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Structure of RLD2 BRX domain bound to LZY3 CCL motif

Analyse Structure of RLD2 BRX domain bound to LZY3 CCL motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6L0V
Type: protein
Length: 306 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.347
Source: Arabidopsis thaliana
Molecule: RLD2; NGR2
UniProt: F4K0X5, Q5XVG3
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · resolution 1.347 · 3 distinct chains · 26% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RLD2	protein	61	30% helix, 38% strand	F4K0X5
B, D, F, H	NGR2	protein	16	0% helix, 50% strand	Q5XVG3
E, G	RLD2	protein	60	30% helix, 35% strand	F4K0X5

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, E, F
PEG · Di(hydroxyethyl)ether · additive · chains A
PGE · Triethylene glycol · additive · chains G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.35	0.74	21	EDO
2	93	0.33	0.73	19	EDO

Interfaces

13 interfaces between chains.

A–B · 675 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 667 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 650 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 648 Å² buried · 11 hydrogen bonds · protein-protein
A–G · 374 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6L0V · Structure of RLD2 brx domain bound to LZY3 ccl motif · the same entry in another collection · chain H against H, TM-score 1.00
Q5XVG3 · AlphaFold monomer V2.0 prediction for protein lazy 4 (Q5XVG3) · a predicted model of the same protein · chain B against A, TM-score 0.26

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt F4K0X5
Every structure of UniProt Q5XVG3
Elsewhere: RCSB PDB 6L0V · PDBe 6L0V · UniProt F4K0X5 · UniProt Q5XVG3

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