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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1mk5
BIOTIN-BINDING PROTEIN HEADER
WILDTYPE CORE-STREPTAVIDIN WITH BIOTIN AT 1.4A. TITLE
STREPTAVIDIN 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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BTN H5100
23A ASN
25A LEU
27A SER
43A TYR
45A SER
47A VAL
48A GLY
49A ASN
50A ALA
79A TRP
86A ALA
88A SER
90A THR
92A TRP
108A TRP
110A LEU
112A SER
120G TRP
128A ASP
BTN D5100
23E ASN
25E LEU
27E SER
43E TYR
45E SER
47E VAL
48E GLY
49E ASN
50E ALA
79E TRP
86E ALA
88E SER
90E THR
92E TRP
108E TRP
110E LEU
112E SER
120C TRP
128E ASP
BTN J5200
23O ASN
25O LEU
27O SER
43O TYR
45O SER
47O VAL
48O GLY
49O ASN
50O ALA
79O TRP
86O ALA
88O SER
90O THR
92O TRP
108O TRP
110O LEU
112O SER
120I TRP
128O ASP
BTN B5200
23G ASN
25G LEU
27G SER
43G TYR
45G SER
47G VAL
48G GLY
49G ASN
50G ALA
79G TRP
86G ALA
88G SER
90G THR
92G TRP
108G TRP
110G LEU
112G SER
120A TRP
128G ASP
BTN L5100
23M ASN
25M LEU
27M SER
43M TYR
45M SER
47M VAL
48M GLY
49M ASN
50M ALA
79M TRP
86M ALA
88M SER
90M THR
92M TRP
108M TRP
110M LEU
112M SER
120K TRP
128M ASP
BTN P5100
23I ASN
25I LEU
27I SER
43I TYR
45I SER
47I VAL
48I GLY
49I ASN
50I ALA
79I TRP
86I ALA
88I SER
90I THR
92I TRP
108I TRP
110I LEU
112I SER
120O TRP
128I ASP
BTN N5200
23K ASN
25K LEU
27K SER
43K TYR
45K SER
47K VAL
48K GLY
49K ASN
50K ALA
79K TRP
86K ALA
88K SER
90K THR
92K TRP
108K TRP
110K LEU
112K SER
120M TRP
128K ASP
BTN F5200
23C ASN
25C LEU
27C SER
43C TYR
45C SER
47C VAL
48C GLY
49C ASN
50C ALA
79C TRP
86C ALA
88C SER
90C THR
92C TRP
108C TRP
110C LEU
112C SER
120E TRP
128C ASP
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):

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
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
1swc Details
other holo-structures
pdb ID Ligand Unique ID
3ry1 MRDF4001 MRDG4006 Details
1swd BTNF_300 Details
BTNB_600
2gh7 BTNR5200 Details
BTNE5100
BTNI5200
BTNN5100
2f01 BTNR5200 Details
BTNE5100
BTNI5200
BTNN5100
1swe BTND_500 Details
BTNB_600
BTNH_300
BTNF_400
3ry2 BTNG5001 Details
BTNU5001
BTNC5001 GOLM4003
BTNJ5001 GOLF4003
BTNX5001 GOLT4003
BTNQ5001 GOLA4003
BTNN5001
BTNB5001
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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BTN NAME: BIOTIN
FORMULA: C10 H16 N2 O3 S1
SMILES: OC(=O)CCCCC1SCC2NC(=O)NC12
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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