MolNFT v1 · #123850 · protein

Crystal structure of ligand-free VRC03 antigen-binding fragment.

5JXA · VRC03 heavy chain: “Crystal structure of ligand-free VRC03 antigen-binding fragment.”. X-ray diffraction, 2 ligands (CU, PO4), 3 pockets (best druggability 0.56). MolNFT v1 #123850 on GenesisL1: 3D structure, binding sites and…

PDB: 5JXA
Type: protein
Length: 440 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VRC03 heavy chain; VRC03 light chain
Ligands: CU, PO4
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	VRC03 heavy chain	protein	231	8% helix, 52% strand	—
L	VRC03 light chain	protein	209	6% helix, 51% strand	—

Ligands and binding sites

CU · Copper (II) ion · metal · 3 copies · chains H, L
PO4 · Phosphate ion · ion · 3 copies · chains H, L
EDO · 1,2-ethanediol · additive · 3 copies · chains H, L

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

Pockets

3 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	344	0.56	0.75	43	empty
2	240	0.56	0.78	38	EDO
3	76	0.34	0.75	17	empty

Interfaces

1 interface between chains.

H–L · 1865 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5JXA · Crystal structure of ligand-free VRC03 antigen-binding fragment. · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 5JXA · PDBe 5JXA

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