MakeTNT-toolkit User Documentation previous

Validated TNT-restraints

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Author: (2004-2006) M. Brandl


TNT-restraints for the following compounds and their linkages have been added to the TNT-standard library:
  • modified amino acids and amino acid modifying groups
    • with PDB-counts of 15 or higher and/or
    • requested by users (please do not hesitate to ask for additional ones)
  • Cofactors: ATP, ADP, ANP, cyclic-AMP, FAD, FADH, NAD, NADH
  • Carbohydrates: pyranoses, NAG, SIA
Restraints are based on standard PDB atom and residue naming documented below. For each compound, please find links to:
  • chemical formula (column2)
  • example PDB-structure (last but one column)
  • superposition (last column) of example PDB-structure (MODEL 1) and structure optimized by Gelly(O.Smart, MODEL 2)

Non-standard Amino Acids

Residue restraints were:
  • derived(PDB2TNT) from Corina-generated structures deposited in the MSDchem database[1]
  • adjusted for charges and conjugation in phosphate groups
Link restraints have either been taken from the standard library or high-resolution PDB-structures

[1]
  • MSDsite: behind the scene: The technology used in database searching and retrieval for the analysis and viewing of bound ligands and active sites. Golovin, A., Dimitropoulos, D., Oldfield, T. and Henrick, K. (2004) The eCheminfo 2004 Conference "Applications of Cheminformatics and Modelling to Drug Discovery 8-19 November.
  • MSD database and MSD database services A. Golovin, T. J. Oldfield, J. G. Tate, S. Velankar, G. J. Barton, H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Hussain, J. M. C. Ionides, M. John, P. A. Keller, E. Krissinel, P. McNeil, A. Naim, R. Newman, A. Pajon, J. Pineda, A. Rachedi, J. Copeland, A. Sitnov, S. Sobhany, A. Suarez-Uruena, J. Swaminathan, M. Tagari, S. Tromm, W. Vranken and K. Henrick (2004) E-MSD: an integrated data Nucleic Acids Research, 32 (Database issue), D211-D216. 2004
modification/modified amino acid 3-letter code/link to formula parent amino acid CATEGORY in connect.dat example coordinates from PDB superposition of PDB/optimised coordinates
3-SULFINOALANINE CSD CYS AAREST CSD-1acd.pdb CSD-1acd-opt.pdb
4-HYDROXYPROLINE HYP PRO AAREST HYP-1ag7.pdb HYP-1ag7-opt.pdb
4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL
-THREONINE 		BMT THR AANME BMT-1bck.pdb BMT-1bck-opt.pdb
5-HYDROXYPROLINE 5HP GLU AAREST 5HP-1a39.pdb 5HP-1a39-opt.pdb
ACETYL_GROUP ACE - ACE ACE-155c.pdb ACE-155c-opt.pdb
ALPHA-AMINOBUTYRIC_ACID ABA ALA AAREST ABA-1a3p.pdb ABA-1a3p-opt.pdb
ALPHA-AMINOISOBUTYRIC_ACID AIB ALA AAREST AIB-1ai1.pdb AIB-1ai1-opt.pdb
AMINO_GROUP NH2 - AAREST NH2-1a0m.pdb NH2-1a0m-opt.pdb
CARBOXY_GROUP CBX - CBX CBX-1an5.pdb CBX-1an5-opt.pdb
CYSTEINE-S-DIOXIDE CSW CYS AAREST CSW-1c0t.pdb CSW-1c0t-opt.pdb
