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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2w5l
HYDROLASE HEADER
RNASE A-NADP COMPLEX TITLE
RIBONUCLEASE PANCREATIC 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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NAP B1125
7B LYS
8B PHE
11B GLN
12B HIS
41B LYS
65B CYS
66B LYS
67B ASN
69B GLN
71B ASN
72B CYS
109B ALA
111B GLU
118B VAL
119B HIS
120B PHE
121B ASP
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
1afu Details
other holo-structures
pdb ID Ligand Unique ID
2xoi SFBA1125 Details
1rca CGPA_150 CGPA_160 PO4A_170 Details
1afk PAPA_125 Details
PAPB_125
3dxg U5PA_125 U5PA_126 Details
U5PB_125
3jw1 U5PB_201 Details
U5PA_201
1o0h ADPB1126 Details
ADPA1125
1w4p UM3B1125 Details
UM3A1125
1rpg CPAA_126 Details
3d7b FLCA_125 U4SA_127 FLCA_126 Details
2w5g ATPB1125 Details
ATPA1125
1rob C2PA_126 Details
8rsa ADTA_125 Details
ADTB_125
1w4o UA3A1125 Details
1rnd DGPA_126 SO4A_125 Details
2w5i ATPB1125 Details
ATPA1125
2e33 BMAB1003 MANB1004 NAGB1002 NAGB1001 MANB1005 Details
1o0m U2PB1201 Details
U2PA1101
1jn4 139A_901 Details
1z6s AMPB1102 Details
AMPA1101
2qca DGPA_200 DGPA_300 Details
2w5k NDPB1125 Details
1qhc PUAB_902 PUAD_902 Details
1rnc 5GPA_161 SO4A_151 Details
3d6q FLCA_125 U3SA_127 FLCA_126 Details
1afl ATRB_125 Details
ATRA_125
1rpf C3PB_125 Details
C3PD_125
1o0n U3PA1101 Details
U3PB1201
3lxo T3PD_601 Details
T3PB_601
1rnn C5PE_200 FMTF_131 Details
C5PB_200 FMTC_131
1u1b PAXB_902 Details
PAXA_901
1z6d IMPE1921 IMPF1920 IMPC1920 Details
IMPB1921 IMPF1920 IMPC1920
2xog SFBA1125 Details
1ruv UVCA_125 Details
1w4q UMFB1125 Details
UMFA1125
1rnm C5PE_200 C5PJ_200 SO4B_125 SO4D_127 SO4I_127 Details
3dxh UDPB_125 Details
UDPA_125 UDPA_126
1o0o A2PB_999 Details
3d8y FLCA_125 T3SA_127 FLCA_126 Details
1eow SO4A_125 U2GA_130 Details
1o0f A3PA1301 Details
A3PB1401
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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NAP NAME: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H28 N7 O17 P3
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
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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