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Anti-TIM3 antibody Fab complex

Analyse Anti-TIM3 antibody Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KQL
Type: protein
Length: 544 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TIM3.18 Fab heavy chain; TIM3.18 Fab light chain; Hepatitis a virus cellular receptor 2
UniProt: Q8TDQ0
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	TIM3.18 Fab heavy chain	protein	219	8% helix, 48% strand	—
L	TIM3.18 Fab light chain	protein	215	7% helix, 50% strand	—
T	Hepatitis a virus cellular receptor 2	protein	110	8% helix, 36% strand	Q8TDQ0

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains H, L

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.58	0.74	54	empty
2	232	0.52	0.76	34	empty
3	158	0.45	0.75	33	empty
4	102	0.40	0.76	20	empty
5	55	0.39	0.80	14	empty

Interfaces

3 interfaces between chains.

H–L · 1827 Å² buried · 19 hydrogen bonds · protein-protein
H–T · 840 Å² buried · 15 hydrogen bonds · protein-protein
L–T · 118 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7KQL · Anti-Tim3 antibody Fab complex · the same entry in another collection · chain L against L, TM-score 1.00
Q8TDQ0 · AlphaFold monomer V2.0 prediction for hepatitis a virus cellular receptor 2 (Q8TDQ0) · a predicted model of the same protein · chain T against A, TM-score 0.88

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 Q8TDQ0
Elsewhere: RCSB PDB 7KQL · PDBe 7KQL · UniProt Q8TDQ0

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