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Crystal structure of human nectin-4 extracellular fragment D1-D2

Analyse Crystal structure of human nectin-4 extracellular fragment D1-D2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FRW
Type: protein
Length: 1,248 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poliovirus receptor-related protein 4
UniProt: Q96NY8
Pockets: 14 · best druggability 0.60

Structure

x-ray diffraction · 6 distinct chains · 3% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Poliovirus receptor-related protein 4	protein	215	4% helix, 55% strand	Q96NY8
B	Poliovirus receptor-related protein 4	protein	213	3% helix, 57% strand	Q96NY8
C	Poliovirus receptor-related protein 4	protein	211	3% helix, 53% strand	Q96NY8
D	Poliovirus receptor-related protein 4	protein	212	1% helix, 55% strand	Q96NY8
E	Poliovirus receptor-related protein 4	protein	208	1% helix, 46% strand	Q96NY8
F	Poliovirus receptor-related protein 4	protein	189	5% helix, 43% strand	Q96NY8

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	267	0.60	0.80	37	empty
2	310	0.58	0.77	41	empty
3	187	0.52	0.78	26	empty
4	177	0.51	0.78	30	empty
5	65	0.41	0.81	20	empty

Interfaces

5 interfaces between chains.

B–C · 759 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 645 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 623 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 474 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 395 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4FRW · Crystal structure of human nectin-4 extracellular fragment D1-D2 · the same entry in another collection · chain F against F, TM-score 1.00
Q96NY8 · AlphaFold monomer V2.0 prediction for nectin-4 (Q96NY8) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 Q96NY8
Elsewhere: RCSB PDB 4FRW · PDBe 4FRW · UniProt Q96NY8

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