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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2xb8
LYASE HEADER
STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (2R)-2-( 4-METHOXYBENZYL)-3-DEHYDROQUINIC ACID 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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XNW W1144
11W PRO
12W ASN
13W LEU
15W ARG
16W LEU
19W ARG
20W GLU
24W TYR
75W ASN
77W GLY
78W GLY
81W HIS
84C VAL
88C ASP
92C GLU
101W HIS
102W ILE
103W SER
105W VAL
108W ARG
112W ARG
XNW Q1144
11Q PRO
12Q ASN
13Q LEU
15Q ARG
16Q LEU
19Q ARG
20Q GLU
24Q TYR
75Q ASN
77Q GLY
78Q GLY
81Q HIS
84A VAL
88A ASP
92A GLU
101Q HIS
102Q ILE
103Q SER
105Q VAL
108Q ARG
112Q ARG
XNW U1144
11U PRO
12U ASN
13U LEU
15U ARG
16U LEU
19U ARG
20U GLU
24U TYR
75U ASN
77U GLY
78U GLY
81U HIS
84E VAL
88E ASP
92E GLU
101U HIS
102U ILE
103U SER
105U VAL
108U ARG
112U ARG
XNW G1144
11G PRO
12G ASN
13G LEU
15G ARG
16G LEU
19G ARG
20G GLU
24G TYR
75G ASN
77G GLY
78G GLY
81G HIS
84W VAL
88W ASP
92W GLU
101G HIS
102G ILE
103G SER
105G VAL
108G ARG
112G ARG
XNW I1144
11I PRO
12I ASN
13I LEU
15I ARG
16I LEU
19I ARG
20I GLU
24I TYR
75I ASN
77I GLY
78I GLY
81I HIS
84U VAL
88U ASP
92U GLU
101I HIS
102I ILE
103I SER
105I VAL
108I ARG
112I ARG
XNW M1144
11M PRO
12M ASN
13M LEU
15M ARG
16M LEU
19M ARG
20M GLU
24M TYR
75M ASN
77M GLY
78M GLY
81M HIS
84Y VAL
88Y ASP
92Y GLU
101M HIS
102M ILE
103M SER
105M VAL
108M ARG
112M ARG
XNW A1144
11A PRO
12A ASN
13A LEU
15A ARG
16A LEU
19A ARG
20A GLU
24A TYR
75A ASN
77A GLY
78A GLY
81A HIS
84O VAL
88O ASP
92O GLU
101A HIS
102A ILE
103A SER
105A VAL
108A ARG
112A ARG
XNW O1144
11O PRO
12O ASN
13O LEU
15O ARG
16O LEU
19O ARG
20O GLU
24O TYR
75O ASN
77O GLY
78O GLY
81O HIS
84Q VAL
88Q ASP
92Q GLU
101O HIS
102O ILE
103O SER
105O VAL
108O ARG
112O ARG
XNW C1144
11C PRO
12C ASN
13C LEU
15C ARG
16C LEU
19C ARG
20C GLU
24C TYR
75C ASN
77C GLY
78C GLY
81C HIS
84G VAL
88G ASP
92G GLU
101C HIS
102C ILE
103C SER
105C VAL
108C ARG
112C ARG
XNW K1144
11K PRO
12K ASN
13K LEU
15K ARG
16K LEU
19K ARG
20K GLU
24K TYR
75K ASN
77K GLY
78K GLY
81K HIS
84M VAL
88M ASP
92M GLU
101K HIS
102K ILE
103K SER
105K VAL
108K ARG
112K ARG
XNW Y1144
11Y PRO
12Y ASN
13Y LEU
15Y ARG
16Y LEU
19Y ARG
20Y GLU
24Y TYR
75Y ASN
77Y GLY
78Y GLY
81Y HIS
84K VAL
88K ASP
92K GLU
101Y HIS
102Y ILE
103Y SER
105Y VAL
108Y ARG
112Y ARG
XNW E1144
11E PRO
12E ASN
13E LEU
15E ARG
16E LEU
19E ARG
20E GLU
24E TYR
75E ASN
77E GLY
78E GLY
81E HIS
84I VAL
88I ASP
92I GLU
101E HIS
102E ILE
103E SER
105E VAL
108E ARG
112E ARG
SO4 P1146
81O HIS
111A PHE
114O HIS
115O SER
116O TYR
SO4 Z1146
81Y HIS
111M PHE
114Y HIS
115Y SER
116Y TYR
SO4 V1146
81U HIS
111I PHE
