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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1tta
TRANSPORT(THYROXINE) HEADER
THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL30MET VARIANT TO 1.7 ANGSTROMS RESOLUTION TITLE
TRANSTHYRETIN 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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13 MET
15 LYS
17 LEU
24 PRO
52 SER
54 GLU
56 HIS
106 THR
108 ALA
109 ALA
110 LEU
115 SER
116 TYR
117 SER
118 THR
119 THR
121 VAL
123 THR
127 GLU
215 LYS
217 LEU
306 THR
308 ALA
309 ALA
310 LEU
317 SER
318 THR
319 THR
321 VAL
1013 MET
1015 LYS
1017 LEU
1106 THR
1108 ALA
1109 ALA
1110 LEU
1117 SER
1118 THR
1119 THR
1121 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
2f7i 26CD_325 26CH_325 34 119 Details
26CB_326 26CF_326 34 109
1y1d FHIB2000 FHIF2000 38 130 Details
FHID3000 FHIH3000 38 141
1tz8 DESJ_128 20 103 Details
DESL_128 20 99
1e5a TBPB_999 TBPF_999 20 79 Details
TBPD_998 TBPH_998 20 87
3ipb JZDA_128 49 123 Details
2qgd MR5D_201 MR5H_201 36 128 Details
MR5B_200 MR5F_200 36 125
1tt6 DESB_128 DESG_128 40 125 Details
DESK_129 DESL_129 40 125
3ipe JZEB_128 45 130 Details
1e4h PBRF_998 PBRL_998 24 134 Details
PBRC_999 PBRI_999 24 97
3b56 DIUB2000 DIUF2000 24 96 Details
DIUD3000 DIUH3000 24 102
2fbr 44CB_173 44CE_173 74 237 Details
2b15 DNFC_130 DNFI_130 26 92 Details
DNFF_128 DNFL_128 26 88
2roy P28B_128 P28F_128 58 175 Details
P28D_128 P28H_128 58 167
2f8i 205D1001 205H1001 40 128 Details
205B1002 205F1002 40 136
2qge MR6D_200 MR6H_200 34 109 Details
MR6B_201 MR6F_201 34 119
2g9k NE1D_500 NE1H_500 36 107 Details
NE1B_501 NE1F_501 36 107
2qgc MR4D_128 MR4H_128 36 112 Details
MR4B_128 MR4F_128 36 116
2rox T44E_128 T44J_128 48 146 Details
T44C_128 T44H_128 48 138
1z7j T4AD_129 T4AH_129 44 135 Details
3cn3 LJ4A_128 LJ4C_128 32 123 Details
LJ4B_128 LJ4D_128 32 119
2b77 3CAD_239 3CAH_239 36 122 Details
3CAB_240 3CAF_240 36 116
3p3r 3M1D_128 3M1H_128 40 132 Details
3M1B_128 3M1F_128 40 130
1tyr READ_130 REAH_130 44 154 Details
REAB_131 REAF_131 44 149
1u21 P2CC_211 P2CD_211 42 146 Details
P2CG_221 P2CH_221 42 126
3d2t 1FLB_502 1FLF_502 36 116 Details
1FLD_500 1FLH_500 36 122
3p3u 3M4D_128 3M4H_128 40 152 Details
3M4B_128 3M4F_128 40 141
2gab NE2G_502 NE2H_502 34 110 Details
NE2C_501 NE2D_501 34 122
3hj0 A93B_128 A93D_128 38 127 Details
A93A_128 A93C_128 38 124
3gs4 7BDB_500 7BDD_500 40 140 Details
7BDA_501 7BDC_501 40 143
2flm 6CAB_201 6CAE_201 78 270 Details
3kgu GEND3071 GENH3071 40 145 Details
GENB3071 GENF3071 40 127
2g5u PCQC_240 PCQD_240 36 111 Details
3p3t 3M3D_128 3M3H_128 36 134 Details
3M3B_128 3M3F_128 36 142
3p3s 3M2B_128 3M2H_128 36 107 Details
3M2E_128 3M2K_128 36 97
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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