MolNFT v1 · #159289 · protein

OX40R (TNFRSF4) bound to Fab 1A7

6OKN · Fab 1A7 heavy chain: “OX40R (TNFRSF4) bound to Fab 1A7”. X-ray diffraction, 7 pockets (best druggability 0.73). MolNFT v1 #159289 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OKN
Type: protein
Length: 1,038 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 1A7 heavy chain; Fab 1A7 light chain; Tumor necrosis factor receptor superfamily…
UniProt: P43489
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab 1A7 heavy chain	protein	217	9% helix, 50% strand	—
B, D	Fab 1A7 light chain	protein	213	7% helix, 51% strand	—
C	Fab 1A7 heavy chain	protein	220	7% helix, 49% strand	—
E	Tumor necrosis factor receptor superfamily member 4	protein	81	4% helix, 23% strand	P43489
R	Tumor necrosis factor receptor superfamily member 4	protein	94	0% helix, 24% strand	P43489

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	1125	0.73	0.77	99	empty
2	683	0.65	0.74	50	empty
3	642	0.64	0.74	55	EPE
4	93	0.37	0.75	18	empty
5	94	0.34	0.74	21	empty

Interfaces

9 interfaces between chains.

C–D · 1845 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1782 Å² buried · 16 hydrogen bonds · protein-protein
C–E · 580 Å² buried · 2 hydrogen bonds · protein-protein
A–R · 567 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 464 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 19 disulfide (disulfide).

Compared structures

6OKN · OX40R (TNFRSF4) bound to Fab 1A7 · the same entry in another collection · chain R against R, 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 0.96

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 6OKN · PDBe 6OKN · UniProt P43489

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