university lille north of france LigASite database of binding sites
Home
News
Introduction
Methods
Flow Chart
References
Download
About
FAQ
Search
LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
(click to remove window)
Browse dataset
holo-structureHelp

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

(click anywhere in this window to remove it)
2yzn
LIGASE HEADER
CRYSTAL STRUCTURE OF D-ALANINE:D-ALANINE LIGASE WITH AMPPNP FROM THERMUS THERMOPHILUS HB8. TITLE
D-ALANINE-D-ALANINE LIGASE 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)
ANP H 403
13G GLU
116G LYS
131G VAL
151G PHE
153G LYS
159G SER
160G SER
163G ILE
189G GLU
190G LYS
191G ALA
192G LEU
195G VAL
197G GLU
218G TYR
219C GLU
220C ALA
221C PRO
222C PHE
268G ARG
270G ASP
272G PHE
281G ASN
282G GLU
284G ASN
ANP F 403
13E GLU
116E LYS
131E VAL
151E PHE
153E LYS
159E SER
160E SER
163E ILE
189E GLU
190E LYS
191E ALA
192E LEU
195E VAL
197E GLU
218E TYR
219K GLU
220K ALA
221K PRO
222K PHE
268E ARG
270E ASP
272E PHE
281E ASN
282E GLU
284E ASN
ANP D 402
87C GLU
113C CYS
114C MET
116C LYS
131C VAL
151C PHE
153C LYS
157C THR
158C GLY
159C SER
160C SER
163C ILE
165C ARG
189C GLU
190C LYS
191C ALA
192C LEU
195C VAL
197C GLU
218C TYR
219G GLU
220G ALA
221G PRO
270C ASP
272C PHE
281C ASN
282C GLU
284C ASN
ANP L 402
87K GLU
113K CYS
114K MET
116K LYS
131K VAL
151K PHE
153K LYS
157K THR
158K GLY
159K SER
160K SER
163K ILE
189K GLU
190K LYS
191K ALA
192K LEU
195K VAL
197K GLU
218K TYR
219E GLU
220E ALA
221E PRO
270K ASP
272K PHE
281K ASN
282K GLU
284K ASN
ANP J 401
116I LYS
131I VAL
151I PHE
153I LYS
154I PRO
155I ALA
156I ASN
157I THR
160I SER
163I ILE
189I GLU
190I LYS
192I LEU
195I VAL
197I GLU
270I ASP
272I PHE
281I ASN
282I GLU
ANP B 401
116A LYS
131A VAL
151A PHE
153A LYS
154A PRO
155A ALA
156A ASN
157A THR
160A SER
163A ILE
165A ARG
189A GLU
190A LYS
192A LEU
195A VAL
197A GLU
270A ASP
272A PHE
281A ASN
282A 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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
» 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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
2yzg Details
other holo-structures
pdb ID Ligand Unique ID
2zdq ATPD1502 DALC_403 DALC_404 Details
ATPB1501 DALA_401 DALA_402
2zdh ADPN_704 _MGO_817 Details
ADPF_702 _MGH_813
ADPB_701 _MGC_811 _MGD_812
ADPJ_703 _MGL_815
2zdg ADPI_404 _MGJ_602 Details
ADPD_402
ADPF_403 _MGG_601
ADPB_401
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)
ANP NAME: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
FORMULA: C10 H17 N6 O12 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)NP(O)(O)=O)C(O)C3O
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: 0.4506 seconds