MolNFT v1 · #126269 · protein

Coiled-coil protein

5LXN · Transforming acidic coiled-coil-containing protein 3: “Coiled-coil protein”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.67). MolNFT v1 #126269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LXN
Type: protein
Length: 639 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transforming acidic coiled-coil-containing protein 3
UniProt: Q9Y6A5
Ligands: SO4
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 95% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Transforming acidic coiled-coil-containing protein 3	protein	81	95% helix, 0% strand	Q9Y6A5
B, D, H	Transforming acidic coiled-coil-containing protein 3	protein	80	95% helix, 0% strand	Q9Y6A5
F	Transforming acidic coiled-coil-containing protein 3	protein	76	96% helix, 0% strand	Q9Y6A5
G	Transforming acidic coiled-coil-containing protein 3	protein	80	95% helix, 0% strand	Q9Y6A5

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains C, D, H
PGE · Triethylene glycol · additive · 7 copies · chains A, G, H, B, F, C, D

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

Pockets

6 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	564	0.67	0.77	49	PGE
2	362	0.61	0.77	49	PGE
3	286	0.55	0.76	37	PGE
4	185	0.53	0.78	23	empty
5	77	0.36	0.76	18	empty

Interfaces

18 interfaces between chains.

C–D · 1873 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1837 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 1829 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 1702 Å² buried · 5 hydrogen bonds · protein-protein
B–F · 1081 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified, 2 disulfide (engineered, disulfide).

Compared structures

5LXN · Coiled-coil protein · the same entry in another collection · chain H against H, TM-score 1.00
Q9Y6A5 · AlphaFold monomer V2.0 prediction for transforming acidic coiled- coil-containing protein… · a predicted model of the same protein · chain F against A, TM-score 0.92

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 Q9Y6A5
Elsewhere: RCSB PDB 5LXN · PDBe 5LXN · UniProt Q9Y6A5

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