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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2auu
HYDROLASE HEADER
INORGANIC PYROPHOSPHATASE COMPLEXED WITH MAGNESIUM PYROPHOSPHATE AND FLUORIDE TITLE
INORGANIC PYROPHOSPHATASE 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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MG C 202
20Y GLU
29Y LYS
31Y GLU
57Y TYR
67Y ASP
68Y PRO
70Y ASP
MG E 202
20A GLU
29A LYS
31A GLU
57A TYR
67A ASP
68A PRO
70A ASP
MG S 202
20O GLU
29O LYS
31O GLU
57O TYR
67O ASP
68O PRO
70O ASP
MG Y 202
20U GLU
29U LYS
31U GLU
55U TYR
57U TYR
67U ASP
68U PRO
70U ASP
MG O 202
20K GLU
29K LYS
31K GLU
57K TYR
67K ASP
68K PRO
70K ASP
MG I 202
20E GLU
29E LYS
31E GLU
55E TYR
57E TYR
67E ASP
68E PRO
70E ASP
POP G 180
29Y LYS
31Y GLU
43Y ARG
51Y TYR
55Y TYR
65Y ASP
67Y ASP
70Y ASP
97Y ASP
98Y GLU
99Y ALA
102Y ASP
104Y LYS
141Y TYR
142Y LYS
148Y LYS
POP I 180
29A LYS
31A GLU
43A ARG
51A TYR
55A TYR
65A ASP
67A ASP
70A ASP
97A ASP
98A GLU
99A ALA
102A ASP
104A LYS
141A TYR
142A LYS
148A LYS
POP W 180
29O LYS
31O GLU
43O ARG
51O TYR
55O TYR
65O ASP
67O ASP
70O ASP
97O ASP
98O GLU
99O ALA
102O ASP
104O LYS
141O TYR
142O LYS
148O LYS
POP C 180
29U LYS
31U GLU
43U ARG
51U TYR
55U TYR
65U ASP
67U ASP
70U ASP
97U ASP
98U GLU
99U ALA
102U ASP
104U LYS
141U TYR
142U LYS
148U LYS
POP S 180
29K LYS
31K GLU
43K ARG
51K TYR
55K TYR
65K ASP
67K ASP
70K ASP
97K ASP
98K GLU
99K ALA
102K ASP
104K LYS
141K TYR
142K LYS
148K LYS
POP M 180
29E LYS
31E GLU
43E ARG
51E TYR
55E TYR
65E ASP
67E ASP
70E ASP
97E ASP
98E GLU
99E ALA
102E ASP
104E LYS
141E TYR
142E LYS
148E LYS
MG F 204
31Y GLU
42Y ASP
43Y ARG
67Y ASP
98Y GLU
148Y LYS
MG H 204
31A GLU
42A ASP
43A ARG
67A ASP
98A GLU
148A LYS
MG V 204
31O GLU
42O ASP
43O ARG
67O ASP
98O GLU
148O LYS
MG B 204
31U GLU
42U ASP
43U ARG
67U ASP
98U GLU
148U LYS
MG R 204
31K GLU
42K ASP
43K ARG
67K ASP
98K GLU
148K LYS
MG L 204
31E GLU
42E ASP
43E ARG
67E ASP
98E GLU
148E LYS
MG U 201
63O SER
65O ASP
68O PRO
70O ASP
102O ASP
MG Q 201
63K SER
65K ASP
68K PRO
70K ASP
102K ASP
F X 211
65O ASP
67O ASP
68O PRO
70O ASP
F T 211
65K ASP
67K ASP
68K PRO
70K ASP
F J 211
65A ASP
67A ASP
68A PRO
70A ASP
F H 211
65Y ASP
67Y ASP
68Y PRO
70Y ASP
MG E 201
65Y ASP
68Y PRO
70Y ASP
102Y ASP
MG D 203
65Y ASP
97Y ASP
99Y ALA
102Y ASP
104Y LYS
141Y TYR
MG G 201
65A ASP
68A PRO
70A ASP
102A ASP
MG F 203
65A ASP
97A ASP
99A ALA
102A ASP
104A LYS
141A TYR
MG T 203
65O ASP
97O ASP
99O ALA
102O ASP
104O LYS
141O TYR
MG Z 203
65U ASP
97U ASP
99U ALA
102U ASP
104U LYS
141U TYR
F D 211
65U ASP
67U ASP
68U PRO
70U ASP
MG A 201
65U ASP
68U PRO
70U ASP
102U ASP
MG P 203
65K ASP
97K ASP
99K ALA
102K ASP
104K LYS
141K TYR
F N 211
65E ASP
67E ASP
68E PRO
70E ASP
MG K 201
65E ASP
68E PRO
70E ASP
102E ASP
MG J 203
65E ASP
97E ASP
99E ALA
102E ASP
104E LYS
141E TYR
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
1igp Details
other holo-structures
pdb ID Ligand Unique ID
2au8 PO4P_180 _MNS_201 _MNT_204 _MNQ_203 _CLO_208 _MNR_202 Details
PO4T_180 _MNU_203 _MNW_201 _CLS_208 _MNX_204 _MNV_202
2au6 POPT_182 _MNS_203 __FX_211 _MNV_201 _MNU_202 Details
POPP_182 _MNQ_202 _MNR_201 __FT_211 _MNO_203
POPH_182 _MNG_203 _MNI_202 __FL_211 _MNJ_201
POPR_182 _MNQ_203 _MNS_202 _MNT_201 __FV_211
POPF_182 _MNG_202 _MNH_201 __FJ_211 _MNE_203
POPD_182 __FH_211 _MNE_202 _MNC_203 _MNF_201
1i6t POPD_411 _CAZ_302 _CAB_303 _CAA_301 Details
POPX_411 _CAV_303 _CAU_301 _CAT_302
POPT_411 _CAP_302 _CAR_303 _CAQ_301
POPJ_411 _CAH_303 _CAG_301 _CAF_302
POPH_411 _CAF_303 _CAE_301 _CAD_302
POPN_411 _CAL_303 _CAK_301 _CAJ_302
2au9 POPS_180 _MNU_204 _MNQ_203 _MNT_201 _MNR_202 _CLP_208 __FV_211 Details
POPH_180 _MNI_201 _CLE_208 _MNG_202 _MNJ_204 __FK_211 _MNF_203
POPO_180 _MNM_203 _MNQ_204 _MNP_201 _MNN_202 _CLL_208 __FR_211
POPK_180 _MNI_203 _CLH_208 _MNL_201 _MNJ_202 __FN_211 _MNM_204
POPD_180 _MNC_202 _MNE_201 _CLA_208 _MNF_204 _MNB_203 __FG_211
POPZ_180 _CLW_208 _MNB_204 __FC_211 _MNX_203 _MNA_201 _MNY_202
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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POP NAME: PYROPHOSPHATE 2-
FORMULA: H2 O7 P2
SMILES: OP([O-])(=O)OP(O)([O-])=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
F NAME: FLUORIDE ION
FORMULA: F1
SMILES: [F-]
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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