CYSTEINESULFONIC_ACID OCS CYS AAREST OCS-1cs8.pdb OCS-1cs8-opt.pdb
D-ALANINE DAL ALA AAREST DAL-1cwj.pdb DAL-1cwj-opt.pdb
D-ARGININE DAR ARG AAREST DAR-1cvq.pdb DAR-1cvq-opt.pdb
D-ASPARAGINE DSG ASN AAREST DSG-1t5m.pdb DSG-1t5m-opt.pdb
D-ASPARTATE DSP ASP AAREST DSP-1bfw.pdb DSP-1bfw-opt.pdb
D-CYSTEINE DCY CYS AAREST DCY-1czq.pdb DCY-1czq-opt.pdb
DECARBOXY(PARAHYDROXYBENZYLIDENE-
IMIDAZOLIDINONE)THREONINE 		CRO CRO CRO CRO-1c4f.pdb CRO-1c4f-opt.pdb
D-GLUTAMATE DGL GLU AAREST DGL-1czq.pdb DGL-1czq-opt.pdb
D-GLUTAMINE DGN GLN AAREST DGN-1yj1.pdb DGN-1yj1-opt.pdb
D-HISTIDINE DHI HIS AAREST DHI-1czq.pdb DHI-1czq-opt.pdb
D-ISOLEUCINE DIL ILE AAREST DIL-1cvq.pdb DIL-1cvq-opt.pdb
D-ISOVALINE DIV VAL AAREST DIV-1ee7.pdb DIV-1ee7-opt.pdb
D-LEUCINE DLE LEU AAREST DLE-1bdw.pdb DLE-1bdw-opt.pdb
D-LYSINE DLY LYS AAREST DLY-1c4b.pdb DLY-1c4b-opt.pdb
D-PHENYLALANINE DPN PHE AAREST DPN-1b0q.pdb DPN-1b0q-opt.pdb
D-PROLINE DPR PRO AAREST DPR-1ic9.pdb DPR-1ic9-opt.pdb
D-SERINE DSN SER AAREST DSN-1t5n.pdb DSN-1t5n-opt.pdb
D-THREONINE DTH THR AAREST DTH-1a7z.pdb DTH-1a7z-opt.pdb
D-TRYPTOPHANE DTR DTR AAREST DTR-1czq.pdb DTR-1czq-opt.pdb
D-TYROSINE DTY TYR AAREST DTY-1uno.pdb DTY-1uno-opt.pdb
D-VALINE DVA VAL AAREST DVA-1mic.pdb DVA-1mic-opt.pdb
FORMYL_GROUP FOR - FOR FOR-1al4.pdb FOR-1al4-opt.pdb
GAMMA-CARBOXY-GLUTAMIC_ACID CGU GLU AAREST CGU-1awy.pdb CGU-1awy-opt.pdb
ISOVALERIC_ACID IVA - AAREST IVA-1apt.pdb IVA-1apt-opt.pdb
LYSINE_NZ-CARBOXYLIC_ACID KCX LYS AAREST KCX-1aa1.pdb KCX-1aa1-opt.pdb
LYSINE-PYRIDOXAL-5'-PHOSPHATE LLP LYS AAREST LLP-1a8i.pdb LLP-1a8i-opt.pdb
N-CARBOXYMETHIONINE CXM MET AAREST CXM-1aiq.pdb CXM-1aiq-opt.pdb
N-FORMYLMETHIONINE FME MET AAREST FME-1bq9.pdb FME-1bq9-opt.pdb
N-METHYLLEUCINE MLE LEU AANME MLE-1bck.pdb MLE-1bck-opt.pdb
N-METHYLVALINE MVA VAL AANME MVA-1c5f.pdb MVA-1c5f-opt.pdb
NORLEUCINE NLE LEU AAREST NLE-1a8k.pdb NLE-1a8k-opt.pdb
O-PHOSPHOTYROSINE PTR TYR AAREST PTR-1a1b.pdb PTR-1a1b-opt.pdb
ORNITHINE ORN ALA AAREST ORN-1b2h.pdb ORN-1b2h-opt.pdb
PHOSPHOSERINE SEP SER AAREST SEP-1b4g.pdb SEP-1b4g-opt.pdb
PHOSPHOTHREONINE TPO THR AAREST TPO-1bkx.pdb TPO-1bkx-opt.pdb
PYROGLUTAMIC_ACID PCA GLU AAREST PCA-1a8j.pdb PCA-1a8j-opt.pdb
PYRUVOYL_GROUP PVL - PVL PVL-1hq6.pdb PVL-1hq6-opt.pdb
SARCOSINE SAR GLY AANME SAR-1bck.pdb SAR-1bck-opt.pdb
S-HYDROXY-CYSTEINE CEA CYS AAREST CEA-1cxp.pdb CEA-1cxp-opt.pdb
S-HYDROXYCYSTEINE CSO CYS AAREST CSO-1dmp.pdb CSO-1dmp-opt.pdb
S-MERCAPTOCYSTEINE CSS CYS AAREST CSS-1bi0.pdb CSS-1bi0-opt.pdb
S-OXY_CYSTEINE CSX CYS AAREST CSX-1fw8.pdb CSX-1fw8-opt.pdb
S,S-(2-HYDROXYETHYL)THIOCYSTEINE CME CYS AAREST CME-1a1v.pdb CME-1a1v-opt.pdb
SULFONATED_TYROSINE TYS TYR AAREST TYS-1a2c.pdb TYS-1a2c-opt.pdb
TERT-BUTYLOXYCARBONYL_GROUP BOC - BOC BOC-1btw.pdb BOC-1btw-opt.pdb
TOPO-QUINONE TPQ PHE AAREST TPQ-1a2v.pdb TPQ-1a2v-opt.pdb
TYROSINE-O-SULPHONIC_ACID STY TYR AAREST STY-1c5l.pdb STY-1c5l-opt.pdb