114U HIS
115U SER
116U TYR
SO4 B1146
81A HIS
111Q PHE
114A HIS
115A SER
116A TYR
SO4 L1146
81K HIS
111Y PHE
114K HIS
115K SER
116K TYR
SO4 D1146
81C HIS
111W PHE
114C HIS
115C SER
116C TYR
SO4 J1146
81I HIS
111E PHE
114I HIS
115I SER
116I TYR
SO4 N1146
81M HIS
111K PHE
114M HIS
115M SER
116M TYR
SO4 H1146
81G HIS
111C PHE
114G HIS
115G SER
116G TYR
SO4 X1146
81W HIS
111G PHE
114W HIS
115W SER
116W TYR
SO4 R1146
81Q HIS
111O PHE
114Q HIS
115Q SER
116Q TYR
SO4 F1146
81E HIS
111U PHE
114E HIS
115E SER
116E TYR
SO4 U1150
87O ARG
109A GLU
110A GLU
111A PHE
113G ARG
115O SER
119O PRO
SO4 E1150
87Y ARG
109M GLU
110M GLU
111M PHE
113Q ARG
115Y SER
119Y PRO
SO4 A1150
87U ARG
109I GLU
110I GLU
111I PHE
113M ARG
115U SER
119U PRO
SO4 G1150
87A ARG
109Q GLU
110Q GLU
111Q PHE
113I ARG
115A SER
119A PRO
SO4 Q1150
87K ARG
109Y GLU
110Y GLU
111Y PHE
113C ARG
115K SER
119K PRO
SO4 I1150
87C ARG
109W GLU
110W GLU
111W PHE
113K ARG
115C SER
119C PRO
SO4 O1150
87I ARG
109E GLU
110E GLU
111E PHE
113A ARG
115I SER
119I PRO
SO4 S1150
87M ARG
109K GLU
110K GLU
111K PHE
113U ARG
115M SER
119M PRO
SO4 M1150
87G ARG
109C GLU
110C GLU
111C PHE
113O ARG
115G SER
119G PRO
SO4 C1150
87W ARG
109G GLU
110G GLU
111G PHE
113E ARG
115W SER
119W PRO
SO4 W1150
87Q ARG
109O GLU
110O GLU
111O PHE
113Y ARG
115Q SER
119Q PRO
SO4 K1150
87E ARG
109U GLU
110U GLU
111U PHE
113W ARG
115E SER
119E PRO
SO4 S1148
106G HIS
110G GLU
113G ARG
114O HIS
115O SER
118O SER
119O PRO
SO4 C1148
106Q HIS
110Q GLU
113Q ARG
114Y HIS
115Y SER
118Y SER
119Y PRO
SO4 Y1148
106M HIS
110M GLU
113M ARG
114U HIS
115U SER
118U SER
119U PRO
SO4 E1148
106I HIS
110I GLU
113I ARG
114A HIS
115A SER
118A SER
119A PRO
SO4 O1148
106C HIS
110C GLU
113C ARG
114K HIS
115K SER
118K SER
119K PRO
SO4 G1148
106K HIS
110K GLU
113K ARG
114C HIS
115C SER
118C SER
119C PRO
SO4 M1148
106A HIS
110A GLU
113A ARG
114I HIS
115I SER
118I SER
119I PRO
SO4 Q1148
106U HIS
110U GLU
113U ARG
114M HIS
115M SER
118M SER
119M PRO
SO4 K1148
106O HIS
110O GLU
113O ARG
114G HIS
115G SER
118G SER
119G PRO
SO4 A1148
106E HIS
110E GLU
113E ARG
114W HIS
115W SER
118W SER
119W PRO
SO4 U1148
106Y HIS
110Y GLU
113Y ARG
114Q HIS
115Q SER
118Q SER
119Q PRO
SO4 I1148
106W HIS
110W GLU
113W ARG
114E HIS
115E SER
118E SER
119E PRO
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
2y77 CB8P1144 Details
CB8R1144
CB8B1144
CB8T1144
CB8V1144
CB8F1144
CB8N1144
CB8X1144
CB8L1144
CB8D1144
CB8H1144
CB8J1144
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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SO4 NAME: SULFATE ION
FORMULA: O4 S1
SMILES: [O-]S([O-])(=O)=O
XNW 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: 3.762 seconds