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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2y77
LYASE HEADER
STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE COMPLEXED WITH (1R,4S,5R)-3-(BENZO(B) THIOPHEN-2-YLMETHOXY)-1,4,5-TRIHYDROXY-2-(THIOPHEN-2- YLMETHYL)CYCLOHEX-2-ENECARBOXYLATE TITLE
3-DEHYDROQUINATE DEHYDRATASE 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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CB8 P1144
11K PRO
12K ASN
13K LEU
15K ARG
16K LEU
17K GLY
18K ARG
75K ASN
77K GLY
78K GLY
81K HIS
88E ASP
101K HIS
102K ILE
103K SER
105K VAL
108K ARG
112K ARG
CB8 R1144
11M PRO
12M ASN
13M LEU
15M ARG
16M LEU
17M GLY
18M ARG
75M ASN
77M GLY
78M GLY
81M HIS
88Y ASP
101M HIS
102M ILE
103M SER
105M VAL
108M ARG
112M ARG
CB8 B1144
11W PRO
12W ASN
13W LEU
15W ARG
16W LEU
17W GLY
75W ASN
77W GLY
78W GLY
81W HIS
88G ASP
101W HIS
102W ILE
103W SER
105W VAL
108W ARG
112W ARG
CB8 T1144
11O PRO
12O ASN
13O LEU
15O ARG
16O LEU
17O GLY
18O ARG
75O ASN
77O GLY
78O GLY
81O HIS
88S ASP
101O HIS
102O ILE
103O SER
105O VAL
108O ARG
112O ARG
CB8 V1144
11Q PRO
12Q ASN
13Q LEU
15Q ARG
16Q LEU
17Q GLY
75Q ASN
77Q GLY
78Q GLY
81Q HIS
88W ASP
101Q HIS
102Q ILE
103Q SER
105Q VAL
108Q ARG
112Q ARG
CB8 F1144
11A PRO
12A ASN
13A LEU
15A ARG
16A LEU
17A GLY
75A ASN
77A GLY
78A GLY
81A HIS
88M ASP
101A HIS
102A ILE
103A SER
105A VAL
108A ARG
112A ARG
CB8 N1144
11I PRO
12I ASN
13I LEU
15I ARG
16I LEU
17I GLY
75I ASN
77I GLY
78I GLY
81I HIS
88K ASP
101I HIS
102I ILE
103I SER
105I VAL
108I ARG
112I ARG
CB8 X1144
11S PRO
12S ASN
13S LEU
15S ARG
16S LEU
17S GLY
75S ASN
77S GLY
78S GLY
81S HIS
88C ASP
101S HIS
102S ILE
103S SER
105S VAL
108S ARG
112S ARG
CB8 L1144
11G PRO
12G ASN
13G LEU
15G ARG
16G LEU
17G GLY
18G ARG
75G ASN
77G GLY
78G GLY
81G HIS
88Q ASP
101G HIS
102G ILE
103G SER
105G VAL
108G ARG
112G ARG
CB8 D1144
11Y PRO
12Y ASN
13Y LEU
15Y ARG
16Y LEU
17Y GLY
18Y ARG
75Y ASN
77Y GLY
78Y GLY
81Y HIS
88A ASP
101Y HIS
102Y ILE
103Y SER
105Y VAL
108Y ARG
112Y ARG
CB8 H1144
11C PRO
12C ASN
13C LEU
15C ARG
16C LEU
17C GLY
75C ASN
77C GLY
78C GLY
81C HIS
88O ASP
101C HIS
102C ILE
103C SER
105C VAL
108C ARG
112C ARG
CB8 J1144
11E PRO
12E ASN
13E LEU
15E ARG
16E LEU
17E GLY
18E ARG
75E ASN
77E GLY
78E GLY
81E HIS
88I ASP
101E HIS
102E ILE
103E SER
105E VAL
108E ARG
112E 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:

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
2dhq Details
other holo-structures
pdb ID Ligand Unique ID
2xb8 SO4P1146 SO4S1148 SO4U1150 Details
SO4C1148 SO4E1150 SO4Z1146
XNWW1144
SO4A1150 SO4Y1148 SO4V1146
SO4B1146 SO4G1150 SO4E1148
XNWQ1144
SO4L1146 SO4Q1150 SO4O1148
SO4D1146 SO4G1148 SO4I1150
SO4J1146 SO4M1148 SO4O1150
SO4N1146 SO4Q1148 SO4S1150
XNWU1144
XNWG1144
SO4H1146 SO4M1150 SO4K1148
SO4A1148 SO4X1146 SO4C1150
XNWI1144
XNWM1144
SO4R1146 SO4W1150 SO4U1148
XNWA1144
XNWO1144
XNWC1144
SO4F1146 SO4K1150 SO4I1148
XNWK1144
XNWY1144
XNWE1144
1h0s FA6H_200 Details
FA6R_200
2y76 CB7J1144 Details
CB7R1144
CB7L1144
CB7F1144
CB7B1144
CB7X1144
CB7T1144
CB7D1144
CB7H1144
CB7N1144
CB7V1144
CB7P1144
2y71 CB6L1144 Details
CB6V1144
CB6D1144
CB6P1144
CB6B1144
CB6F1144
CB6T1144
CB6J1144
CB6N1144
CB6X1144
CB6R1144
CB6H1144
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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CB8 NAME: not_found
FORMULA: not_found
SMILES: not_found
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
Script execution time: 3.372 seconds