Research workbench

C-type lectin from bothrops jararacussu

Analyse C-type lectin from bothrops jararacussu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F2Q
Type: protein
Length: 1,344 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-type lectin bjcul
UniProt: P83519
Ligands: CA, NA
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F, G, H, J	C-type lectin bjcul	protein	134	22% helix, 35% strand	P83519
B, C, E, I	C-type lectin bjcul	protein	135	21% helix, 32% strand	P83519

Ligands and binding sites

CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

12 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	966	0.71	0.75	90	empty
2	1045	0.70	0.75	105	NA
3	958	0.70	0.75	96	NA
4	884	0.68	0.75	87	empty
5	665	0.65	0.75	64	NA

Interfaces

20 interfaces between chains.

F–G · 673 Å² buried · 17 hydrogen bonds · protein-protein
H–I · 659 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 657 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 656 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 655 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 37 disulfide (disulfide).

Compared structures

5F2Q · C-type lectin from Bothrops jararacussu · the same entry in another collection · chain J against J, TM-score 1.00
P83519 · AlphaFold monomer V2.0 prediction for C-type lectin bjcul (P83519) · a predicted model of the same protein · chain A 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 P83519
Elsewhere: RCSB PDB 5F2Q · PDBe 5F2Q · UniProt P83519

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