ceitec_PPT_podklad_uvod logo+napis_en OPVaVpI_loga-eu_pos_H_EN partner_logo_2 Validation - ligands Radka Svobodová CEITEC_logo_pos Can we still find wrong structures in PDB? Example: Nipah G attachment glycoprotein (PDB ID 3D12, PNAS) Contains 30 instances of 11 different carbohydrates, each with one ring and five chiral atoms. Results: •13 of these ligands have incorrect chirality •In a few cases, all chiral atoms exhibit incorrect chirality 2 CEITEC_logo_pos Can we still find wrong structures in PDB? 3 Unfortunately yes CEITEC_logo_pos Validation approaches 4 What to validate? How? Software Geometry (3D) Against tabular values Proteins and nucl. acids: WHAT_CHECK, PROCHECK, PROCHECK-NMR, AQUA, MolProbity, OOPS Ligands: ValLigURL, Mogul, Coot, PHENIX Topology (2D) Against a template Proteins and nucl. acids: -||- Ligands: pdb-care, MotiveValidator, ValidatorDB http://www.rcsb.org/pdb/images/MAN_600.gif C:\Users\dave\Downloads\chirality\pairing.png 1.5 Å 120° 1.7 Å Compilation: PDB validation reports CEITEC_logo_pos Improved data quality §Cleaned up mmCIF data §Standard vocabularies §Experimental details, binding sites, secondary structure, antibiotic/inhibitor information, nucleic-acid parameters §Clean mmCIF files are used in production § CEITEC_logo_pos Validation reports §Summary §Quality vs. all PDB §Quality vs. entries at similar resolution §Overview of residue- based quality for every polymer §Table of ligands that may need your attention §Shortcut: pdbe.org/valrep/1cbs 1CBS CEITEC_logo_pos 7 Topology validation (= validation of annotation) http://www.rcsb.org/pdb/images/MAN_600.gif C:\Users\dave\Downloads\chirality\pairing.png CEITEC_logo_pos Topology validation – basic terms 8 Residue §Any component of a biomacromolecule §Examples: amino acids, nucleotides, saccharides, ions, … §In PDB, residue is annotated via “Residue ID” – a unique 3-letter code http://www.rcsb.org/pdb/images/FUC_600.gif FUC, alpha-L-fucose http://www.rcsb.org/pdb/images/PHE_600.gif PHE, phenylalanine CEITEC_logo_pos Topology validation – basic terms 9 Types of residues: Standard residues: §amino acids §nucleotides § Non-standard residues: §modified amino acids and nucleotides Ligands: §Chemical compounds which form a complex with a biomacromolecule (e.g., sugar, drug, heme). §Also ions are often referred as ligands CEITEC_logo_pos Topology validation – basic terms 10 Principles of topology validation: §Subjects of topology validation are residues §Validated residue is compared with a model residue, which has the same Residue ID §The model residues are taken from a reference database §Differences between the model residue and the validated residue are reported CEITEC_logo_pos Topology validation – approach 11 Complication with “shared atoms”: §When some residues bind together, one of them can lose an atom: § http://www.rcsb.org/pdb/images/FUC_600.gif http://www.rcsb.org/pdb/images/MAG_600.gif MAG FUC PDB ID 1g1t H20 •Solution: When we validate a residue, we must include also its close surrounding MAG-FUC CEITEC_logo_pos Input motif = validated residue + surrounding Topology validation - approach 12 C:\Users\dave\Downloads\chirality\inputMotif_edit.png Validated motif mapped to the Model Residue C:\Users\dave\Downloads\chirality\pairing.png Input PDB entry Selection of validated residue and its close surrounding Mapping of input motif to the model residue (via subgraph matching) C:\Users\dave\Downloads\chirality\1_2.jpg CEITEC_logo_pos Topology validation – types of validation analyses 13 §Completeness analyses §Missing atoms §Missing rings § §Chirality analyses §Chirality on C atom, metal atom, high bond order atom, planarity § §Advanced analyses §Substitution §Different atom naming §Foreign atoms CEITEC_logo_pos C:\Users\dave\Downloads\chirality\motif.png Topology validation – types of validation analyses Prerequisite: Can we map the validated and the model residue? 14 Degenerated structure Correct residue 1IVG_17_7716 (MAN) CEITEC_logo_pos C:\Users\dave\Downloads\chirality\motif.png C:\Users\dave\Downloads\chirality\missingRing.png C:\Users\dave\Downloads\chirality\missingAtom.png Topology validation – types of validation analyses ERRORS – INCOMPLETE STRUCTURE 15 Missing atom Missing ring Correct residue CEITEC_logo_pos Topology validation – types of validation analyses ERRORS – CHIRALITY 16 Wrong chirality on metal atom 1E4M_16_4280 (MAN) Wrong chirality on C atoms http://www.rcsb.org/pdb/images/MAN_600.gif MAN http://www.rcsb.org/pdb/images/AVC_600.gif AVC 2P7E_0_95 (AVC) CEITEC_logo_pos Topology validation – types of validation analyses ERRORS – CHIRALITY II 17 1BZ0_1_4428 (HEM) Wrong chirality (planar) http://www.rcsb.org/pdb/images/CMP_600.gif 4A2U_2_13909 (CMP) CMP Wrong chirality on atom having high order bonds HEM Correct chirality (Tolerant) = Correct residues + residues having only these issues: •Wrong chirality (planar) •Wrong chirality on atom having high order bonds CEITEC_logo_pos C:\Users\dave\Downloads\chirality\motif.png Topology validation – types of validation analyses WARNINGS 18 Substitution Foreign atom (= atom from neighboring residue) Different atom name O1 instead O5 C:\Users\dave\Downloads\chirality\substitution.png C:\Users\dave\Downloads\chirality\foreignAtom.png C:\Users\dave\Downloads\chirality\motif.png Correct residue C:\Users\dave\Downloads\chirality\inputMotif_edit.png ADVANCED WARNINGS: Alternate locations Zero RMSD with model • • CEITEC_logo_pos Different atom names - example 19 CEITEC_logo_pos Topology validation Software tools • PDB care (Lütteke et al., 2006): •Tool focused on carbohydrates validation •First application, which implements topology validation •Performs basic validation analyses (missing atoms, missing rings, wrong chirality) MotiveValidator (http://ncbr.muni.cz/MotiveValidator) : •Tool, which allows validation of all residues •Performs basic validation analyses + reports basic warnings (substitutions, foreign atoms, different naming) ValidatorDB (http://ncbr.muni.cz/ValidatorDB): •Database, containing validation results for all* ligands and non-standard residues in PDB (weekly updated) •Performs basic validation analyses + advanced validation analyses (report degenerated residue, distinguish type of chirality error) •Reports basic warnings + next warnings (Alternate locations, Zero RMSD with model) * Except amino acids, nucleotides, and small residues (<7 heavy atoms) ceitec_PPT_podklad_uvod CEITEC_logo_pos_RGB OPVaVpI_loga-eu_pos_H_EN partner_logo_2_col Central European Institute of Technology Masaryk University Kamenice 753/5 625 00 Brno, Czech Republic www.ceitec.muni.cz | info@ceitec.muni.cz Thank you for your attention