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)
1nht
LIGASE HEADER
ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SITE OF CRYSTALLINE ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI DATA COLLECTED AT 100K TITLE
ADENYLOSUCCINATE SYNTHETASE 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)
PGS B 440
11A TRP
12A GLY
13A ASP
16A LYS
38A ASN
39A ALA
40A GLY
41A HIS
114A ASP
126A ILE
127A GLY
128A THR
129A THR
130A GLY
131A ARG
133A ILE
134A GLY
143E ARG
223A ALA
224A GLN
228A LEU
237A TYR
238A VAL
239A THR
240A SER
272A ARG
273A VAL
274A GLY
275A ALA
303A ARG
PGS F 440
11E TRP
12E GLY
13E ASP
16E LYS
38E ASN
39E ALA
40E GLY
41E HIS
114E ASP
126E ILE
127E GLY
128E THR
129E THR
130E GLY
131E ARG
133E ILE
134E GLY
143A ARG
223E ALA
224E GLN
228E LEU
237E TYR
238E VAL
239E THR
240E SER
272E ARG
273E VAL
274E GLY
275E ALA
303E ARG
MG D 435
13A ASP
40A GLY
GDP G 432
13E ASP
14E GLU
15E GLY
16E LYS
17E GLY
18E LYS
40E GLY
41E HIS
42E THR
44E VAL
293E GLN
294E GLY
295E ASN
299E ALA
305E ARG
330E THR
331E LYS
333E ASP
334E VAL
383E PHE
414E SER
416E GLY
417E PRO
MG H 435
13E ASP
40E GLY
HAD E 437
13E ASP
38E ASN
40E GLY
129E THR
273E VAL
298E GLY
299E ALA
300E THR
301E THR
303E ARG
305E ARG
HAD A 437
13A ASP
38A ASN
40A GLY
129A THR
273A VAL
298A GLY
299A ALA
300A THR
301A THR
303A ARG
305A ARG
GDP C 432
13A ASP
14A GLU
15A GLY
16A LYS
17A GLY
18A LYS
40A GLY
41A HIS
42A THR
44A VAL
293A GLN
294A GLY
295A ASN
299A ALA
305A ARG
330A THR
331A LYS
333A ASP
334A VAL
383A PHE
414A SER
416A GLY
417A PRO
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
1ade Details
other holo-structures
pdb ID Ligand Unique ID
1cg0 GDPB_432 HDAE_437 IMOC_440 _MGD_435 Details
GDPG_432 IMOH_440 HDAJ_437 _MGI_435
2gcq DOIG_451 _MGH_435 GDPF_432 HADE_437 Details
DOIC_451 HADA_437 GDPB_432 _MGD_435
1hoo GNHB_432 GNPC_432 Details
1gim GDPG_432 HADF_438 IMPH_440 _MGI_435 NO3J_433 Details
GDPB_432 HADA_438 _MGD_435 IMPC_440 NO3E_433
1qf5 GDPB_434 _MGE_433 RPLC_435 PO4D_432 Details
GDPG_434 _MGJ_433 PO4I_432 RPLH_435
1qf4 GDPG_434 _MGJ_433 PO4I_432 RPDH_435 Details
GDPB_434 RPDC_435 _MGE_433 PO4D_432
1juy GDPB_432 H5PC_433 _PID_434 HDAF_438 _MGE_435 Details
GDPH_432 HDAL_438 _PIJ_434 H5PI_433 _MGK_435
1hon GNHB_432 Details
1hop GCPD_433 Details
GCPB_432
1soo H5PE_453 SO4D_442 _NAF_547 SO4C_443 Details
H5PL_453 SO4K_442 SO4J_443 _NAM_547
1son AMPB_453 Details
AMPE_453
1cib GDPH_432 HDAK_437 _MGJ_434 IMPI_440 NO3L_433 Details
GDPB_432 HDAE_437 NO3F_433 _MGD_434 IMPC_440
1gin GDPB_432 IMPD_440 _MGC_435 HADA_438 NO3E_433 Details
GDPG_432 _MGH_435 IMPI_440 HADF_438 NO3J_433
1ksz GDPC_432 PGSB_440 HADA_437 _MGD_435 Details
GDPG_432 _MGH_435 PGSF_440 HADE_437
1ch8 GPXH_432 IMPI_440 NO3L_433 _MGK_434 HDAJ_437 Details
GPXB_432 NO3F_433 HDAD_437 IMPC_440 _MGE_434
IMPI_440 NO3L_433 HDAJ_437
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)
GDP NAME: GUANOSINE-5'-DIPHOSPHATE
FORMULA: C10 H15 N5 O11 P2
SMILES: NC1=Nc2[n](cnc2C(=O)N1)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
PGS NAME: 2-DEAZO-6-THIOPHOSPHATE GUANOSINE-5'-MONOPHOSPHATE
FORMULA: C10 H15 N4 O10 P2 S1
SMILES: OC1C(COP(O)(O)=O)OC(C1O)[n]2cnc3c(SP(O)(O)=O)[nH+]cnc23
HAD NAME: (CARBOXYHYDROXYAMINO)ETHANOIC ACID
FORMULA: C3 H5 N1 O5
SMILES: ON(CC(O)=O)C(O)=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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: 2.9846 seconds