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Structural tuning of CD81LEL (space group P31)

Analyse Structural tuning of CD81LEL (space group P31) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M3D
Type: protein
Length: 359 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD81 antigen
UniProt: P60033
Ligands: PO4
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD81 antigen	protein	90	70% helix, 0% strand	P60033
B	CD81 antigen	protein	91	68% helix, 0% strand	P60033
C, D	CD81 antigen	protein	89	65% helix, 0% strand	P60033

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains B, A, C, D
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	173	0.40	0.72	27	empty
2	60	0.37	0.79	14	EDO

Interfaces

3 interfaces between chains.

A–D · 998 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 946 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 58 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5M3D · Structural tuning of CD81LEL (space group P31) · the same entry in another collection · chain C against C, TM-score 1.00
P60033 · AlphaFold monomer V2.0 prediction for CD81 antigen (P60033) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P60033
Elsewhere: RCSB PDB 5M3D · PDBe 5M3D · UniProt P60033

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