MolNFT v1 · #38979 · protein

Crystal structure of HBR3 bound to CB3S-Fab

2HFG · CB3S Fab light chain (kappa): “Crystal structure of HBR3 bound to CB3S-Fab”. X-ray diffraction, 5 pockets (best druggability 0.57). MolNFT v1 #38979 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2HFG
Type: protein
Length: 460 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CB3S Fab light chain (kappa); CB3S Fab heavy chain; Tumor necrosis factor receptor…
UniProt: Q6PIH7, Q6N093, Q96RJ3
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	CB3S Fab light chain (kappa)	protein	213	7% helix, 51% strand	Q6PIH7
H	CB3S Fab heavy chain	protein	220	7% helix, 57% strand	Q6N093
R	Tumor necrosis factor receptor superfamily member 13C	protein	27	0% helix, 37% strand	Q96RJ3

Pockets

5 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	393	0.57	0.74	47	empty
2	62	0.52	0.87	20	empty
3	155	0.41	0.74	30	empty
4	103	0.36	0.74	22	empty
5	60	0.27	0.73	19	empty

Interfaces

3 interfaces between chains.

L–H · 1860 Å² buried · 18 hydrogen bonds · protein-protein
H–R · 665 Å² buried · 7 hydrogen bonds · protein-protein
L–R · 243 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

2HFG · Crystal structure of hBR3 bound to CB3s-Fab · the same entry in another collection · chain L against L, TM-score 1.00
Q96RJ3 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain R against A, TM-score 0.71

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 Q6PIH7
Every structure of UniProt Q6N093
Every structure of UniProt Q96RJ3
Elsewhere: RCSB PDB 2HFG · PDBe 2HFG · UniProt Q6PIH7 · UniProt Q6N093 · UniProt Q96RJ3

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