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Structure of the 3ALPHAM13 high-affinity mutant of the 2C TCR in complex with LD/QL9

Analyse Structure of the 3ALPHAM13 high-affinity mutant of the 2C TCR in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3E3Q
Type: protein
Length: 3,232 residues
Chains: 32
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, L-D alpha chain; QL9 peptide; T-cell receptor…
UniProt: P01897, P01738
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, c, H, L, P, U, Y	H-2 class I histocompatibility antigen, L-D alpha chain	protein	175	39% helix, 34% strand	P01897
Q, G, f, K, O, T, X, b	QL9 peptide	protein	9	0% helix, 0% strand	—
D, C, d, I, M, R, V, Z	T-cell receptor alpha chain V region PHDS58	protein	109	3% helix, 49% strand	P01738
E, F, e, J, N, S, W, a	TCR beta chain	protein	111	3% helix, 51% strand	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1046	0.75	0.78	109	empty
2	403	0.67	0.80	50	empty
3	401	0.67	0.80	50	empty
4	465	0.67	0.79	48	empty
5	480	0.66	0.78	52	empty

Interfaces

67 interfaces between chains.

H–P · 1393 Å² buried · 23 hydrogen bonds · protein-protein
L–Y · 1382 Å² buried · 23 hydrogen bonds · protein-protein
U–X · 940 Å² buried · 15 hydrogen bonds · protein-protein
L–O · 940 Å² buried · 15 hydrogen bonds · protein-protein
Y–b · 938 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

3E3Q · Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 · the same entry in another collection · chain O against O, 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
Every structure of UniProt P01897
Every structure of UniProt P01738
Elsewhere: RCSB PDB 3E3Q · PDBe 3E3Q · UniProt P01897 · UniProt P01738

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