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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2rmb
ISOMERASE HEADER
CRYSTAL STRUCTURES OF CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A AND N-METHYL-4-[(E)-2-BUTENYL]-4,4- DIMETHYLTHREONINE CYCLOSPORIN A TITLE
CYCLOPHILIN A 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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SAR F 3
54E HIS
63E GLN
71E ASN
72E GLY
73E THR
SAR P 3
54O HIS
63O GLN
71O ASN
72O GLY
73O THR
SAR J 3
54I HIS
63I GLN
71I ASN
72I GLY
73I THR
SAR R 3
54Q HIS
63Q GLN
71Q ASN
72Q GLY
73Q THR
SAR T 3
54S HIS
63S GLN
71S ASN
72S GLY
73C THR
SAR D 3
54C HIS
63C GLN
71C ASN
72C GLY
73S THR
SAR L 3
54K HIS
63K GLN
71K ASN
72K GLY
73A THR
SAR B 3
54A HIS
63A GLN
71A ASN
72A GLY
73K THR
SAR N 3
54M HIS
63M GLN
71M ASN
72M GLY
73G THR
SAR H 3
54G HIS
63G GLN
71G ASN
72G GLY
73M THR
DMT P 1
55O ARG
63O GLN
102O ASN
103O ALA
104O GLY
107E THR
126O HIS
DMT F 1
55E ARG
63E GLN
102E ASN
103E ALA
104E GLY
107O THR
126E HIS
DMT J 1
55I ARG
63I GLN
102I ASN
103I ALA
104I GLY
107Q THR
126I HIS
DMT R 1
55Q ARG
63Q GLN
102Q ASN
103Q ALA
104Q GLY
107I THR
126Q HIS
DMT T 1
55S ARG
63S GLN
102S ASN
103S ALA
104S GLY
107C THR
126S HIS
DMT D 1
55C ARG
63C GLN
102C ASN
103C ALA
104C GLY
107S THR
126C HIS
DMT L 1
55K ARG
63K GLN
102K ASN
103A ALA
104K GLY
107A THR
126K HIS
DMT B 1
55A ARG
63A GLN
102A ASN
103A ALA
104A GLY
107K THR
126A HIS
DMT N 1
55M ARG
63M GLN
102M ASN
103M ALA
104M GLY
107G THR
126M HIS
DMT H 1
55G ARG
63G GLN
102G ASN
103G ALA
104G GLY
107M THR
126G HIS
ABA R 2
63Q GLN
72Q GLY
101Q ALA
102Q ASN
103Q ALA
107Q THR
111Q GLN
ABA H 2
72G GLY
101G ALA
102G ASN
103G ALA
107G THR
111G GLN
ABA F 2
72E GLY
101E ALA
102E ASN
103E ALA
107E THR
111E GLN
ABA P 2
72O GLY
101O ALA
102O ASN
103O ALA
107O THR
111O GLN
ABA J 2
72I GLY
73I THR
101I ALA
102I ASN
103I ALA
107I THR
111I GLN
ABA D 2
72C GLY
101C ALA
102C ASN
103C ALA
107C THR
111C GLN
ABA T 2
72S GLY
101S ALA
102S ASN
103S ALA
107S THR
111S GLN
ABA B 2
72A GLY
101A ALA
102A ASN
103A ALA
107A THR
111A GLN
ABA L 2
72K GLY
101K ALA
102K ASN
103K ALA
107K THR
111K GLN
ABA N 2
72M GLY
101M ALA
102M ASN
103M ALA
107M THR
111M GLN
MLE F 4
73O THR
74O GLY
75O GLY
81O GLU
82O LYS
103O ALA
107O THR
111O GLN
MLE P 4
73E THR
74E GLY
75E GLY
81E GLU
82E LYS
103E ALA
107E THR
MLE J 4
73Q THR
74Q GLY
75Q GLY
81Q GLU
82Q LYS
103Q ALA
107Q THR
MLE R 4
73I THR
74I GLY
75I GLY
81I GLU
82I LYS
103I ALA
107I THR
111I GLN
MLE T 4
73C THR
74C GLY
75C GLY
81C GLU
82C LYS
103C ALA
107C THR
111C GLN
MLE D 4
73S THR
74S GLY
75S GLY
81S GLU
82S LYS
103S ALA
107S THR
111S GLN
MLE L 4
73A THR
74A GLY
75A GLY
82A LYS
103A ALA
107A THR
MLE B 4
73K THR
74K GLY
75K GLY
81K GLU
82K LYS
103K ALA
107K THR
MLE H 4
73M THR
74M GLY
75M GLY
82M LYS
103M ALA
107M THR
MLE N 4
73G THR
74G GLY
75G GLY
81G GLU
82G LYS
103G ALA
107G THR
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).

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apo-structure
pdb ID
3k0n Details
other holo-structures
pdb ID Ligand Unique ID
1cwb ABAB___2 DMTB___1 MLEB___4 SARB___3 Details
3odl ABAB___6 MVAB___4 SARB___7 YYAB___5 MLEB___2 DALB___1 MLEB___3 MLEB___8 Details
2rma ABAF___2 BMTP___1 MLEF___4 MLEP___4 ABAP___2 BMTF___1 SARF___3 SARP___3 Details
ABAH___2 BMTR___1 MLEH___4 ABAR___2 SARR___3 MLER___4 BMTH___1 SARH___3
ABAJ___2 MLEJ___4 MLET___4 BMTT___1 SART___3 SARJ___3 ABAT___2 BMTJ___1
ABAB___2 MLEL___4 SARL___3 BMTB___1 SARB___3 ABAL___2 BMTL___1 MLEB___4
ABAD___2 BMTD___1 MLEN___4 MLED___4 BMTN___1 ABAN___2 SARD___3 SARN___3
3cys ABAB_202 SARB_203 BMTB_201 MLEB_204 Details
1cwl ABAB___2 MHLB___4 SARB___3 BMTB___1 Details
1cwh ABAB___2 DSEB___3 MLEB___4 BMTB___1 Details
1cwc BMTB___1 DBBB___2 SARB___3 MNLB___4 Details
1ynd SFAB_401 SFAD_402 Details
1mf8 ABAG___2 BMTG___1 MLEG___4 SARG___3 Details
1mik AA4B___2 MLEB___4 SARB___3 BMTB___1 Details
3odi ABAB___6 MVAB___4 SARB___7 MLEB___2 DALB___1 MLEB___3 XXAB___5 MLEB___8 Details
1nmk SFMA_166 SFMB_201 Details
1cwm ABAB___2 TBMB___1 IMLB___4 SARB___3 Details
1cwa ABAB___2 MLEB___4 SARB___3 BMTB___1 Details
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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ABA NAME: alpha-aminobutyric acid
FORMULA: C4 H8 N1 O2
SMILES: CCC(N)C(O)=OALPHA-AMINOBUTYRIC ACID
DMT NAME: 3-HYDROXY-4,4-DIMETHYL-2-(METHYLAMINO)-6-OCTENOIC ACID
FORMULA: C11 H21 N1 O3
SMILES: CNC(C(O)C(C)(C)CC=CC)C(O)=O
MLE NAME: N-methylleucine
FORMULA: C7 H14 N1 O2
SMILES: CNC(CC(C)C)C(O)=ON-METHYLLEUCINE
SAR NAME: sarcosine
FORMULA: C3 H6 N1 O2
SMILES: CNCC(O)=OSARCOSINE
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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