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Dimer structure of murine nectin-1 D1

Analyse Dimer structure of murine nectin-1 D1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5B21
Type: protein
Length: 228 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Murine nectin-1 D1
UniProt: Q9JKF6
Pockets: 1 · best druggability 0.33

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Murine nectin-1 D1	protein	114	3% helix, 58% strand	Q9JKF6

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.33	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 1094 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5B21 · Dimer structure of murine Nectin-1 D1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9JKF6 · AlphaFold monomer V2.0 prediction for nectin-1 (Q9JKF6) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q9JKF6
Elsewhere: RCSB PDB 5B21 · PDBe 5B21 · UniProt Q9JKF6

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