MolNFT v1 · #42155 · protein

Structure of emilin-1 C1Q-like domain

2KA3: “Structure of emilin-1 C1Q-like domain”. Solution nmr, 5 pockets (best druggability 0.74). MolNFT v1 #42155 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2KA3
Type: protein
Length: 393 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Emilin-1
UniProt: Q9Y6C2
Pockets: 5 · best druggability 0.74

Structure

solution nmr · 1 distinct chain · 0% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Emilin-1	protein	131	0% helix, 33% strand	Q9Y6C2

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	523	0.74	0.82	45	empty
2	507	0.72	0.81	50	empty
3	477	0.72	0.82	50	empty
4	821	0.71	0.77	83	empty
5	728	0.69	0.76	71	empty

Interfaces

3 interfaces between chains.

B–C · 595 Å² buried · 1 hydrogen bond · protein-protein
A–C · 584 Å² buried · 1 hydrogen bond · protein-protein
A–B · 466 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2KA3 · Structure of EMILIN-1 C1Q-like domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y6C2 · AlphaFold monomer V2.0 prediction for emilin-1 (Q9Y6C2) · a predicted model of the same protein · chain C against A, TM-score 0.61

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 Q9Y6C2
Elsewhere: RCSB PDB 2KA3 · PDBe 2KA3 · UniProt Q9Y6C2

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