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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1e5q
OXIDOREDUCTASE HEADER
TERNARY COMPLEX OF SACCHAROPINE REDUCTASE FROM MAGNAPORTHE GRISEA, NADPH AND SACCHAROPINE TITLE
SACCHAROPINE REDUCTASE 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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NDP F 500
9F LEU
10F GLY
11F SER
12F GLY
13F PHE
14F VAL
15F THR
32F ALA
33F CYS
34F ARG
35F THR
38F SER
54F LEU
55F ASP
56F VAL
57F ASN
74F SER
75F LEU
76F ILE
77F PRO
78F TYR
80F PHE
81F HIS
98F THR
99F SER
124F GLY
125F LEU
126F ASP
127F PRO
174F TRP
175F SER
176F SER
178F GLY
395F MET
399F VAL
NDP A 500
9A LEU
10A GLY
11A SER
12A GLY
13A PHE
14A VAL
15A THR
32A ALA
33A CYS
34A ARG
35A THR
38A SER
54A LEU
55A ASP
56A VAL
57A ASN
74A SER
75A LEU
76A ILE
77A PRO
78A TYR
80A PHE
81A HIS
98A THR
99A SER
124A GLY
125A LEU
126A ASP
127A PRO
174A TRP
175A SER
176A SER
178A GLY
395A MET
399A VAL
NDP H 500
9H LEU
10H GLY
11H SER
12H GLY
13H PHE
14H VAL
15H THR
32H ALA
33H CYS
34H ARG
35H THR
38H SER
54H LEU
55H ASP
56H VAL
57H ASN
74H SER
75H LEU
76H ILE
77H PRO
78H TYR
80H PHE
81H HIS
98H THR
99H SER
124H GLY
125H LEU
126H ASP
127H PRO
174H TRP
175H SER
176H SER
178H GLY
395H MET
399H VAL
NDP D 500
9D LEU
10D GLY
11D SER
12D GLY
13D PHE
14D VAL
15D THR
32D ALA
33D CYS
34D ARG
35D THR
38D SER
54D LEU
55D ASP
56D VAL
57D ASN
74D SER
75D LEU
76D ILE
77D PRO
78D TYR
80D PHE
81D HIS
98D THR
99D SER
124D GLY
125D LEU
126D ASP
127D PRO
174D TRP
175D SER
176D SER
178D GLY
395D MET
399D VAL
NDP C 500
9C LEU
10C GLY
11C SER
12C GLY
13C PHE
14C VAL
15C THR
32C ALA
33C CYS
34C ARG
35C THR
38C SER
54C LEU
55C ASP
56C VAL
57C ASN
74C SER
75C LEU
76C ILE
77C PRO
78C TYR
80C PHE
81C HIS
98C THR
99C SER
124C GLY
125C LEU
126C ASP
127C PRO
174C TRP
175C SER
176C SER
178C GLY
395C MET
399C VAL
NDP B 500
9B LEU
10B GLY
11B SER
12B GLY
13B PHE
14B VAL
15B THR
32B ALA
33B CYS
34B ARG
35B THR
38B SER
54B LEU
55B ASP
56B VAL
57B ASN
74B SER
75B LEU
76B ILE
77B PRO
78B TYR
80B PHE
81B HIS
98B THR
99B SER
124B GLY
125B LEU
126B ASP
127B PRO
174B TRP
175B SER
176B SER
178B GLY
395B MET
399B VAL
NDP E 500
9E LEU
10E GLY
11E SER
12E GLY
13E PHE
14E VAL
15E THR
32E ALA
33E CYS
34E ARG
35E THR
38E SER
54E LEU
55E ASP
56E VAL
57E ASN
74E SER
75E LEU
76E ILE
77E PRO
78E TYR
80E PHE
81E HIS
98E THR
99E SER
124E GLY
125E LEU
126E ASP
127E PRO
174E TRP
175E SER
176E SER
178E GLY
395E MET
399E VAL
NDP G 500
9G LEU
10G GLY
11G SER
12G GLY
13G PHE
14G VAL
15G THR
32G ALA
33G CYS
34G ARG
35G THR
38G SER
54G LEU
55G ASP
56G VAL
57G ASN
74G SER
75G LEU
76G ILE
77G PRO
78G TYR
80G PHE
81G HIS
98G THR
99G SER
124G GLY
125G LEU
126G ASP
127G PRO
174G TRP
175G SER
176G SER
178G GLY
395G MET
399G VAL
SHR F 501
78F TYR
99F SER
100F TYR
125F LEU
126F ASP
127F PRO
155F CYS
156F GLY
157F GLY
174F TRP
178F GLY
182F ALA
223F ASN
224F ARG
245F THR
247F ARG
395F MET
SHR A 501
78A TYR
99A SER
100A TYR
125A LEU
126A ASP
127A PRO
155A CYS
156A GLY
157A GLY
174A TRP
178A GLY
182A ALA
223A ASN
224A ARG
245A THR
247A ARG
395A MET
SHR H 501
78H TYR
99H SER
100H TYR
125H LEU
126H ASP
127H PRO
155H CYS
156H GLY
157H GLY
174H TRP
178H GLY
182H ALA
223H ASN
224H ARG
245H THR
247H ARG
395H MET
SHR D 501
78D TYR
99D SER
100D TYR
125D LEU
126D ASP
127D PRO
155D CYS
156D GLY
157D GLY
174D TRP
178D GLY
182D ALA
223D ASN
224D ARG
245D THR
247D ARG
395D MET
SHR C 501
78C TYR
99C SER
100C TYR
125C LEU
126C ASP
127C PRO
155C CYS
157C GLY
174C TRP
178C GLY
182C ALA
223C ASN
224C ARG
245C THR
247C ARG
395C MET
SHR B 501
78B TYR
99B SER
100B TYR
125B LEU
126B ASP
127B PRO
155B CYS
156B GLY
157B GLY
170B TYR
174B TRP
178B GLY
182B ALA
223B ASN
224B ARG
245B THR
247B ARG
395B MET
SHR E 501
78E TYR
99E SER
100E TYR
125E LEU
126E ASP
127E PRO
155E CYS
157E GLY
174E TRP
178E GLY
182E ALA
223E ASN
224E ARG
245E THR
247E ARG
395E MET
SHR G 501
78G TYR
99G SER
100G TYR
125G LEU
126G ASP
127G PRO
155G CYS
156G GLY
157G GLY
174G TRP
178G GLY
182G ALA
223G ASN
224G ARG
245G THR
247G ARG
395G MET
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
1e5l Details
other holo-structures
pdb ID Ligand Unique ID
none
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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NDP NAME: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H30 N7 O17 P3
SMILES: NC(=O)C1=CN(C=CC1)C2OC(COP(O)(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
SHR NAME: N-(5-AMINO-5-CARBOXYPENTYL)GLUTAMIC ACID
FORMULA: C11 H20 N2 O6
SMILES: NC(CCCCNC(CCC(O)=O)C(O)=O)C(O)=O
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: 0.4376 seconds