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

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

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1rat
HYDROLASE (NUCLEIC ACID,RNA) HEADER
EFFECTS OF TEMPERATURE ON PROTEIN STRUCTURE AND DYNAMICS: X- RAY CRYSTALLOGRAPHIC STUDIES OF THE PROTEIN RIBONUCLEASE-A AT NINE DIFFERENT TEMPERATURES FROM 98 TO 320 K TITLE
RIBONUCLEASE A 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).

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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.

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2 GLU
3 THR
4 ALA
7 LYS
8 PHE
10 ARG
11 GLN
12 HIS
31 LYS
32 SER
34 ASN
35 LEU
37 LYS
38 ASP
39 ARG
41 LYS
42 PRO
43 VAL
44 ASN
45 THR
65 CYS
66 LYS
67 ASN
69 GLN
71 ASN
72 CYS
83 ASP
84 CYS
85 ARG
109 ALA
111 GLU
118 VAL
119 HIS
120 PHE
121 ASP
122 ALA
123 SER
124 VAL
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:

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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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.

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pdb ID Ligand Unique ID #atoms #contacts
2xoi SFBA1125 39 110 Details
1rca CGPA_150 CGPA_160 PO4A_170 28 84 Details
1afk PAPA_125 31 87 Details
PAPB_125 31 98
3dxg U5PA_125 U5PA_126 42 133 Details
U5PB_125 21 71
3jw1 U5PB_201 21 80 Details
U5PA_201 21 73
1o0h ADPB1126 27 77 Details
ADPA1125 27 83
1w4p UM3B1125 20 79 Details
UM3A1125 20 76
1rpg CPAA_126 37 111 Details
3d7b FLCA_125 U4SA_127 FLCA_126 47 149 Details
2w5g ATPB1125 31 82 Details
ATPA1125 31 86
1rob C2PA_126 21 70 Details
8rsa ADTA_125 20 72 Details
ADTB_125 20 71
1w4o UA3A1125 21 77 Details
1rnd DGPA_126 SO4A_125 28 85 Details
2w5i ATPB1125 31 91 Details
ATPA1125 31 95
2e33 BMAB1003 MANB1004 NAGB1002 NAGB1001 MANB1005 61 111 Details
1o0m U2PB1201 21 78 Details
U2PA1101 21 71
2w5l NAPB1125 27 70 Details
1jn4 139A_901 42 127 Details
1z6s AMPB1102 23 78 Details
AMPA1101 23 74
2qca DGPA_200 DGPA_300 46 126 Details
2w5k NDPB1125 27 71 Details
1qhc PUAB_902 PUAD_902 100 291 Details
1rnc 5GPA_161 SO4A_151 29 91 Details
3d6q FLCA_125 U3SA_127 FLCA_126 48 144 Details
1afl ATRB_125 31 96 Details
ATRA_125 31 93
1rpf C3PB_125 21 73 Details
C3PD_125 21 73
1o0n U3PA1101 21 74 Details
U3PB1201 21 72
3lxo T3PD_601 21 89 Details
T3PB_601 21 91
1rnn C5PE_200 FMTF_131 24 86 Details
C5PB_200 FMTC_131 24 83
1u1b PAXB_902 51 136 Details
PAXA_901 51 141
1z6d IMPE1921 IMPF1920 IMPC1920 69 232 Details
IMPB1921 IMPF1920 IMPC1920 69 231
2xog SFBA1125 40 115 Details
1ruv UVCA_125 21 80 Details
1w4q UMFB1125 21 82 Details
UMFA1125 21 79
1rnm C5PE_200 C5PJ_200 SO4B_125 SO4D_127 SO4I_127 57 202 Details
3dxh UDPB_125 25 72 Details
UDPA_125 UDPA_126 50 136
1o0o A2PB_999 27 80 Details
3d8y FLCA_125 T3SA_127 FLCA_126 48 140 Details
1eow SO4A_125 U2GA_130 25 92 Details
1o0f A3PA1301 27 70 Details
A3PB1401 27 77
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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