MolNFT v1 · #116508 · protein

Crystal structure of human CD81 large extracellular loop in complex with single chain fv fragment K13

5DFW · CD81 antigen: “Crystal structure of human CD81 large extracellular loop in complex with single chain fv fragment K13”. X-ray diffraction, 2 pockets (best druggability 0.62). MolNFT v1 #116508 on GenesisL1: 3D structure, binding…

PDB: 5DFW
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD81 antigen; Single chain fv fragment
UniProt: P60033
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD81 antigen	protein	90	66% helix, 0% strand	P60033
H	Single chain fv fragment	protein	222	5% helix, 47% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	204	0.62	0.82	38	empty
2	79	0.31	0.74	19	empty

Interfaces

1 interface between chains.

A–H · 796 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5DFW · Crystal structure of human CD81 large extracellular loop in complex with single chain fv… · the same entry in another collection · chain A against A, 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 0.83

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 5DFW · PDBe 5DFW · UniProt P60033

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