MolNFT v1 · #38788 · protein

Crystal structure of phage derived Fab BDF1 with human death receptor 5 (DR5)

2H9G · Fab BDF1, light chain: “Crystal structure of phage derived Fab BDF1 with human death receptor 5 (DR5)”. X-ray diffraction, 12 pockets (best druggability 0.58). MolNFT v1 #38788 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2H9G
Type: protein
Length: 1,024 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab BDF1, light chain; Fab BDF1, heavy chain; Tumor necrosis factor receptor superfamily…
UniProt: O14763
Pockets: 12 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, L	Fab BDF1, light chain	protein	211	6% helix, 51% strand	—
B, H	Fab BDF1, heavy chain	protein	215	8% helix, 52% strand	—
R	Tumor necrosis factor receptor superfamily member 10B precursor	protein	108	0% helix, 30% strand	O14763
S	Tumor necrosis factor receptor superfamily member 10B precursor	protein	64	0% helix, 27% strand	O14763

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	441	0.58	0.74	55	empty
2	59	0.57	0.90	21	empty
3	382	0.56	0.74	46	empty
4	415	0.56	0.73	38	empty
5	228	0.54	0.78	24	empty

Interfaces

7 interfaces between chains.

A–B · 1798 Å² buried · 15 hydrogen bonds · protein-protein
L–H · 1797 Å² buried · 15 hydrogen bonds · protein-protein
B–H · 679 Å² buried · 15 hydrogen bonds · protein-protein
H–S · 576 Å² buried · 4 hydrogen bonds · protein-protein
B–R · 567 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide (disulfide).

Compared structures

2H9G · Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5) · the same entry in another collection · chain H against H, TM-score 1.00
O14763 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain S against A, TM-score 0.94

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 O14763
Elsewhere: RCSB PDB 2H9G · PDBe 2H9G · UniProt O14763

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