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Cl-K1 trimer

Analyse Cl-K1 trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YLI
Type: protein
Length: 919 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Collectin-11
UniProt: Q9BWP8
Ligands: CA, CL
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Collectin-11	protein	154	34% helix, 27% strand	Q9BWP8
C	Collectin-11	protein	153	35% helix, 27% strand	Q9BWP8
D	Collectin-11	protein	155	34% helix, 27% strand	Q9BWP8
E	Collectin-11	protein	149	32% helix, 28% strand	Q9BWP8

Ligands and binding sites

CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 13 copies · chains A, B, C, D, E, F

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

Pockets

7 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	936	0.82	0.84	105	empty
2	918	0.80	0.82	64	empty
3	120	0.44	0.77	18	empty
4	109	0.41	0.76	18	empty
5	82	0.36	0.76	16	empty

Interfaces

8 interfaces between chains.

D–E · 761 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 747 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 706 Å² buried · 3 hydrogen bonds · protein-protein
D–F · 699 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 680 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4YLI · CL-K1 trimer · the same entry in another collection · chain F against F, TM-score 1.00
Q9BWP8 · AlphaFold monomer V2.0 prediction for collectin-11 (Q9BWP8) · a predicted model of the same protein · chain B 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 Q9BWP8
Elsewhere: RCSB PDB 4YLI · PDBe 4YLI · UniProt Q9BWP8

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