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The crystal structure of TNF family member eda-A2

Analyse The crystal structure of TNF family member eda-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RJ8
Type: protein
Length: 840 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ectodysplasin-a isoform eda-A2
UniProt: Q92838
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, G	Ectodysplasin-a isoform eda-A2	protein	140	5% helix, 59% strand	Q92838

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	332	0.74	0.86	58	empty
2	280	0.68	0.84	39	empty
3	103	0.40	0.76	17	empty
4	85	0.36	0.75	12	empty
5	84	0.35	0.75	14	empty

Interfaces

9 interfaces between chains.

F–G · 1084 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1019 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1018 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1010 Å² buried · 15 hydrogen bonds · protein-protein
E–G · 976 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1RJ8 · The crystal structure of TNF family member EDA-A2 · the same entry in another collection · chain G against G, TM-score 1.00
Q92838 · AlphaFold monomer V2.0 prediction for ectodysplasin-a (Q92838) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 Q92838
Elsewhere: RCSB PDB 1RJ8 · PDBe 1RJ8 · UniProt Q92838

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