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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3l2d
TRANSFERASE HEADER
GLYCOCYAMINE KINASE, BETA-BETA HOMODIMER FROM MARINE WORM NAMALYCASTIS SP. TITLE
GLYCOCYAMINE KINASE BETA CHAIN 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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82 LYS
83 LYS
84 THR
85 GLY
139 SER
140 CYS
141 ARG
143 ARG
199 ILE
202 HIS
204 LEU
205 PHE
206 GLU
212 LEU
239 TRP
242 GLU
243 GLU
247 ARG
251 MET
252 GLN
294 CYS
296 THR
297 ASN
303 ARG
305 SER
306 VAL
307 HIS
331 ARG
333 THR
334 GLY
335 GLY
336 GLU
337 SER
346 ASP
350 TRP
352 ARG
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
3l2f ADPB_602 _MGB_702 NMGB_502 NO3B_802 40 169 Details
ADPE_605 NO3E_805 NMGE_505 _MGE_705 40 166
ADPC_603 NO3C_803 NMGC_503 _MGC_703 40 175
ADPH_608 NO3H_808 NMGH_508 _MGH_708 40 164
ADPR_618 _MGR_718 NMGR_518 NO3R_818 40 167
ADPI_609 NMGI_509 _MGI_709 NO3I_809 40 170
ADPO_615 NMGO_515 _MGO_715 NO3O_815 40 168
ADPP_616 NO3P_816 NMGP_516 _MGP_716 40 164
ADPD_604 _MGD_704 NMGD_504 NO3D_804 40 159
ADPJ_610 NMGJ_510 _MGJ_710 NO3J_810 40 160
ADPQ_617 _MGQ_717 NO3Q_817 NMGQ_517 40 159
ADPA_601 NO3A_801 _MGA_701 NMGA_501 40 181
ADPG_607 NMGG_507 _MGG_707 NO3G_807 40 155
ADPM_613 NMGM_513 _MGM_713 NO3M_813 40 165
ADPF_606 NO3F_806 _MGF_706 NMGF_506 40 163
ADPK_611 _MGK_711 NMGK_511 NO3K_811 40 162
ADPL_612 _MGL_712 NO3L_812 NMGL_512 40 167
ADPN_614 _MGN_714 NMGN_514 NO3N_814 40 164
3l2g ADPB_618 NMGD_518 NO3E_818 _MGC_718 40 166 Details
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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