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Crystal structure of peptide-HLA-A24 bound to S19-2 V-DELTA/V-beta TCR

Analyse Crystal structure of peptide-HLA-A24 bound to S19-2 V-DELTA/V-beta TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XOV
Type: protein
Length: 1,672 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-24 alpha chain; Beta-2-microglobulin; HIV-1…
UniProt: P05534, P61769
Pockets: 20 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-24 alpha chain	protein	274	27% helix, 40% strand	P05534
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	HIV-1 NEF138-10 peptide	protein	10	0% helix, 0% strand	—
I, G	V-delta chain of T cell receptor	protein	207	5% helix, 44% strand	—
J, H	V-beta chain of T cell receptor	protein	245	7% helix, 50% strand	—

Pockets

20 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	891	0.70	0.75	63	empty
2	875	0.69	0.75	62	empty
3	612	0.68	0.77	57	empty
4	506	0.67	0.78	45	empty
5	423	0.61	0.76	47	empty

Interfaces

15 interfaces between chains.

I–J · 2270 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2268 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 1347 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1342 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 980 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5XOV · Crystal structure of peptide-HLA-A24 bound to S19-2 V-delta/V-beta TCR · the same entry in another collection · chain H against H, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P05534
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5XOV · PDBe 5XOV · UniProt P05534 · UniProt P61769

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