MolNFT v1 · #26351 · protein

Crystal structure of the UNC5H2 death domain

1WMG · Netrin receptor UNC5H2: “Crystal structure of the UNC5H2 death domain”. X-ray diffraction, 2 ligands (SO3, SO4). MolNFT v1 #26351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1WMG
Type: protein
Length: 522 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Netrin receptor UNC5H2
UniProt: Q8K1S3
Ligands: SO3, SO4

Structure

x-ray diffraction · 6 distinct chains · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Netrin receptor UNC5H2	protein	90	68% helix, 0% strand	Q8K1S3
B	Netrin receptor UNC5H2	protein	83	70% helix, 0% strand	Q8K1S3
C	Netrin receptor UNC5H2	protein	88	63% helix, 0% strand	Q8K1S3
D	Netrin receptor UNC5H2	protein	86	65% helix, 0% strand	Q8K1S3
E	Netrin receptor UNC5H2	protein	88	61% helix, 0% strand	Q8K1S3
F	Netrin receptor UNC5H2	protein	87	57% helix, 0% strand	Q8K1S3

Ligands and binding sites

SO3 · Sulfite ion · ion · 7 copies · chains A, C, D, E
SO4 · Sulfate ion · ion · 3 copies · chains C, E, F

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

Interfaces

5 interfaces between chains.

A–B · 698 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 695 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 626 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 587 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 524 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

1WMG · Crystal structure of the UNC5H2 death domain · the same entry in another collection · chain F against F, TM-score 1.00
Q8K1S3 · AlphaFold monomer V2.0 prediction for netrin receptor UNC5B (Q8K1S3) · a predicted model of the same protein · chain F against A, TM-score 0.89

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 Q8K1S3
Elsewhere: RCSB PDB 1WMG · PDBe 1WMG · UniProt Q8K1S3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.