university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1o24
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.0 A RESOLUTION TITLE
THYMIDYLATE SYNTHASE THYX COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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26 ALA
27 ALA
29 VAL
30 SER
31 PHE
44 LEU
47 TYR
48 LEU
52 GLY
53 HIS
54 GLU
55 THR
56 PRO
58 GLU
70 ILE
71 PHE
73 ALA
74 ARG
75 GLN
77 PHE
78 ARG
79 HIS
80 ARG
81 ILE
82 ALA
83 SER
84 TYR
85 ASN
86 GLU
87 LEU
88 SER
89 GLY
90 ARG
91 TYR
92 SER
147 ARG
156 THR
161 THR
163 ASN
165 ARG
166 SER
169 ASN
173 LEU
174 ARG
176 ASP
178 HIS
179 ALA
180 GLN
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
1kq4 FADB_315 FADH_305 106 427 Details
FADD_300 FADF_310 106 395
1o2b FADE_600 FADH_610 106 399 Details
FADC_615 FADK_605 106 397
1o26 PGEL_640 FADJ_610 63 228 Details
FADB_615 PGEQ_635 UMPO_613 UMPH_618 PGEL_640 UMPK_608 FADN_605 FADG_600 PGEE_620 PGEP_625 UMPC_603 FADJ_610 332 1163
UMPO_613 PGEP_625 FADJ_610 83 301
1o2a FADD_700 FADF_710 106 390 Details
FADB_715 FADH_705 106 422
1o27 BRUF_618 FADK_605 FADB_615 127 452 Details
BRUI_608 FADK_605 FADB_615 127 452
BRUC_603 FADE_600 FADH_610 BRUL_613 148 523
1o29 FADE_800 UFPC_803 UFPL_813 FADH_810 148 516 Details
FADB_815 UFPI_808 UFPF_818 FADK_805 148 505
UFPL_813 FADH_810 74 263
1o28 EPED_700 UFPB_703 36 140 Details
EPEC_710 UFPP_713 36 139
EPEK_715 PGEJ_735 UFPI_718 46 203
EPEN_705 UFPM_708 36 145
PGEG_725 10 76
1o25 UMPH_613 20 82 Details
UMPF_608 20 82
UMPB_603 20 81
UMPD_618 20 82
v9.7
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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