Research workbench

Selenomethionine derivative of xenopus laevis embryonic epidermal lectin carbohydrate-binding domain

Analyse Selenomethionine derivative of xenopus laevis embryonic epidermal lectin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WMO
Type: protein
Length: 1,662 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xeel protein
UniProt: Q5PPM0
Ligands: CA
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, C, B, D, E, A	Xeel protein	protein	277	21% helix, 27% strand	Q5PPM0

Ligands and binding sites

CA · Calcium ion · metal · 18 copies · chains F, C, B, D, E, A
1PE · Pentaethylene glycol · additive · 14 copies · chains F, C, B, D, E, A

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

Pockets

11 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	1083	0.86	0.87	124	empty
2	1103	0.86	0.87	126	empty
3	92	0.40	0.77	19	empty
4	78	0.39	0.78	19	empty
5	78	0.39	0.78	18	empty

Interfaces

9 interfaces between chains.

B–A · 848 Å² buried · 12 hydrogen bonds · protein-protein
F–E · 845 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 844 Å² buried · 14 hydrogen bonds · protein-protein
C–B · 835 Å² buried · 11 hydrogen bonds · protein-protein
F–D · 834 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified, 24 disulfide (engineered, disulfide).

Compared structures

4WMO · Selenomethionine derivative of Xenopus laevis embryonic epidermal lectin… · the same entry in another collection · chain B against B, TM-score 1.00
Q5PPM0 · AlphaFold monomer V2.0 prediction for intelectin-1 (Q5PPM0) · a predicted model of the same protein · chain F against A, TM-score 1.00

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 Q5PPM0
Elsewhere: RCSB PDB 4WMO · PDBe 4WMO · UniProt Q5PPM0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.