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

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

(click anywhere in this window to remove it)
1o26
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND DUMP AT 1.6 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
PGE Q 635
26A ALA
27A ALA
30A SER
31A PHE
48A LEU
52A GLY
53A HIS
54A GLU
55A THR
56A PRO
85I ASN
91I TYR
165A ARG
173M LEU
PGE L 640
27F ALA
30F SER
31F PHE
44F LEU
47F TYR
48F LEU
52F GLY
53F HIS
54F GLU
55F THR
56F PRO
85M ASN
91M TYR
173I LEU
FAD B 615
30M SER
53M HIS
54M GLU
55M THR
58M GLU
78A ARG
79A HIS
80A ARG
81M ILE
82F ALA
83F SER
85F ASN
86F GLU
88F SER
90F ARG
91F TYR
163M ASN
165M ARG
166M SER
169A ASN
173A LEU
174A ARG
178A HIS
179A ALA
FAD J 610
30F SER
53F HIS
54F GLU
55F THR
58F GLU
78I ARG
79I HIS
80I ARG
81F ILE
82M ALA
83M SER
85M ASN
86M GLU
88M SER
90M ARG
91M TYR
163F ASN
165F ARG
166F SER
169I ASN
173I LEU
174I ARG
178I HIS
179I ALA
FAD N 605
30A SER
53A HIS
54A GLU
55A THR
58A GLU
78M ARG
79M HIS
80M ARG
81A ILE
82I ALA
83I SER
85I ASN
86I GLU
88I SER
90I ARG
91I TYR
163A ASN
165A ARG
166A SER
169M ASN
173M LEU
174M ARG
178M HIS
179M ALA
FAD G 600
30I SER
53I HIS
54I GLU
55I THR
58I GLU
78F ARG
79F HIS
80F ARG
81I ILE
82A ALA
83A SER
85A ASN
86A GLU
88A SER
90A ARG
91A TYR
163I ASN
165I ARG
166I SER
169F ASN
173F LEU
174F ARG
178F HIS
179F ALA
PGE E 620
70A ILE
73A ALA
74A ARG
77A PHE
78F ARG
86A GLU
PGE P 625
70M ILE
73M ALA
74I ARG
77M PHE
78I ARG
86M GLU
156I THR
UMP O 613
71I PHE
74I ARG
75I GLN
78I ARG
86M GLU
87M LEU
88M SER
89M GLY
90M ARG
91M TYR
147M ARG
174I ARG
180I GLN
UMP H 618
71A PHE
74A ARG
75A GLN
78A ARG
86F GLU
87F LEU
88F SER
89F GLY
90F ARG
91F TYR
147F ARG
174A ARG
180A GLN
UMP K 608
71M PHE
74M ARG
75M GLN
78M ARG
86I GLU
87I LEU
88I SER
89I GLY
90I ARG
91I TYR
147I ARG
174M ARG
180M GLN
UMP C 603
71F PHE
74F ARG
75F GLN
78F ARG
86A GLU
87A LEU
88A SER
89A GLY
90A ARG
91A TYR
147A ARG
174F ARG
180F 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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
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
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
1o29 FADE_800 UFPC_803 UFPL_813 FADH_810 Details
FADB_815 UFPI_808 UFPF_818 FADK_805
UFPL_813 FADH_810
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.

(click anywhere in this window to remove it)
PGE NAME: TRIETHYLENE GLYCOL
FORMULA: C6 H14 O4
SMILES: OCCOCCOCCO
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
UMP NAME: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
FORMULA: C9 H13 N2 O8 P1
SMILES: OC1CC(OC1COP(O)(O)=O)N2C=CC(=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
Script execution time: 2.727 seconds