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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3k88
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF NADH:FAD OXIDOREDUCTASE (TFTC) - FAD, NADH COMPLEX TITLE
CHLOROPHENOL-4-MONOOXYGENASE COMPONENT 1 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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NAD L 501
22J PHE
23J ARG
26J LEU
27J SER
31J THR
50J SER
51J ALA
67J ASN
144J SER
145J HIS
166J TYR
169J ARG
1054G SER
1055G VAL
1056G CYS
1057G ASP
NAD R 501
22P PHE
23P ARG
26P LEU
27P SER
31P THR
50P SER
51P ALA
67P ASN
144P SER
145P HIS
166P TYR
169P ARG
1054M SER
1055M VAL
1056M CYS
1057M ASP
NAD F 501
22D PHE
23D ARG
26D LEU
27D SER
31D THR
50D SER
51D ALA
67D ASN
144D SER
145D HIS
166D TYR
169D ARG
1054A SER
1055A VAL
1056A CYS
1057A ASP
FAD K 500
33J VAL
47J LEU
48J THR
49J CYS
50J SER
51J ALA
65J CYS
66J ILE
67J ASN
69J LYS
70J SER
71J TYR
72J ALA
96J GLN
98J PHE
99J ALA
100J GLY
103J SER
104J VAL
105J PRO
106J MET
109J ARG
166J TYR
171J TYR
FAD Q 500
33P VAL
47P LEU
48P THR
49P CYS
50P SER
51P ALA
65P CYS
66P ILE
67P ASN
69P LYS
70P SER
71P TYR
72P ALA
96P GLN
98P PHE
99P ALA
100P GLY
103P SER
104P VAL
105P PRO
106P MET
109P ARG
166P TYR
171P TYR
FAD E 500
33D VAL
47D LEU
48D THR
49D CYS
50D SER
51D ALA
65D CYS
66D ILE
67D ASN
69D LYS
70D SER
71D TYR
72D ALA
96D GLN
98D PHE
99D ALA
100D GLY
103D SER
104D VAL
105D PRO
106D MET
109D ARG
166D TYR
171D TYR
FAD B1500
41J PRO
42J PHE
57D ASP
58D ARG
77J LYS
78J SER
79J ASN
80J GLY
81J VAL
135J THR
136J ILE
137J ALA
1033A VAL
1047A LEU
1048A THR
1049A CYS
1050A SER
1051A ALA
1065A CYS
1066A ILE
1067A ASN
1069A LYS
1070A SER
1095A SER
1096A GLN
1098A PHE
1099A ALA
1100A GLY
1101A VAL
1144A SER
1145A HIS
1166A TYR
1171A TYR
FAD N1500
41D PRO
42D PHE
57P ASP
58P ARG
77D LYS
78D SER
79D ASN
80D GLY
81D VAL
135D THR
136D ILE
137D ALA
1033M VAL
1047M LEU
1048M THR
1049M CYS
1050M SER
1051M ALA
1065M CYS
1066M ILE
1067M ASN
1069M LYS
1070M SER
1095M SER
1096M GLN
1098M PHE
1099M ALA
1100M GLY
1144M SER
1145M HIS
1166M TYR
1171M TYR
FAD H1500
41P PRO
42P PHE
57J ASP
58J ARG
77P LYS
78P SER
79P ASN
80P GLY
81P VAL
135P THR
136P ILE
137P ALA
1033G VAL
1047G LEU
1048G THR
1049G CYS
1050G SER
1051G ALA
1065G CYS
1066G ILE
1067G ASN
1069G LYS
1070G SER
1095G SER
1096G GLN
1098G PHE
1099G ALA
1100G GLY
1101G VAL
1144G SER
1145G HIS
1166G TYR
1171G TYR
NAD C1501
54D SER
55D VAL
56D CYS
57D ASP
1022A PHE
1023A ARG
1026A LEU
1027A SER
1031A THR
1050A SER
1051A ALA
1067A ASN
1069A LYS
1145A HIS
1166A TYR
1169A ARG
NAD O1501
54P SER
55P VAL
56P CYS
57P ASP
1022M PHE
1023M ARG
1026M LEU
1027M SER
1031M THR
1050M SER
1051M ALA
1067M ASN
1069M LYS
1145M HIS
1166M TYR
1169M ARG
NAD I1501
54J SER
55J VAL
56J CYS
57J ASP
1022G PHE
1023G ARG
1026G LEU
1027G SER
1031G THR
1050G SER
1051G ALA
1067G ASN
1069G LYS
1145G HIS
1166G TYR
1169G 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
3k86 Details
other holo-structures
pdb ID Ligand Unique ID
3k87 FADB_600 Details
FADD_500
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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FAD NAME: FLAVIN-ADENINE DINUCLEOTIDE
FORMULA: C27 H33 N9 O15 P2
SMILES: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CC(O)C(O)C(O)COP(O)(=O)OP(O)(=O)OCC4OC(C(O)C4O)[n]5cnc6c(N)ncnc56)c2cc1C
NAD NAME: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
FORMULA: C21 H27 N7 O14 P2
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
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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