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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2yvo
HYDROLASE HEADER
CRYSTAL STRUCTURE OF NDX2 IN COMPLEX WITH MG2+ AND AMP FROM THERMUS THERMOPHILUS HB8 TITLE
MUTT/NUDIX FAMILY PROTEIN 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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AMP J2001
16F PRO
17F VAL
32A LEU
33A THR
34A TYR
35A VAL
60F GLN
62F ARG
74F ALA
75F GLY
76F LYS
90F GLU
94F GLU
113A SER
114A PHE
136F GLU
137F GLU
138F GLY
139F GLU
AMP E2001
16A PRO
17A VAL
32F LEU
33F THR
34F TYR
35F VAL
60A GLN
62A ARG
74A ALA
75A GLY
76A LYS
90A GLU
113F SER
114F PHE
136A GLU
137A GLU
138A GLY
139A GLU
MG G1002
60F GLN
62F ARG
74F ALA
94F GLU
139F GLU
MG B1002
60A GLN
62A ARG
74A ALA
94A GLU
139A GLU
MG H1003
76F LYS
78F ASP
89F ARG
90F GLU
136F GLU
MG C1003
76A LYS
78A ASP
89A ARG
90A GLU
136A GLU
MG I1001
90F GLU
93F GLU
94F GLU
136F GLU
139F GLU
MG D1001
90A GLU
93A GLU
94A GLU
136A GLU
139A GLU
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).

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

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apo-structure
pdb ID
2yvn Details
other holo-structures
pdb ID Ligand Unique ID
2yvp RBYB_186 _MGD_185 _MGC_183 _MGE_184 Details
RBYG_186 _MGH_183 _MGJ_184 _MGI_185
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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AMP NAME: ADENOSINE MONOPHOSPHATE
FORMULA: C10 H14 N5 O7 P1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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