MolNFT v1 · #134819 · protein

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

5TGB · 02-cb Fab heavy chain: “Structure of chimeric 02-cb Fab, a VRC01-like germline antibody”. X-ray diffraction, 7 pockets (best druggability 0.57). MolNFT v1 #134819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TGB
Type: protein
Length: 846 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 02-cb Fab heavy chain; 02-cb Fab light chain
Pockets: 7 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	02-cb Fab heavy chain	protein	210	7% helix, 51% strand	—
L	02-cb Fab light chain	protein	208	6% helix, 51% strand	—
A	02-cb Fab heavy chain	protein	221	9% helix, 52% strand	—
B	02-cb Fab light chain	protein	207	6% helix, 52% strand	—

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.57	0.90	20	empty
2	352	0.54	0.74	48	empty
3	254	0.50	0.75	29	empty
4	61	0.49	0.86	21	empty
5	118	0.43	0.77	22	empty

Interfaces

2 interfaces between chains.

A–B · 1839 Å² buried · 19 hydrogen bonds · protein-protein
H–L · 1622 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5TGB · Structure of chimeric 02-CB 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 5TGB · PDBe 5TGB

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