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

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

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1o29
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND FDUMP AT 2.0 A RESOLUTION TITLE
THYMIDYLATE SYNTHASE THYX COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

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

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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FAD B 815
27J ALA
53J HIS
54J GLU
55J THR
58J GLU
78A ARG
79A HIS
80A ARG
81J ILE
82D ALA
83D SER
85D ASN
86D GLU
88D SER
90D ARG
91D TYR
163J ASN
165J ARG
166J SER
169A ASN
173A LEU
174A ARG
178A HIS
179A ALA
FAD E 800
30G SER
53G HIS
54G GLU
55G THR
58G GLU
78D ARG
79D HIS
80D ARG
81G ILE
82A ALA
83A SER
85A ASN
86A GLU
88A SER
90A ARG
91A TYR
163G ASN
165G ARG
166G SER
169D ASN
173D LEU
174D ARG
178D HIS
179D ALA
FAD H 810
30D SER
53D HIS
54D GLU
55D THR
58D GLU
78G ARG
79G HIS
80G ARG
81D ILE
82J ALA
83J SER
85J ASN
86J GLU
88J SER
90J ARG
91J TYR
163D ASN
165D ARG
166D SER
169G ASN
173G LEU
174G ARG
178G HIS
179G ALA
FAD K 805
30A SER
53A HIS
54A GLU
55A THR
58A GLU
78J ARG
79J HIS
80J ARG
81A ILE
82G ALA
83G SER
85G ASN
86G GLU
88G SER
90G ARG
91G TYR
163A ASN
165A ARG
166A SER
169J ASN
173J LEU
174J ARG
178J HIS
179J ALA
UFP C 803
71D PHE
74D ARG
75D GLN
77A PHE
78D ARG
86A GLU
87A LEU
88A SER
89A GLY
90A ARG
91A TYR
147A ARG
174D ARG
179D ALA
180D GLN
UFP L 813
71G PHE
74G ARG
75G GLN
77J PHE
78G ARG
86J GLU
87J LEU
88J SER
89J GLY
90J ARG
91J TYR
147J ARG
174G ARG
179G ALA
180G GLN
UFP I 808
71J PHE
74J ARG
75J GLN
77G PHE
78J ARG
86G GLU
87G LEU
88G SER
89G GLY
90G ARG
91G TYR
147G ARG
174J ARG
179J ALA
180J GLN
UFP F 818
71A PHE
74A ARG
75A GLN
77D PHE
78A ARG
86D GLU
87D LEU
88D SER
89D GLY
90D ARG
91D TYR
147D ARG
174A ARG
179A ALA
180A 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:

LigPlot (hosted at the EBI):

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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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1o24 Details
other holo-structures
pdb ID Ligand Unique ID
1kq4 FADB_315 FADH_305 Details
FADD_300 FADF_310
1o2b FADE_600 FADH_610 Details
FADC_615 FADK_605
1o26 PGEL_640 FADJ_610 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
UMPO_613 PGEP_625 FADJ_610
1o2a FADD_700 FADF_710 Details
FADB_715 FADH_705
1o27 BRUF_618 FADK_605 FADB_615 Details
BRUI_608 FADK_605 FADB_615
BRUC_603 FADE_600 FADH_610 BRUL_613
1o28 EPED_700 UFPB_703 Details
EPEC_710 UFPP_713
EPEK_715 PGEJ_735 UFPI_718
EPEN_705 UFPM_708
PGEG_725
1o25 UMPH_613 Details
UMPF_608
UMPB_603
UMPD_618
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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FAD NAME: FLAVIN-ADENINE DINUCLEOTIDE
FORMULA: C27 H33 N9 O15 P2
SMILES: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CC(O)C(O)C(O)COP(O)(=O)OP(O)(=O)OCC4OC(C(O)C4O)[n]5cnc6c(N)ncnc56)c2cc1C
UFP NAME: 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
FORMULA: C9 H12 N2 O8 F1 P1
SMILES: OC1CC(OC1COP(O)(O)=O)N2C=C(F)C(=O)NC2=O
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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