university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (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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1nly
HYDROLASE HEADER
CRYSTAL STRUCTURE OF THE TRAFFIC ATPASE OF THE HELICOBACTER PYLORI TYPE IV SECRETION SYSTEM IN COMPLEX WITH ATPGAMMAS TITLE
VIRB11 HOMOLOG 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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2PE G 600
38B ASP
39B PHE
41B LYS
43B GLU
55B VAL
67B PRO
68B PHE
69B ASP
70B VAL
71B ARG
73B ARG
2PE I 600
38F ASP
39F PHE
41F LYS
43F GLU
55F VAL
67F PRO
68F PHE
69F ASP
70F VAL
71F ARG
73F ARG
2PE H 600
38C ASP
39C PHE
41C LYS
43C GLU
55C VAL
67C PRO
68C PHE
69C ASP
70C VAL
71C ARG
73C ARG
ATG G 400
44A ASN
45A ILE
46A THR
61A ASN
113A ARG
133A ARG
134A ILE
135A PRO
136A SER
137A LYS
138A THR
140A TYR
144A PHE
145A PHE
148A GLN
150A PHE
180A THR
181A GLY
182A SER
183A GLY
184A LYS
185A THR
186A THR
209A GLU
248A GLU
271A THR
273A HIS
320A LYS
ATG I 500
44F ASN
45F ILE
46F THR
61F ASN
113F ARG
133F ARG
134F ILE
135F PRO
136F SER
137F LYS
138F THR
140F TYR
144F PHE
145F PHE
148F GLN
150F PHE
180F THR
181F GLY
182F SER
183F GLY
184F LYS
185F THR
186F THR
209F GLU
248F GLU
271F THR
273F HIS
320F LYS
ATG I 400
44E ASN
45E ILE
46E THR
61E ASN
113E ARG
133E ARG
134E ILE
135E PRO
136E SER
137E LYS
138E THR
140E TYR
144E PHE
145E PHE
148E GLN
150E PHE
180E THR
181E GLY
182E SER
183E GLY
184E LYS
185E THR
186E THR
209E GLU
248E GLU
271E THR
273E HIS
320E LYS
ATG H 500
44C ASN
45C ILE
46C THR
61C ASN
113C ARG
133C ARG
134C ILE
135C PRO
136C SER
137C LYS
138C THR
140C TYR
144C PHE
145C PHE
148C GLN
150C PHE
180C THR
181C GLY
182C SER
183C GLY
184C LYS
185C THR
186C THR
209C GLU
248C GLU
271C THR
273C HIS
320C LYS
ATG G 500
44B ASN
45B ILE
46B THR
61B ASN
113B ARG
133B ARG
134B ILE
135B PRO
136B SER
137B LYS
138B THR
140B TYR
144B PHE
145B PHE
148B GLN
150B PHE
180B THR
181B GLY
182B SER
183B GLY
184B LYS
185B THR
186B THR
209B GLU
248B GLU
271B THR
273B HIS
320B LYS
ATG H 400
44D ASN
45D ILE
46D THR
61D ASN
113D ARG
133D ARG
134D ILE
135D PRO
136D SER
137D LYS
138D THR
140D TYR
144D PHE
145D PHE
148D GLN
150D PHE
180D THR
181D GLY
182D SER
183D GLY
184D LYS
185D THR
186D THR
209D GLU
248D GLU
273D HIS
320D LYS
SO4 I 800
181F GLY
182F SER
183F GLY
184F LYS
185F THR
SO4 H 800
181C GLY
182C SER
183C GLY
184C LYS
185C THR
SO4 G 800
181B GLY
182B SER
183B GLY
184B LYS
185B THR
MG G 700
185A THR
209A GLU
247A GLY
248A GLU
271A THR
MG I 700
185E THR
209E GLU
247E GLY
248E GLU
271E THR
MG H 700
185D THR
209D GLU
247D GLY
248D GLU
271D 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:

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

LigPlot (hosted at the EBI):

» SO4 » Jmol
» ATG » Jmol
» 2PE » Jmol
» MG » Jmol
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
2pt7 Details
other holo-structures
pdb ID Ligand Unique ID
1g6o PEGI_500 PEGI_503 PEGI_504 PEGI_502 PEGI_501 Details
ADPH_401
PEGG_500 PEGG_503 PEGG_502 PEGG_504 PEGG_501
ADPI_401
ADPG_402
ADPH_402
ADPG_401
ADPI_402
PEGH_500 PEGH_502 PEGH_504 PEGH_503 PEGH_501
1opx 2PEI2000 Details
2PEH2000
2PEG2000
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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ATG NAME: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
FORMULA: C10 H16 N5 O12 P3 S1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(S)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
2PE NAME: NONAETHYLENE GLYCOL
FORMULA: C18 H38 O10
SMILES: OCCOCCOCCOCCOCCOCCOCCOCCOCCO
SO4 NAME: SULFATE ION
FORMULA: O4 S1
SMILES: [O-]S([O-])(=O)=O
v6.0
October 2008		 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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