data_2VVK # _entry.id 2VVK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2VVK PDBE EBI-36511 WWPDB D_1290036511 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2H46 unspecified 'NATIVE DOMAIN-SWAPPED DIMER CRYSTAL STRUCTURE OF THE GRB2SH2 DOMAIN' PDB 1QG1 unspecified 'GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXEDWITH AN SHC-DERIVED PEPTIDE' PDB 1CJ1 unspecified 'GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN)COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE' PDB 1BM2 unspecified 'GRB2-SH2 DOMAIN IN COMPLEX WITH CYCLO-[N- ALPHA-ACETYL-L-THI ALYSYL-O-PHOSPHOTYROSYL- VALYL-ASPARAGYL-VALYL-PROLYL] (PKF273-791)' PDB 1GFD unspecified . PDB 1FYR unspecified 'DIMER FORMATION THROUGH DOMAIN SWAPPING IN THE CRYSTALSTRUCTURE OF THE GRB2-SH2 AC- PYVNV COMPLEX' PDB 1JYU unspecified 'XRAY STRUCTURE OF GRB2 SH2 DOMAIN' PDB 1BMB unspecified 'GRB2-SH2 DOMAIN IN COMPLEX WITH KPFYVNVEF ( PKF270-974)' PDB 1JYQ unspecified 'XRAY STRUCTURE OF GRB2 SH2 DOMAIN COMPLEXED WITH A HIGHLYAFFINE PHOSPHO PEPTIDE' PDB 1GFC unspecified . PDB 2AOB unspecified 'CRYSTAL STRUCTURES OF A HIGH-AFFINITY MACROCYCLIC PEPTIDEMIMETIC IN COMPLEX WITH THE GRB2 SH2 DOMAIN' PDB 1X0N unspecified 'NMR STRUCTURE OF GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2DOMAIN COMPLEXED WITH THE INHIBITOR' PDB 1TZE unspecified ;SIGNAL TRANSDUCTION ADAPTOR GROWTH FACTOR, GRB2 SH2 DOMAIN COMPLEXED WITH PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN- VAL-NH2 (KFPPYVNC-NH2) ; PDB 1AZE unspecified 'NMR STRUCTURE OF THE COMPLEX BETWEEN THE C32S-Y7V MUTANT OF THE NSH3 DOMAIN OF GRB2 WITH A PEPTIDE FROM SOS, 10 STRUCTURES' PDB 1GRI unspecified GRB2 PDB 1IO6 unspecified 'GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 (GRB2 ) C-TERMINALSH3 DOMAIN COMPLEXED WITH A LIGAND PEPTIDE (NMR, MINIMIZEDMEAN STRUCTURE)' PDB 1FHS unspecified ;THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE SRCHOMOLOGY DOMAIN-2 OF THE GROWTH FACTOR RECEPTOR BOUNDPROTEIN-2, NMR, 18 STRUCTURES ; PDB 1ZFP unspecified 'GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXEDWITH A PHOSPHOTYROSYL PENTAPEPTIDE' PDB 1GCQ unspecified 'CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS' PDB 1GHU unspecified 'NMR SOLUTION STRUCTURE OF GROWTH FACTOR RECEPTOR-BOUNDPROTEIN 2 (GRB2) SH2 DOMAIN, 24 STRUCTURES' PDB 2AOA unspecified 'CRYSTAL STRUCTURES OF A HIGH-AFFINITY MACROCYCLIC PEPTIDEMIMETIC IN COMPLEX WITH THE GRB2 SH2 DOMAIN' PDB 1JYR unspecified 'XRAY STRUCTURE OF GRB2 SH2 DOMAIN COMPLEXED WITH APHOSPHORYLATED PEPTIDE' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2VVK _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2008-06-09 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Harkiolaki, M.' 1 'Tsirka, T.' 2 'Feller, S.M.' 3 # _citation.id primary _citation.title 'Distinct Binding Modes of Two Epitopes in Gab2 that Interact with the Sh3C Domain of Grb2.' _citation.journal_abbrev Structure _citation.journal_volume 17 _citation.page_first 809 _citation.page_last ? _citation.year 2009 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19523899 _citation.pdbx_database_id_DOI 10.1016/J.STR.2009.03.017 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Harkiolaki, M.' 1 primary 'Tsirka, T.' 2 primary 'Lewitzky, M.' 3 primary 'Simister, P.C.' 4 primary 'Joshi, D.' 5 primary 'Bird, L.E.' 6 primary 'Jones, E.Y.' 7 primary ;O'Reilly, N. ; 8 primary 'Feller, S.M.' 9 # _cell.entry_id 2VVK _cell.length_a 25.405 _cell.length_b 38.681 _cell.length_c 50.870 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VVK _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # 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 polymer man 'GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2' 6363.956 1 ? ? 