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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1f6a
IMMUNE SYSTEM HEADER
STRUCTURE OF THE HUMAN IGE-FC BOUND TO ITS HIGH AFFINITY RECEPTOR FC(EPSILON)RI(ALPHA) TITLE
IG EPSILON CHAIN C REGION 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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CPS a 102
331I SER
332I ASN
333I PRO
334H ARG
335H GLY
427H ARG
CPS Y 102
331D SER
332D ASN
333D PRO
334B ARG
335B GLY
427B ARG
CPS Z 102
331F SER
332F ASN
333F PRO
334E ARG
335E GLY
427E ARG
CPS Y 103
333D PRO
334D ARG
335D GLY
336D VAL
362D ASP
364D ALA
365D PRO
422D HIS
424D HIS
425D LEU
CPS Z 103
333F PRO
334F ARG
335F GLY
336F VAL
362F ASP
364F ALA
365F PRO
422F HIS
424F HIS
425F LEU
CPS a 103
333I PRO
334I ARG
335I GLY
336I VAL
362I ASP
364I ALA
365I PRO
422I HIS
424I HIS
425I LEU
NAG V 695
334D ARG
339D TYR
359D LEU
361D VAL
362D ASP
390D GLU
392D GLN
398D THR
NAG V 694
334D ARG
361D VAL
362D ASP
392D GLN
394D ASN
396D THR
398D THR
NAG W 695
334F ARG
339F TYR
359F LEU
361F VAL
362F ASP
390F GLU
392F GLN
398F THR
NAG W 694
334F ARG
361F VAL
362F ASP
392F GLN
394F ASN
396F THR
398F THR
NAG X 694
334I ARG
361I VAL
362I ASP
392I GLN
394I ASN
396I THR
398I THR
NAG X 695
334I ARG
339I TYR
359I LEU
361I VAL
362I ASP
390I GLU
392I GLN
398I THR
NAG U 695
337H SER
339H TYR
359H LEU
361H VAL
362H ASP
390H GLU
392H GLN
398H THR
NAG S 695
337B SER
339B TYR
359B LEU
361B VAL
362B ASP
390B GLU
392B GLN
398B THR
NAG T 695
337E SER
339E TYR
359E LEU
361E VAL
362E ASP
390E GLU
392E GLN
398E THR
MAN V 696
339D TYR
341D SER
359D LEU
MAN U 696
339H TYR
341H SER
359H LEU
MAN U 698
339H TYR
MAN S 696
339B TYR
341B SER
359B LEU
MAN S 698
339B TYR
MAN W 696
339F TYR
341F SER
359F LEU
MAN T 696
339E TYR
341E SER
359E LEU
MAN T 698
339E TYR
MAN X 696
339I TYR
341I SER
359I LEU
MAN U 697
341H SER
MAN S 697
341B SER
MAN T 697
341E SER
NAG U 694
361H VAL
362H ASP
392H GLN
393H ARG
394H ASN
396H THR
398H THR
NAG S 694
361B VAL
362B ASP
392B GLN
393B ARG
394B ASN
396B THR
398B THR
NAG T 694
361E VAL
362E ASP
392E GLN
393E ARG
394E ASN
396E THR
398E THR
CPS Z 105
365F PRO
366F SER
367F LYS
368F GLY
423F PRO
424F HIS
CPS a 105
365I PRO
366I SER
367I LYS
368I GLY
423I PRO
424I HIS
CPS Y 105
365D PRO
366D SER
367D LYS
368D GLY
423D PRO
424D HIS
MAN O 246
419I ARG
427I ARG
428I ALA
430I MET
MAN N 246
419F ARG
427F ARG
428F ALA
430F MET
MAN M 246
419D ARG
427D ARG
428D ALA
430D MET
CPS Y 101
423D PRO
424D HIS
CPS a 101
423I PRO
424I HIS
CPS Z 101
423F PRO
424F HIS
MAN U 699
494H GLN
496I ARG
MAN S 699
494B GLN
496D ARG
MAN T 699
494E GLN
496F 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):

» NAG-NAG-MAN-FUC » Jmol
» NAG-NAG-MAN-MAN-
MAN 		» Jmol
» NAG-NAG-FUC » Jmol
» NAG-NAG-MAN-MAN-
MAN-MAN 		» Jmol
» NAG-NAG-MAN » Jmol
» SO4 » Jmol
» CPS » 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
1fp5 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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MAN NAME: ALPHA-D-MANNOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
NAG NAME: N-ACETYL-D-GLUCOSAMINE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
CPS NAME: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
FORMULA: C32 H58 N2 O7 S1
SMILES: CC(CCC(=O)NCCC[N+](C)(C)CCCS([O-])(=O)=O)C1CCC2C3C(O)CC4CC(O)CCC4(C)C3CC(O)C12C
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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