Cofactors

Residue restraints were generated in 4 steps:
  • a high-resolution structure from the hiccup database was chosen as a starting point
  • the structure was corrected for atom-typing and charged groups and its geometry optimized using the MMFF force field and a constant dielectric constant of 80(water)
  • PDB2TNT was run on the resulting optimized structure
  • P=O bonds were normalized manually to correct for electron delocalization

cofactor 3-letter code/link to formula example coordinates from the Hiccup database superposition of Hiccup/optimised coordinates
ADP ADP adp_exp.pdb adp-opt.pdb
AMP AMP amp_exp.pdb amp-opt.pdb
ATP ATP atp_exp.pdb atp-opt.pdb
cAMP CMP cmp_exp.pdb cmp-opt.pdb
COENZYME A[1] COA coa_exp.pdb coa-opt.pdb
FAD FAD fad_exp.pdb fad-opt.pdb
FLAVIN_MONONUCLEOTIDE FMN fmn_exp.pdb fmn-opt.pdb
NADP NAP nap_exp.pdb nap-opt.pdb
NADPH NDP ndp_exp.pdb ndp-opt.pdb
[1] MMMFFs optimized Ac-CoA has been used as a template structure

Carbohydrates

TNT-restraints for:
  • all sugars listed in the table below
  • all O-glycosidic linkages between those monomers (please use MakeLINK to add the appropriate link to your TNT-sequence file)
  • N-glycosidic linkage between ASN and any pyranose (including NAG), O-glycosidic linkages between SER/THR and any pyranose (including MAN; please use MakeLINK to add to your sequence file)

cofactor 3-letter code/link to formula example monomer coordinates from the Hiccup database superposition of PDB/optimised coordinates for monomer example environment optimized example environment
D-GLUCOSE BGC GLC bgc_msd.pdb glc_msd.pdb bgc_msd-opt.pdb glc_msd-opt.pdb 1od3.pdb 3chb.pdb 1od3-opt.pdb 3chb-opt.pdb
D-MANNOSE MAN BMA bma_msd.pdb man_msd.pdb bma_msd-opt.pdb man_msd-opt.pdb 1ib4.pdb 1oh4.pdb 1ib4-opt.pdb 1oh4-opt.pdb
FUCOSE FUC fuc_msd.pdb fuc_msd-opt.pdb 1e4m.pdb 1e4m-opt.pdb
D-GALACTOSE GAL GLA gal_msd.pdb gla_msd.pdb gal_msd-opt.pdb gla_msd-opt.pdb 3chb.pdb 1oh4.pdb 3chb-opt.pdb 1oh4-opt.pdb
N-ACETYL-D-GLUCOSAMINE NAG nag_msd.pdb nag_msd-opt.pdb 1e4m.pdb 1e4m-opt.pdb
N-ACETYL-D-GALACTOSAMINE NGA nga_msd.pdb nga_msd-opt.pdb 3chb.pdb 3chb-opt.pdb
O-SIALIC_ACID SIA sia_msd.pdb sia_msd-opt.pdb 3chb.pdb 3chb-opt.pdb
D-XYLOPYRANOSE XYS xys_msd.pdb xys_msd-opt.pdb 1e4m.pdb 1e4m-opt.pdb

Maria Brandl,<buster-develop@GlobalPhasing.com>
Last modification: 16.02.11