'SH3 DOMAIN, RESIDUES 161-214' 'N TERMINAL GS OVERHAND DUE TO THROMBIN CLEAVAGE' 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 77 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'ADAPTER PROTEIN GRB2, SH2/SH3 ADAPTER GRB2, PROTEIN ASH, GRB2 SH3C' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GSVQALFDFDPQEDGELGFRRGDFIHVMDNSDPNWWKGACHGQTGMFPRNYVTPVN _entity_poly.pdbx_seq_one_letter_code_can GSVQALFDFDPQEDGELGFRRGDFIHVMDNSDPNWWKGACHGQTGMFPRNYVTPVN _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 SER n 1 3 VAL n 1 4 GLN n 1 5 ALA n 1 6 LEU n 1 7 PHE n 1 8 ASP n 1 9 PHE n 1 10 ASP n 1 11 PRO n 1 12 GLN n 1 13 GLU n 1 14 ASP n 1 15 GLY n 1 16 GLU n 1 17 LEU n 1 18 GLY n 1 19 PHE n 1 20 ARG n 1 21 ARG n 1 22 GLY n 1 23 ASP n 1 24 PHE n 1 25 ILE n 1 26 HIS n 1 27 VAL n 1 28 MET n 1 29 ASP n 1 30 ASN n 1 31 SER n 1 32 ASP n 1 33 PRO n 1 34 ASN n 1 35 TRP n 1 36 TRP n 1 37 LYS n 1 38 GLY n 1 39 ALA n 1 40 CYS n 1 41 HIS n 1 42 GLY n 1 43 GLN n 1 44 THR n 1 45 GLY n 1 46 MET n 1 47 PHE n 1 48 PRO n 1 49 ARG n 1 50 ASN n 1 51 TYR n 1 52 VAL n 1 53 THR n 1 54 PRO n 1 55 VAL n 1 56 ASN n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name HUMAN _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'HOMO SAPIENS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PGEX-2T _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 2VVK 1 ? ? 2VVK ? 2 UNP GRB2_HUMAN 1 ? ? P62993 ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2VVK A 1 ? 2 ? 2VVK 1 ? 2 ? 1 2 2 2 2VVK A 3 ? 56 ? P62993 161 ? 214 ? 3 56 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2VVK _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.97 _exptl_crystal.density_percent_sol 37.5 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '8% PEG 4K, 0.1M NAACETATE PH 4.6' # _diffrn.id 1 _diffrn.ambient_temp 77 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2007-04-16 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SI(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.976 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength 0.976 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2VVK _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30.00 _reflns.d_resolution_high 1.60 _reflns.number_obs 6917 _reflns.number_all ? _reflns.percent_possible_obs 98.4 _reflns.pdbx_Rmerge_I_obs 0.03 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 89.20 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 13.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.66 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.03 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 14.40 _reflns_shell.pdbx_redundancy 14.4 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2VVK _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 6559 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.79 _refine.ls_d_res_high 1.60 _refine.ls_percent_reflns_obs 98.5 _refine.ls_R_factor_obs 0.160 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.159 _refine.ls_R_factor_R_free 0.178 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.800 _refine.ls_number_reflns_R_free 330 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.951 _refine.correlation_coeff_Fo_to_Fc_free 0.937 _refine.B_iso_mean 8.68 _refine.aniso_B[1][1] -0.11000 _refine.aniso_B[2][2] 0.02000 _refine.aniso_B[3][3] 0.08000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model 'PDB ENTRY 1IO6' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.091 _refine.pdbx_overall_ESU_R_Free 0.083 _refine.overall_SU_ML 0.044 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.214 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 448 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 77 _refine_hist.number_atoms_total 531 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 30.79 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.008 0.021 ? 478 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.165 1.908 ? 650 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.726 5.000 ? 59 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 32.130 24.483 ? 29 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 15.461 15.000 ? 66 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 11.724 15.000 ? 3 'X-RAY DIFFRACTION' ? r_chiral_restr 0.085 0.200 ? 60 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 398 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.188 0.200 ? 210 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.310 0.200 ? 315 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.143 0.200 ? 52 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.200 0.200 ? 33 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.095 0.200 ? 22 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.742 1.500 ? 289 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.200 2.000 ? 453 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 1.728 3.000 ? 219 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 2.616 4.500 ? 195 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.60 _refine_ls_shell.d_res_low 1.64 _refine_ls_shell.number_reflns_R_work 458 _refine_ls_shell.R_factor_R_work 0.1510 _refine_ls_shell.percent_reflns_obs 99.18 _refine_ls_shell.R_factor_R_free 0.1900 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 23 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2VVK _struct.title 'Grb2 SH3C (1)' _struct.pdbx_descriptor 'GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2VVK _struct_keywords.pdbx_keywords 'PROTEIN BINDING' _struct_keywords.text ;GRB2 SH3, SH3 DOMAIN, SH2 DOMAIN, PHOSPHOPROTEIN, HOST-VIRUS INTERACTION, PROTEIN-BINDING, GOLGI APPARATUS, ALTERNATIVE SPLICING, PROTEIN BINDING ; # 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 ? # _struct_biol.id 1 # _struct_sheet.id AA _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? anti-parallel AA 2 3 ? anti-parallel AA 3 4 ? anti-parallel AA 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 GLN A 43 ? PRO A 48 ? GLN A 43 PRO A 48 AA 2 TRP A 35 ? CYS A 40 ? TRP A 35 CYS A 40 AA 3 PHE A 24 ? ASP A 29 ? PHE A 24 ASP A 29 AA 4 SER A 2 ? ALA A 5 ? SER A 2 ALA A 5 AA 5 VAL A 52 ? PRO A 54 ? VAL A 52 PRO A 54 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA 1 2 N PHE A 47 ? N PHE A 47 O TRP A 36 ? O TRP A 36 AA 2 3 N ALA A 39 ? N ALA A 39 O HIS A 26 ? O HIS A 26 AA 3 4 N ILE A 25 ? N ILE A 25 O VAL A 3 ? O VAL A 3 AA 4 5 N GLN A 4 ? N GLN A 4 O THR A 53 ? O THR A 53 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 10 _struct_site.details 'BINDING SITE FOR RESIDUE GOL A 1057' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 10 GLY A 1 ? GLY A 1 . ? 