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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1mxo
HYDROLASE HEADER
AMPC BETA-LACTAMASE IN COMPLEX WITH AN M.CARBOXYPHENYLGLYCYLBORONIC ACID BEARING THE CEPHALOTHIN R1 SIDE CHAIN TITLE
BETA-LACTAMASE 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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SM2 B 964
64A SER
119A LEU
120A GLN
150A TYR
152A ASN
211A VAL
221A TYR
289A ASN
293A LEU
315A LYS
316A THR
317A GLY
318A ALA
319A THR
320A GLY
343A ASN
346A ASN
SM2 E 964
64D SER
119D LEU
120D GLN
150D TYR
152D ASN
204D ARG
211D VAL
221D TYR
289D ASN
293D LEU
315D LYS
316D THR
317D GLY
318D ALA
319D THR
320D GLY
343D ASN
346D ASN
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
2bls Details
other holo-structures
pdb ID Ligand Unique ID
2rcx SM4F_964 Details
PO4C___1 SM4B_964
1ga9 ETPF_964 Details
ETPC_964
3o86 BSFB___2 Details
2r9x DMSF___1 WH6A_365 Details
PO4H_363 WH6G_365
3gv9 DMSB_363 GV9B___1 PO4B___3 Details
GV9A_364 PEGA_365
2hdu F12J1002 Details
F12H1001 F12I1003 F12K1006
1my8 SM3E_964 Details
SM3B_964
1ke0 CVBE_364 Details
1xgi NSTB_416 Details
1llb PCNC_964 Details
1ke3 BDBA_364 Details
BDBB_364
3gsg GF1A_366 Details
DMSB_363 GF1B_365
1kvm CEOD_864 Details
3bm6 C9PB___2 Details
C9PA___1
2hds 4MBC1603 4MBI1602 Details
4MBE1601 PO4B1301 SUCD1201
1ll9 AXLC_964 Details
1l2s STCE2115 Details
STCC3115
STCB1115
1iem CB4B_964 Details
CB4A_964
3o87 BSGA___1 Details
BSGB___2
1xgj HTCA_777 Details
HTCB_888
2pu4 OX6A_901 Details
OX7B_902
2pu2 DK2A_702 Details
DK2B_701
1ll5 IM2B_370 Details
IM2A_370
3grj PO4G___1 G14F_363 Details
DMSN_368 PO4G___1 G14F_363
2r9w 23CH___2 PO4I_362 Details
23CA_365 PO4B_364
2i72 VA1D_964 Details
VA1B_964
1c3b BZBA_362 Details
3gvb 3GVA___1 Details
1fco MOXD_961 Details
MOXB_961
1iel CAZA_964 Details
CAZB_964
3o88 BSHA___1 Details
BSHB___2
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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SM2 NAME: (1R)-1-(2-THIENYLACETYLAMINO)-1-(3-CARBOXYPHENYL)METHYLBORONIC ACID
FORMULA: C14 H14 N1 O5 B1 S1
SMILES: OB(O)C(NC(=O)Cc1sccc1)c2cccc(c2)C(O)=O
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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