university lille north of france LigASite database of binding sites
holo-structureHelp

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

(click anywhere in this window to remove it)
3ry2
BIOTIN-BINDING PROTEIN HEADER
WILD-TYPE CORE STREPTAVIDIN-BIOTIN COMPLEX AT ATOMIC RESOLUT 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.

(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)
BTN G5001
23H ASN
25H LEU
27H SER
43H TYR
45H SER
47H VAL
48H GLY
49H ASN
50H ALA
79H TRP
86H ALA
88H SER
90H THR
92H TRP
108H TRP
110H LEU
112H SER
120D TRP
128H ASP
BTN U5001
23V ASN
25V LEU
27V SER
43V TYR
45V SER
47V VAL
48V GLY
49V ASN
50V ALA
79V TRP
86V ALA
88V SER
90V THR
92V TRP
108V TRP
110V LEU
112V SER
120R TRP
128V ASP
BTN C5001
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
120A TRP
128K ASP
BTN J5001
23D ASN
25D LEU
27D SER
43D TYR
45D SER
47D VAL
49D ASN
50D ALA
79D TRP
86D ALA
88D SER
90D THR
92D TRP
108D TRP
110D LEU
112D SER
120H TRP
128D ASP
BTN X5001
23R ASN
25R LEU
27R SER
43R TYR
45R SER
47R VAL
48R GLY
49R ASN
50R ALA
79R TRP
86R ALA
88R SER
90R THR
92R TRP
108R TRP
110R LEU
112R SER
120V TRP
128R ASP
BTN Q5001
23Y ASN
25Y LEU
27Y SER
43Y TYR
45Y SER
47Y VAL
49Y ASN
50Y ALA
79Y TRP
86Y ALA
88Y SER
90Y THR
92Y TRP
108Y TRP
110Y LEU
112Y SER
120O TRP
128Y ASP
BTN N5001
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
120K TRP
128A ASP
BTN B5001
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
120Y TRP
128O ASP
GOL M4003
48K GLY
49K ASN
110K LEU
112K SER
120A TRP
121A LYS
124K LEU
GOL F4003
48D GLY
49D ASN
110D LEU
112D SER
120H TRP
121H LYS
124D LEU
GOL T4003
48R GLY
49R ASN
110R LEU
112R SER
120V TRP
121V LYS
124R LEU
GOL A4003
48Y GLY
49Y ASN
110Y LEU
112Y SER
120O TRP
121O LYS
124Y LEU
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:

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.

(click anywhere in this window to remove it)
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
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
1mk5 BTNH5100 Details
BTND5100
BTNJ5200
BTNB5200
BTNL5100
BTNP5100
BTNN5200
BTNF5200
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)
BTN NAME: BIOTIN
FORMULA: C10 H16 N2 O3 S1
SMILES: OC(=O)CCCCC1SCC2NC(=O)NC12
GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
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: 0.6337 seconds