1_555 ? 2 AC1 10 VAL A 3 ? VAL A 3 . ? 1_555 ? 3 AC1 10 VAL A 27 ? VAL A 27 . ? 1_555 ? 4 AC1 10 ASN A 30 ? ASN A 30 . ? 1_555 ? 5 AC1 10 ASN A 50 ? ASN A 50 . ? 4_556 ? 6 AC1 10 PRO A 54 ? PRO A 54 . ? 1_555 ? 7 AC1 10 HOH C . ? HOH A 2026 . ? 3_645 ? 8 AC1 10 HOH C . ? HOH A 2075 . ? 1_555 ? 9 AC1 10 HOH C . ? HOH A 2076 . ? 1_555 ? 10 AC1 10 HOH C . ? HOH A 2077 . ? 1_555 ? # _database_PDB_matrix.entry_id 2VVK _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2VVK _atom_sites.fract_transf_matrix[1][1] 0.039362 _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] 0.025852 _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] 0.019658 _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_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 1 1 GLY GLY A . n A 1 2 SER 2 2 2 SER SER A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 GLN 4 4 4 GLN GLN A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 LEU 6 6 6 LEU LEU A . n A 1 7 PHE 7 7 7 PHE PHE A . n A 1 8 ASP 8 8 8 ASP ASP A . n A 1 9 PHE 9 9 9 PHE PHE A . n A 1 10 ASP 10 10 10 ASP ASP A . n A 1 11 PRO 11 11 11 PRO PRO A . n A 1 12 GLN 12 12 12 GLN GLN A . n A 1 13 GLU 13 13 13 GLU GLU A . n A 1 14 ASP 14 14 14 ASP ASP A . n A 1 15 GLY 15 15 15 GLY GLY A . n A 1 16 GLU 16 16 16 GLU GLU A . n A 1 17 LEU 17 17 17 LEU LEU A . n A 1 18 GLY 18 18 18 GLY GLY A . n A 1 19 PHE 19 19 19 PHE PHE A . n A 1 20 ARG 20 20 20 ARG ARG A . n A 1 21 ARG 21 21 21 ARG ARG A . n A 1 22 GLY 22 22 22 GLY GLY A . n A 1 23 ASP 23 23 23 ASP ASP A . n A 1 24 PHE 24 24 24 PHE PHE A . n A 1 25 ILE 25 25 25 ILE ILE A . n A 1 26 HIS 26 26 26 HIS HIS A . n A 1 27 VAL 27 27 27 VAL VAL A . n A 1 28 MET 28 28 28 MET MET A . n A 1 29 ASP 29 29 29 ASP ASP A . n A 1 30 ASN 30 30 30 ASN ASN A . n A 1 31 SER 31 31 31 SER SER A . n A 1 32 ASP 32 32 32 ASP ASP A . n A 1 33 PRO 33 33 33 PRO PRO A . n A 1 34 ASN 34 34 34 ASN ASN A . n A 1 35 TRP 35 35 35 TRP TRP A . n A 1 36 TRP 36 36 36 TRP TRP A . n A 1 37 LYS 37 37 37 LYS LYS A . n A 1 38 GLY 38 38 38 GLY GLY A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 CYS 40 40 40 CYS CYS A . n A 1 41 HIS 41 41 41 HIS HIS A . n A 1 42 GLY 42 42 42 GLY GLY A . n A 1 43 GLN 43 43 43 GLN GLN A . n A 1 44 THR 44 44 44 THR THR A . n A 1 45 GLY 45 45 45 GLY GLY A . n A 1 46 MET 46 46 46 MET MET A . n A 1 47 PHE 47 47 47 PHE PHE A . n A 1 48 PRO 48 48 48 PRO PRO A . n A 1 49 ARG 49 49 49 ARG ARG A . n A 1 50 ASN 50 50 50 ASN ASN A . n A 1 51 TYR 51 51 51 TYR TYR A . n A 1 52 VAL 52 52 52 VAL VAL A . n A 1 53 THR 53 53 53 THR THR A . n A 1 54 PRO 54 54 54 PRO PRO A . n A 1 55 VAL 55 55 55 VAL VAL A . n A 1 56 ASN 56 56 56 ASN ASN A . n # 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 GOL 1 1057 1057 GOL GOL A . C 3 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . C 3 HOH 4 2004 2004 HOH HOH A . C 3 HOH 5 2005 2005 HOH HOH A . C 3 HOH 6 2006 2006 HOH HOH A . C 3 HOH 7 2007 2007 HOH HOH A . C 3 HOH 8 2008 2008 HOH HOH A . C 3 HOH 9 2009 2009 HOH HOH A . C 3 HOH 10 2010 2010 HOH HOH A . C 3 HOH 11 2011 2011 HOH HOH A . C 3 HOH 12 2012 2012 