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Structure of the first-in-class checkpoint inhibitor ipilimumab bound to human ctla-4

Analyse Structure of the first-in-class checkpoint inhibitor ipilimumab bound to human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TRU
Type: protein
Length: 1,081 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ipilimumab Fab light chain; Ipilimumab Fab heavy chain; Cytotoxic T-lymphocyte protein 4
UniProt: P16410
Pockets: 14 · best druggability 0.57

Structure

x-ray diffraction · 6 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Ipilimumab Fab light chain	protein	213	6% helix, 51% strand	—
H	Ipilimumab Fab heavy chain	protein	215	6% helix, 50% strand	—
l	Ipilimumab Fab light chain	protein	212	7% helix, 50% strand	—
h	Ipilimumab Fab heavy chain	protein	212	6% helix, 52% strand	—
c	Cytotoxic T-lymphocyte protein 4	protein	115	0% helix, 57% strand	P16410
C	Cytotoxic T-lymphocyte protein 4	protein	114	3% helix, 55% strand	P16410

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	59	0.57	0.90	24	empty
2	360	0.56	0.75	49	empty
3	357	0.55	0.74	47	empty
4	86	0.55	0.86	18	empty
5	50	0.53	0.89	21	empty

Interfaces

7 interfaces between chains.

l–h · 1645 Å² buried · 13 hydrogen bonds · protein-protein
L–H · 1613 Å² buried · 9 hydrogen bonds · protein-protein
h–c · 618 Å² buried · 4 hydrogen bonds · protein-protein
H–C · 582 Å² buried · 6 hydrogen bonds · protein-protein
l–c · 404 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5TRU · Structure of the first-in-class checkpoint inhibitor Ipilimumab bound to human CTLA-4 · the same entry in another collection · chain C against C, TM-score 1.00
P16410 · AlphaFold monomer V2.0 prediction for cytotoxic T-lymphocyte protein 4 (P16410) · a predicted model of the same protein · chain c 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 P16410
Elsewhere: RCSB PDB 5TRU · PDBe 5TRU · UniProt P16410

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