Research workbench

1.9 ångström crystal structure of CLEC5A

Analyse 1.9 ångström crystal structure of CLEC5A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YHF
Type: protein
Length: 1,062 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-type lectin domain family 5 member a
UniProt: Q9NY25
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I	C-type lectin domain family 5 member a	protein	118	17% helix, 36% strand	Q9NY25

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1165	0.79	0.81	115	empty
2	1159	0.76	0.79	118	empty
3	88	0.62	0.90	24	empty
4	169	0.59	0.83	28	empty
5	228	0.57	0.79	24	empty

Interfaces

17 interfaces between chains.

A–F · 872 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 864 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 576 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 556 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 555 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 disulfide (disulfide).

Compared structures

2YHF · 1.9 Angstrom Crystal Structure of CLEC5A · the same entry in another collection · chain I against I, TM-score 1.00
Q9NY25 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 5 member a (Q9NY25) · a predicted model of the same protein · chain F against A, TM-score 0.99

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 Q9NY25
Elsewhere: RCSB PDB 2YHF · PDBe 2YHF · UniProt Q9NY25

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