university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

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

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1bzy
PHOSPHORIBOSYLTRANSFERASE HEADER
HUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR TITLE
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE 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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MG S 900
66P VAL
67P LEU
69P GLY
101P LEU
133P GLU
134P ASP
141P THR
IMU B 300
66A VAL
69A GLY
101A LEU
103A SER
104A TYR
109A SER
133A GLU
134A ASP
135A ILE
136A ILE
137A ASP
138A THR
139A GLY
140A LYS
141A THR
142A MET
165A LYS
185A LYS
186A PHE
187A VAL
192A LEU
193A ASP
MG D 900
66A VAL
67A LEU
69A GLY
101A LEU
133A GLU
134A ASP
IMU G 300
66F VAL
69F GLY
103F SER
104F TYR
109F SER
133F GLU
134F ASP
135F ILE
136F ILE
137F ASP
138F THR
139F GLY
140F LYS
141F THR
142F MET
165F LYS
186F PHE
187F VAL
192F LEU
193F ASP
MG I 900
66F VAL
67F LEU
69F GLY
101F LEU
133F GLU
134F ASP
141F THR
MG N 900
66K VAL
67K LEU
69K GLY
101K LEU
133K GLU
134K ASP
POP T 400
67P LEU
68P LYS
69P GLY
100P ARG
101P LEU
102P LYS
103P SER
104P TYR
141P THR
193P ASP
196P GLU
199P ARG
POP E 400
67A LEU
68A LYS
69A GLY
100A ARG
101A LEU
102A LYS
103A SER
104A TYR
141A THR
193A ASP
196A GLU
199A ARG
POP J 400
67F LEU
68F LYS
69F GLY
100F ARG
101F LEU
102F LYS
103F SER
104F TYR
141F THR
196F GLU
199F ARG
POP O 400
67K LEU
68K LYS
69K GLY
100K ARG
101K LEU
102K LYS
103K SER
104K TYR
141K THR
196K GLU
199K ARG
MG M 901
102K LYS
104K TYR
186K PHE
192K LEU
193K ASP
199K ARG
IMU Q 300
103P SER
104P TYR
109P SER
113P ILE
133P GLU
134P ASP
135P ILE
136P ILE
137P ASP
138P THR
139P GLY
140P LYS
141P THR
165P LYS
186P PHE
187P VAL
192P LEU
193P ASP
IMU L 300
103K SER
104K TYR
109K SER
133K GLU
134K ASP
135K ILE
136K ILE
137K ASP
138K THR
139K GLY
140K LYS
141K THR
142K MET
165K LYS
185K LYS
186K PHE
187K VAL
192K LEU
193K ASP
MG R 901
104P TYR
186P PHE
193P ASP
MG C 901
104A TYR
186A PHE
193A ASP
MG H 901
104F TYR
186F PHE
193F ASP
199F ARG
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
1z7g Details
other holo-structures
pdb ID Ligand Unique ID
1hmp 5GPD_800 Details
5GPB_300
5GPH_800
5GPF_300
3ggc H26A_218 Details
H26D_218
H26B_218
H26C_218
3ggj 25HB_218 Details
25HD_218
25HC_218
25HA_218
3gep 24HC_218 Details
24HA_218
24HB_218
24HD_218
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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IMU NAME: PHOSPHORIC ACID MONO-[5-(2-AMINO-4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-3,4-DIHYDROXY-PYRROLIDIN-2-YLMETHYL] ESTER
FORMULA: C11 H16 N5 O7 P1
SMILES: NC1=Nc2c([nH]cc2C3NC(COP(O)(O)=O)C(O)C3O)C(=O)N1
POP NAME: PYROPHOSPHATE 2-
FORMULA: H2 O7 P2
SMILES: OP([O-])(=O)OP(O)([O-])=O
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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