HOH HOH A . C 3 HOH 13 2013 2013 HOH HOH A . C 3 HOH 14 2014 2014 HOH HOH A . C 3 HOH 15 2015 2015 HOH HOH A . C 3 HOH 16 2016 2016 HOH HOH A . C 3 HOH 17 2017 2017 HOH HOH A . C 3 HOH 18 2018 2018 HOH HOH A . C 3 HOH 19 2019 2019 HOH HOH A . C 3 HOH 20 2020 2020 HOH HOH A . C 3 HOH 21 2021 2021 HOH HOH A . C 3 HOH 22 2022 2022 HOH HOH A . C 3 HOH 23 2023 2023 HOH HOH A . C 3 HOH 24 2024 2024 HOH HOH A . C 3 HOH 25 2025 2025 HOH HOH A . C 3 HOH 26 2026 2026 HOH HOH A . C 3 HOH 27 2027 2027 HOH HOH A . C 3 HOH 28 2028 2028 HOH HOH A . C 3 HOH 29 2029 2029 HOH HOH A . C 3 HOH 30 2030 2030 HOH HOH A . C 3 HOH 31 2031 2031 HOH HOH A . C 3 HOH 32 2032 2032 HOH HOH A . C 3 HOH 33 2033 2033 HOH HOH A . C 3 HOH 34 2034 2034 HOH HOH A . C 3 HOH 35 2035 2035 HOH HOH A . C 3 HOH 36 2036 2036 HOH HOH A . C 3 HOH 37 2037 2037 HOH HOH A . C 3 HOH 38 2038 2038 HOH HOH A . C 3 HOH 39 2039 2039 HOH HOH A . C 3 HOH 40 2040 2040 HOH HOH A . C 3 HOH 41 2041 2041 HOH HOH A . C 3 HOH 42 2042 2042 HOH HOH A . C 3 HOH 43 2043 2043 HOH HOH A . C 3 HOH 44 2044 2044 HOH HOH A . C 3 HOH 45 2045 2045 HOH HOH A . C 3 HOH 46 2046 2046 HOH HOH A . C 3 HOH 47 2047 2047 HOH HOH A . C 3 HOH 48 2048 2048 HOH HOH A . C 3 HOH 49 2049 2049 HOH HOH A . C 3 HOH 50 2050 2050 HOH HOH A . C 3 HOH 51 2051 2051 HOH HOH A . C 3 HOH 52 2052 2052 HOH HOH A . C 3 HOH 53 2053 2053 HOH HOH A . C 3 HOH 54 2054 2054 HOH HOH A . C 3 HOH 55 2055 2055 HOH HOH A . C 3 HOH 56 2056 2056 HOH HOH A . C 3 HOH 57 2057 2057 HOH HOH A . C 3 HOH 58 2058 2058 HOH HOH A . C 3 HOH 59 2059 2059 HOH HOH A . C 3 HOH 60 2060 2060 HOH HOH A . C 3 HOH 61 2061 2061 HOH HOH A . C 3 HOH 62 2062 2062 HOH HOH A . C 3 HOH 63 2063 2063 HOH HOH A . C 3 HOH 64 2064 2064 HOH HOH A . C 3 HOH 65 2065 2065 HOH HOH A . C 3 HOH 66 2066 2066 HOH HOH A . C 3 HOH 67 2067 2067 HOH HOH A . C 3 HOH 68 2068 2068 HOH HOH A . C 3 HOH 69 2069 2069 HOH HOH A . C 3 HOH 70 2070 2070 HOH HOH A . C 3 HOH 71 2071 2071 HOH HOH A . C 3 HOH 72 2072 2072 HOH HOH A . C 3 HOH 73 2073 2073 HOH HOH A . C 3 HOH 74 2074 2074 HOH HOH A . C 3 HOH 75 2075 2075 HOH HOH A . C 3 HOH 76 2076 2076 HOH HOH A . C 3 HOH 77 2077 2077 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2009-05-19 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 AMoRE phasing . ? 4 # _pdbx_entry_details.entry_id 2VVK _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'GS TERMINAL OVERHANG (THROMBIN CLEAVAGE)' # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CB _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ASP _pdbx_validate_rmsd_angle.auth_seq_id_1 14 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 B _pdbx_validate_rmsd_angle.auth_atom_id_2 CG _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ASP _pdbx_validate_rmsd_angle.auth_seq_id_2 14 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 B _pdbx_validate_rmsd_angle.auth_atom_id_3 OD2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ASP _pdbx_validate_rmsd_angle.auth_seq_id_3 14 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 B _pdbx_validate_rmsd_angle.angle_value 112.58 _pdbx_validate_rmsd_angle.angle_target_value 118.30 _pdbx_validate_rmsd_angle.angle_deviation -5.72 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 2001 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.03 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water HOH #