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

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

(click anywhere in this window to remove it)
2bls
CEPHALOSPORINASE HEADER
AMPC BETA-LACTAMASE FROM ESCHERICHIA COLI TITLE
AMPC BETA-LACTAMASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

(click anywhere in this window to remove it)
Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

(click anywhere in this window to remove it)
61 SER
63 GLY
64 SER
65 VAL
67 LYS
79 ALA
92 TYR
93 TRP
107 LEU
108 HIS
116 LEU
117 GLN
118 VAL
119 LEU
120 GLN
121 VAL
123 ASP
125 VAL
126 LYS
127 SER
128 SER
131 LEU
144 PRO
145 GLY
147 TYR
148 ARG
149 LEU
150 TYR
152 ASN
157 LEU
160 ALA
161 LEU
164 LYS
204 ARG
208 VAL
209 SER
210 HIS
211 VAL
212 SER
213 PRO
214 GLY
215 ALA
216 LEU
217 ASP
218 TYR
219 GLU
220 ALA
221 TYR
250 GLN
253 GLN
254 LEU
257 SER
259 TYR
260 TRP
272 GLU
286 ASN
287 SER
288 ASP
289 ASN
290 LYS
291 ILE
292 ALA
293 LEU
294 ALA
295 ALA
300 ALA
301 ILE
302 THR
303 PRO
304 PRO
305 THR
306 PRO
307 ALA
312 LYS
313 THR
314 GLY
315 LYS
316 THR
317 GLY
318 ALA
319 THR
320 GLY
340 ASN
343 ASN
344 TYR
346 ASN
349 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.

(click anywhere in this window to remove it)

Links to external databases:

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)
holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

(click anywhere in this window to remove it)
pdb ID Ligand Unique ID #atoms #contacts
2rcx SM4F_964 24 90 Details
PO4C___1 SM4B_964 29 92
1ga9 ETPF_964 27 98 Details
ETPC_964 27 90
3o86 BSFB___2 15 74 Details
2r9x DMSF___1 WH6A_365 34 118 Details
PO4H_363 WH6G_365 35 114
3gv9 DMSB_363 GV9B___1 PO4B___3 21 88 Details
GV9A_364 PEGA_365 19 84
2hdu F12J1002 12 80 Details
F12H1001 F12I1003 F12K1006 36 123
1my8 SM3E_964 19 82 Details
SM3B_964 19 84
1ke0 CVBE_364 14 71 Details
1xgi NSTB_416 21 98 Details
1llb PCNC_964 26 106 Details
1ke3 BDBA_364 18 79 Details
BDBB_364 18 71
3gsg GF1A_366 17 73 Details
DMSB_363 GF1B_365 21 89
1kvm CEOD_864 22 90 Details
1mxo SM2B_964 22 81 Details
SM2E_964 22 95
3bm6 C9PB___2 30 105 Details
C9PA___1 30 95
2hds 4MBC1603 4MBI1602 28 111 Details
4MBE1601 PO4B1301 SUCD1201 42 134
1ll9 AXLC_964 25 82 Details
1l2s STCE2115 19 92 Details
STCC3115 19 101
STCB1115 19 88
1iem CB4B_964 22 105 Details
CB4A_964 22 89
3o87 BSGA___1 18 81 Details
BSGB___2 18 78
1xgj HTCA_777 22 86 Details
HTCB_888 22 100
2pu4 OX6A_901 17 79 Details
OX7B_902 17 78
2pu2 DK2A_702 26 94 Details
DK2B_701 26 102
1ll5 IM2B_370 20 91 Details
IM2A_370 20 70
3grj PO4G___1 G14F_363 19 75 Details
DMSN_368 PO4G___1 G14F_363 23 99
2r9w 23CH___2 PO4I_362 34 114 Details
23CA_365 PO4B_364 34 107
2i72 VA1D_964 18 87 Details
VA1B_964 18 84
1c3b BZBA_362 12 71 Details
3gvb 3GVA___1 16 81 Details
1fco MOXD_961 29 108 Details
MOXB_961 29 101
1iel CAZA_964 31 121 Details
CAZB_964 31 128
3o88 BSHA___1 25 85 Details
BSHB___2 25 85
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: 0.2228 seconds