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Mouse gitr (mgitr) with dta-1 Fab fragment

Analyse Mouse gitr (mgitr) with dta-1 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RFP
Type: protein
Length: 1,114 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor receptor superfamily member 18, enhanced green fluorescent protein…
UniProt: O35714
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 6% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tumor necrosis factor receptor superfamily member 18, enhanced green fluorescent protein	protein	118	3% helix, 23% strand	O35714
H, I	Dta-1 (heavy chain)	protein	218	7% helix, 44% strand	—
L, M	Dta-1 (light chain)	protein	221	6% helix, 46% strand	—

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1117	0.83	0.85	145	empty
2	617	0.78	0.84	93	empty
3	662	0.78	0.83	89	empty
4	738	0.77	0.82	82	empty
5	636	0.73	0.80	101	empty

Interfaces

8 interfaces between chains.

I–M · 644 Å² buried · 0 hydrogen bonds · protein-protein
H–L · 643 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 390 Å² buried · 0 hydrogen bonds · protein-protein
B–M · 263 Å² buried · 0 hydrogen bonds · protein-protein
A–L · 257 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 23 disulfide (disulfide).

Compared structures

7RFP · Mouse GITR (mGITR) with DTA-1 Fab fragment · the same entry in another collection · chain M against M, TM-score 1.00
O35714 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain A against A, TM-score 0.82

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 O35714
Elsewhere: RCSB PDB 7RFP · PDBe 7RFP · UniProt O35714

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