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Crystal structure of a peptide-HLA complex

Analyse Crystal structure of a peptide-HLA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SPV
Type: protein
Length: 383 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-8 alpha chain; Beta-2-microglobulin; Peptide…
UniProt: P30460, P61769, P03206
Ligands: NA
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-8 alpha chain	protein	276	28% helix, 39% strand	P30460
B	Beta-2-microglobulin	protein	99	0% helix, 52% strand	P61769
C	Peptide from trans-activator protein BZLF1	protein	8	0% helix, 0% strand	P03206

Ligands and binding sites

NA · Sodium ion · metal · chains A, C
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	646	0.67	0.76	56	empty
2	52	0.66	0.95	18	empty
3	90	0.43	0.79	23	empty
4	89	0.40	0.78	17	empty
5	70	0.37	0.78	16	ACT

Interfaces

2 interfaces between chains.

A–B · 1331 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 975 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3SPV · Crystal structure of a peptide-HLA complex · the same entry in another collection · chain A against A, 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 P30460
Every structure of UniProt P61769
Every structure of UniProt P03206
Elsewhere: RCSB PDB 3SPV · PDBe 3SPV · UniProt P30460 · UniProt P61769 · UniProt P03206

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