Research workbench

Rational development of high-affinity T-cell receptor-like antibodies

Analyse Rational development of high-affinity T-cell receptor-like antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HAE
Type: protein
Length: 3,264 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Nyeso-1…
UniProt: P01892, P61769
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, J, P	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	26% helix, 41% strand	P01892
B, E, K, Q	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F, M, R	Nyeso-1 peptide	protein	9	0% helix, 0% strand	—
L, G, N, S	Antibody light chain	protein	211	6% helix, 48% strand	—
H, I, O, T	Antibody heavy chain	protein	220	7% helix, 47% strand	—

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	478	0.72	0.82	67	empty
2	681	0.69	0.77	54	empty
3	391	0.69	0.82	40	empty
4	310	0.69	0.83	35	empty
5	650	0.68	0.77	59	empty

Interfaces

35 interfaces between chains.

N–O · 1740 Å² buried · 20 hydrogen bonds · protein-protein
G–I · 1708 Å² buried · 18 hydrogen bonds · protein-protein
L–H · 1692 Å² buried · 12 hydrogen bonds · protein-protein
S–T · 1653 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1405 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

3HAE · Rational development of high-affinity T-cell receptor-like antibodies · the same entry in another collection · chain T against T, 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 P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3HAE · PDBe 3HAE · UniProt P01892 · UniProt P61769

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