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Structure of chimeric 02-K Fab, a VRC01-like germline antibody

Analyse Structure of chimeric 02-K Fab, a VRC01-like germline antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TFS
Type: protein
Length: 424 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 02-K Fab heavy chain; 02-K Fab light chain
Ligands: SO4
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	02-K Fab heavy chain	protein	217	12% helix, 53% strand	—
L	02-K Fab light chain	protein	207	7% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	421	0.57	0.74	51	SO4
2	126	0.40	0.75	25	empty
3	89	0.32	0.73	19	empty

Interfaces

1 interface between chains.

H–L · 1809 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).

Compared structures

5TFS · Structure of chimeric 02-K Fab, a VRC01-like germline antibody · 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 5TFS · PDBe 5TFS

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