MolNFT v1 · #159288 · protein

Human OX40R (TNFRSF4) bound to Fab 3C8

6OKM · Fab 3C8 heavy chain: “Human OX40R (TNFRSF4) bound to Fab 3C8”. X-ray diffraction, 6 pockets (best druggability 0.52). MolNFT v1 #159288 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OKM
Type: protein
Length: 538 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 3C8 heavy chain; Fab 3C8 light chain; Tumor necrosis factor receptor superfamily…
UniProt: P43489
Pockets: 6 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab 3C8 heavy chain	protein	214	7% helix, 50% strand	—
L	Fab 3C8 light chain	protein	214	6% helix, 50% strand	—
R	Tumor necrosis factor receptor superfamily member 4	protein	110	3% helix, 35% strand	P43489

Pockets

6 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	170	0.52	0.79	30	empty
2	305	0.51	0.73	44	empty
3	123	0.43	0.76	20	empty
4	111	0.43	0.77	18	empty
5	107	0.39	0.75	28	empty

Interfaces

3 interfaces between chains.

H–L · 1836 Å² buried · 9 hydrogen bonds · protein-protein
H–R · 550 Å² buried · 7 hydrogen bonds · protein-protein
L–R · 500 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide (disulfide).

Compared structures

6OKM · Human OX40R (TNFRSF4) bound to Fab 3C8 · the same entry in another collection · chain H against H, TM-score 1.00
P43489 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 4… · a predicted model of the same protein · chain R against A, TM-score 0.89

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 P43489
Elsewhere: RCSB PDB 6OKM · PDBe 6OKM · UniProt P43489

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