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Crystal structure of the immunoglobulin variable domain of nectin-2 in monoclinic form

Analyse Crystal structure of the immunoglobulin variable domain of nectin-2 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HZA
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poliovirus receptor-related protein 2
UniProt: Q92692
Pockets: 4 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Poliovirus receptor-related protein 2	protein	124	7% helix, 48% strand	Q92692

Pockets

4 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	148	0.49	0.78	22	empty
2	51	0.37	0.80	18	empty
3	73	0.36	0.77	16	empty
4	51	0.34	0.79	13	empty

Interfaces

1 interface between chains.

A–B · 961 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4HZA · Crystal Structure of the Immunoglobulin variable domain of Nectin-2 in monoclinic form · the same entry in another collection · chain A against A, TM-score 1.00
Q92692 · AlphaFold monomer V2.0 prediction for nectin-2 (Q92692) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q92692
Elsewhere: RCSB PDB 4HZA · PDBe 4HZA · UniProt Q92692

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