MolNFT v1 · #50149 · protein

Crystal structure of lamprey variable lymphocyte receptor 2913 ectodomain

2R9U: “Crystal structure of lamprey variable lymphocyte receptor 2913 ectodomain”. X-ray diffraction, 3 pockets (best druggability 0.79). MolNFT v1 #50149 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2R9U
Type: protein
Length: 696 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Variable lymphocyte receptor
UniProt: Q6E4B4
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Variable lymphocyte receptor	protein	174	14% helix, 17% strand	Q6E4B4

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	774	0.79	0.83	90	empty
2	123	0.55	0.83	27	empty
3	185	0.53	0.79	28	empty

Interfaces

5 interfaces between chains.

A–B · 552 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 547 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 276 Å² buried · 1 hydrogen bond · protein-protein
B–D · 187 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 90 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

2R9U · Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain · the same entry in another collection · chain A against A, TM-score 1.00

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 Q6E4B4
Elsewhere: RCSB PDB 2R9U · PDBe 2R9U · UniProt Q6E4B4

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