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Crystal structure of an acidic pH-selective ipilimumab variant IPI.106 in complex with ctla-4

Analyse Crystal structure of an acidic pH-selective ipilimumab variant IPI.106 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SU1
Type: protein
Length: 540 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; Cytotoxic T-lymphocyte protein 4
UniProt: P16410
Ligands: NAG
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	214	8% helix, 51% strand	—
L	Fab light chain	protein	214	8% helix, 54% strand	—
C	Cytotoxic T-lymphocyte protein 4	protein	112	3% helix, 59% strand	P16410

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C

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

Pockets

5 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	411	0.64	0.78	57	empty
2	432	0.59	0.75	50	empty
3	68	0.58	0.89	26	empty
4	246	0.49	0.74	32	empty
5	124	0.37	0.73	24	empty

Interfaces

3 interfaces between chains.

H–L · 1602 Å² buried · 10 hydrogen bonds · protein-protein
H–C · 522 Å² buried · 4 hydrogen bonds · protein-protein
L–C · 307 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).

Compared structures

7SU1 · Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.106 in complex with… · the same entry in another collection · chain H against H, 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 7SU1 · PDBe 7SU1 · UniProt P16410

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