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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1um0
LYASE HEADER
CRYSTAL STRUCTURE OF CHORISMATE SYNTHASE COMPLEXED WITH FMN TITLE
CHORISMATE SYNTHASE 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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FMN J3400
50E ARG
103E SER
104E HIS
105E ALA
122E GLY
123E ARG
125E SER
126E ALA
129E SER
240E LEU
241E ASN
242E GLY
244E LYS
276F SER
279F VAL
280F LEU
281F GLY
295E PHE
296E LYS
298E THR
299E PRO
300E SER
323E HIS
324E ASP
327E ILE
330E ARG
331E GLY
334E VAL
FMN I3400
50C ARG
103C SER
104C HIS
105C ALA
122C GLY
123C ARG
125C SER
126C ALA
129C SER
240C LEU
241C ASN
242C GLY
244C LYS
276B SER
279B VAL
280B LEU
281B GLY
295C PHE
296C LYS
298C THR
299C PRO
300C SER
323C HIS
324C ASP
327C ILE
330C ARG
331C GLY
334C VAL
FMN J1400
93G TYR
103G SER
104G HIS
105G ALA
122G GLY
123G ARG
125G SER
126G ALA
129G SER
228H LYS
230H ASP
240G LEU
241G ASN
242G GLY
243G VAL
244G LYS
279H VAL
280H LEU
281H GLY
282H GLY
295G PHE
296G LYS
298G THR
299G PRO
300G SER
323G HIS
324G ASP
327G ILE
330G ARG
331G GLY
334G VAL
FMN I1400
93A TYR
103A SER
104A HIS
105A ALA
122A GLY
123A ARG
125A SER
126A ALA
129A SER
228D LYS
230D ASP
240A LEU
241A ASN
242A GLY
243A VAL
244A LYS
279D VAL
280D LEU
281D GLY
282D GLY
295A PHE
296A LYS
298A THR
299A PRO
300A SER
323A HIS
324A ASP
327A ILE
330A ARG
331A GLY
334A VAL
FMN J2400
103F SER
104F HIS
105F ALA
122F GLY
123F ARG
124F SER
125F SER
126F ALA
129F SER
230E ASP
240F LEU
241F ASN
242F GLY
243F VAL
244F LYS
262E TYR
276E SER
279E VAL
280E LEU
281E GLY
282E GLY
295F PHE
296F LYS
298F THR
299F PRO
300F SER
323F HIS
324F ASP
327F ILE
330F ARG
331F GLY
334F VAL
FMN I4400
103D SER
104D HIS
105D ALA
122D GLY
123D ARG
125D SER
126D ALA
129D SER
228A LYS
230A ASP
240D LEU
241D ASN
242D GLY
243D VAL
244D LYS
279A VAL
280A LEU
281A GLY
282A GLY
295D PHE
296D LYS
298D THR
299D PRO
300D SER
323D HIS
324D ASP
327D ILE
330D ARG
331D GLY
334D VAL
FMN I2400
103B SER
104B HIS
105B ALA
122B GLY
123B ARG
124B SER
125B SER
126B ALA
129B SER
230C ASP
240B LEU
241B ASN
242B GLY
243B VAL
244B LYS
262C TYR
276C SER
279C VAL
280C LEU
281C GLY
282C GLY
295B PHE
296B LYS
298B THR
299B PRO
300B SER
323B HIS
324B ASP
327B ILE
330B ARG
331B GLY
334B VAL
FMN J4400
103H SER
104H HIS
105H ALA
122H GLY
123H ARG
125H SER
126H ALA
129H SER
230G ASP
240H LEU
241H ASN
242H GLY
243H VAL
244H LYS
279G VAL
280G LEU
281G GLY
282G GLY
295H PHE
296H LYS
298H THR
299H PRO
300H SER
323H HIS
324H ASP
327H ILE
330H ARG
331H GLY
334H VAL
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):

» 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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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
1umf 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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FMN NAME: FLAVIN MONONUCLEOTIDE
FORMULA: C17 H21 N4 O9 P1
SMILES: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CC(O)C(O)C(O)COP(O)(O)=O)c2cc1C
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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