Research workbench

TCR mimic antibody (Fab fragment) in complex with AFP/HLA-A*02

Analyse TCR mimic antibody (Fab fragment) in complex with AFP/HLA-A*02 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RE7
Type: protein
Length: 1,623 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; MHC class I antigen; Beta-2-microglobulin…
UniProt: Q861F7, P61769
Pockets: 19 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 14% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	Fab heavy chain	protein	218	4% helix, 50% strand	—
J, L	Fab light chain	protein	211	6% helix, 51% strand	—
H	Fab heavy chain	protein	212	4% helix, 51% strand	—
A	MHC class I antigen	protein	276	26% helix, 40% strand	Q861F7
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
D	MHC class I antigen	protein	277	28% helix, 40% strand	Q861F7
C, F	Phe-met-asn-lys-phe-ile-tyr-glu-ile	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 7 copies · chains I, H, A, D, E
PG4 · Tetraethylene glycol · additive · 4 copies · chains H, A, B, D, E
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains I, J, H, L, A, B
PGE · Triethylene glycol · additive · 2 copies · chains B, D, E
P6G · Hexaethylene glycol · additive · chains A, B
1PE · Pentaethylene glycol · additive · chains D
FMT · Formic acid · additive · chains D

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

Pockets

19 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	1003	0.77	0.79	99	PG4
2	611	0.68	0.77	60	P6G
3	590	0.67	0.77	59	FMT, PG4
4	441	0.63	0.77	51	empty
5	516	0.61	0.74	59	EPE

Interfaces

17 interfaces between chains.

H–L · 1641 Å² buried · 15 hydrogen bonds · protein-protein
I–J · 1631 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1439 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1405 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 954 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

7RE7 · TCR mimic antibody (Fab fragment) in complex with AFP/HLA-A*02 · the same entry in another collection · chain F against F, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 Q861F7
Every structure of UniProt P61769
Elsewhere: RCSB PDB 7RE7 · PDBe 7RE7 · UniProt Q861F7 · UniProt P61769

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