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1RKH

crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205
The binding interface of the protein-peptide complex is shown in grey, the peptide is shown in red. Images produced by YASARA. Note that only the interface of the protein-peptide complex is shown. Gaps between residues may occur. The image on the top is borrowed from the PDB.

Clusters

This protein-peptide complex appears in the following clusters

Cluster Images Centroid Images Centroid PDB ID Number of PDBs Threshold Structural Alignment
1GWR 121 3 Å 50 %
1GWR 121 2 Å 50 %
1FM9 119 3 Å 75 %
1GWR 118 1 Å 50 %
1FM9 117 2 Å 75 %
2GTK 111 1 Å 75 %
2ZMH 18 3 Å 95 %
2ZMH 18 2 Å 95 %
2ZMH 13 1 Å 95 %

Properties

C
A
11
General information on the complex, such as the receptor and peptide chains. Click on the PDB icon to see this complex in the PDB

Interface Statistics

94
64
C=6 H=94
C=36 H=64
33.4472
47.9337
The DSSP algorithm was used to assign secondary structure to binding site and peptide. The B-Factors are averaged across the PDB and show the flexibility of the binding site and peptide.

Binding Energy

-23.64 kCal *
-5.42 kCal *
-5.19 kCal *
The binding affinity and contribution of backbone and sidechain hydrogen bonds for the protein-peptide complex were calculated using the FoldX force field.
*: the absolute energies are not precise, however FoldX is accurate for relative energies. Learn More.

Categorization

1rkhA00
d1rkha_
Vitamin D3 receptor
P13053
VDR_RAT
Hormone_recep
Note that only the receptor chain(s) is categorized.

Direct link to External Databases

AffinDB FireDB PLD PROCOGNATE PDBSum 3DID
The links are established based on the PDB Identifier of the protein-peptide complex.

BriX Covers

BriX is a structural classification of protein fragments. The library comprises fragments ranging from 4 to 14 amino acids that are clustered against 6 different distance thresholds. This has lead to an alphabet of around 2000 frequently observed letters or structural classes per chain length. These classes are accessible through a search and a browse interface on the BriX website. The peptide is associated with its corresponding structural class from the database of protein fragment clusters (BriX). In these fragment clusters, sets of protein fragments with highly similar backbone structure are grouped. Each protein fragment class represents a natural variation on a typical backbone conformation, with a given length and starting from the given residue in the original peptide. To find out more, consult this help page.
Peptide Chain Peptide Residue BriX Fragment Length BriX Threshold Covering BriX Class
C 625 10 0.8 Å 2433, 3327, 6426, 14124, 14259
C 626 10 0.8 Å 266, 414, 3362, 3916, 6670, 8813, 10336