MolNFT v1 · #153360 · protein

Crystal structure of the Fab fragment of ipilimumab

6JC2 · Ipilimumab Fab heavy chain: “Crystal structure of the Fab fragment of ipilimumab”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.47). MolNFT v1 #153360 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6JC2
Type: protein
Length: 426 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ipilimumab Fab heavy chain; Ipilimumab Fab light chain
Ligands: SO4
Pockets: 4 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Ipilimumab Fab heavy chain	protein	212	6% helix, 53% strand	—
L	Ipilimumab Fab light chain	protein	214	7% helix, 53% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains H, L

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.47	0.74	37	empty
2	132	0.39	0.74	25	empty
3	116	0.37	0.74	27	empty
4	90	0.33	0.73	23	empty

Interfaces

1 interface between chains.

H–L · 1564 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6JC2 · Crystal structure of the Fab fragment of ipilimumab · the same entry in another collection · chain H against H, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6JC2 · PDBe 6JC2

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