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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2w9s
OXIDOREDUCTASE HEADER
STAPHYLOCOCCUS AUREUS S1:DHFR IN COMPLEX WITH TRIMETHOPRIM TITLE
DIHYDROFOLATE REDUCTASE TYPE 1 FROM TN4003 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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TOP A1160
5A ILE
6A VAL
7A ALA
20A LEU
27A ASP
28A LEU
30A HIS
31A ILE
46A THR
49A SER
50A ILE
54A LEU
92A PHE
98A TYR
109A TYR
111A THR
TOP E1160
5E ILE
6E VAL
7E ALA
14E ILE
15E GLY
18E ASN
19E GLN
20E LEU
27E ASP
28E LEU
30E HIS
31E ILE
33B GLN
46E THR
49E SER
50E ILE
54E LEU
92E PHE
98E TYR
111E THR
TOP D1158
5D ILE
6D VAL
7D ALA
14D ILE
18D ASN
19D GLN
20D LEU
27D ASP
28D LEU
30D HIS
31D ILE
33C GLN
46D THR
49D SER
50D ILE
54D LEU
92D PHE
98D TYR
109D TYR
111D THR
118A GLN
TOP C1160
5C ILE
6C VAL
7C ALA
19C GLN
20C LEU
27C ASP
28C LEU
30C HIS
31C ILE
46C THR
49C SER
50C ILE
54C LEU
92C PHE
98C TYR
111C THR
TOP F1159
5F ILE
6F VAL
7F ALA
14F ILE
15F GLY
18F ASN
19F GLN
20F LEU
27F ASP
28F LEU
30F HIS
31F ILE
33A GLN
46F THR
49F SER
50F ILE
54F LEU
92F PHE
98F TYR
109F TYR
111F THR
TOP B1160
5B ILE
6B VAL
7B ALA
20B LEU
27B ASP
28B LEU
30B HIS
31B ILE
46B THR
49B SER
50B ILE
54B LEU
92B PHE
98B TYR
111B THR
NDP A1159
6A VAL
7A ALA
14A ILE
15A GLY
16A TYR
18A ASN
19A GLN
20A LEU
22A TRP
43A ALA
44A ARG
45A LYS
46A THR
49A SER
62A LEU
63A THR
64A ASN
65A GLN
77A ASN
78A SER
79A LEU
92A PHE
93A GLY
94A GLY
95A GLN
96A THR
97A LEU
98A TYR
100A ALA
120A ASP
121A THR
NDP C1159
6C VAL
7C ALA
14C ILE
15C GLY
16C TYR
18C ASN
19C GLN
20C LEU
22C TRP
43C ALA
44C ARG
45C LYS
46C THR
49C SER
62C LEU
63C THR
64C ASN
65C GLN
77C ASN
78C SER
79C LEU
92C PHE
93C GLY
94C GLY
95C GLN
96C THR
97C LEU
98C TYR
120C ASP
121C THR
NDP B1159
6B VAL
7B ALA
14B ILE
15B GLY
16B TYR
18B ASN
19B GLN
20B LEU
22B TRP
43B ALA
44B ARG
45B LYS
46B THR
49B SER
62B LEU
63B THR
64B ASN
65B GLN
77B ASN
78B SER
79B LEU
92B PHE
93B GLY
94B GLY
95B GLN
96B THR
97B LEU
98B TYR
120B ASP
121B THR
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
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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).

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apo-structure
pdb ID
2w9t Details
other holo-structures
pdb ID Ligand Unique ID
none
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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NDP NAME: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H30 N7 O17 P3
SMILES: NC(=O)C1=CN(C=CC1)C2OC(COP(O)(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
TOP NAME: TRIMETHOPRIM
FORMULA: C14 H18 N4 O3
SMILES: COc1cc(Cc2cnc(N)nc2N)cc(OC)c1OC
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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