MolNFT v1 · #61999 · protein

Structure of the M67 high-affinity mutant of the 2C TCR in complex with LD/QL9

3E2H · H-2 class I histocompatibility antigen, L-D alpha chain: “Structure of the M67 high-affinity mutant of the 2C TCR in complex with LD/QL9”. X-ray diffraction, 3 pockets (best druggability 0.56). MolNFT v1 #61999 on GenesisL1: 3D…

PDB: 3E2H
Type: protein
Length: 403 residues
Chains: 4
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: 3 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, L-D alpha chain	protein	175	37% helix, 27% strand	P01897
Q	QL9 peptide	protein	9	0% helix, 0% strand	—
B	T-cell receptor alpha chain V region PHDS58	protein	109	0% helix, 46% strand	P01738
C	M67 TCR beta chain	protein	110	3% helix, 50% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	160	0.56	0.81	22	empty
2	194	0.50	0.77	30	empty
3	95	0.36	0.75	16	empty

Interfaces

6 interfaces between chains.

A–Q · 929 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 826 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 493 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 318 Å² buried · 3 hydrogen bonds · protein-protein
Q–C · 218 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3E2H · Structure of the m67 high-affinity mutant of the 2C TCR in complex with Ld/QL9 · the same entry in another collection · chain A against A, TM-score 1.00
P01897 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, L-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
P01738 · AlphaFold monomer V2.0 prediction for T-cell receptor alpha chain V region PHDS58 (P01738) · a predicted model of the same protein · chain B 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 P01897
Every structure of UniProt P01738
Elsewhere: RCSB PDB 3E2H · PDBe 3E2H · UniProt P01897 · UniProt P01738

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