GAL ? H62 1
HETATM 73 H H6O . GAL A 1 . ? 16.920 3.910 16.910 1.00 0.00 ? 3 GAL ? H6O 1
HETATM 74 H H4O . GAL A 1 . ? 18.850 7.910 18.790 1.00 0.00 ? 3 GAL ? H4O 1
HETATM 75 H H2O . GAL A 1 . ? 16.710 10.760 16.150 1.00 0.00 ? 3 GAL ? H2O 1
HETATM 76 H HO1 . ROH B 2 . ? 8.220 6.920 12.100 1.00 0.00 ? 1 ROH ? HO1 1
HETATM 77 O O1 . ROH B 2 . ? 8.400 7.860 12.000 1.00 0.00 ? 1 ROH ? O1 1
#