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Crystal structure of HLA B*3508 LPEP158G, HLA mutant GLY158

Analyse Crystal structure of HLA B*3508 LPEP158G, HLA mutant GLY158 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VFP
Type: protein
Length: 388 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Lpep peptide from EBV, lpeplpqgqltay
UniProt: C5MK56, P61769
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	27% helix, 39% strand	C5MK56
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Lpep peptide from EBV, lpeplpqgqltay	protein	13	0% helix, 0% strand	—

Ligands and binding sites

ACT · Acetate ion · additive · chains A, B

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

Pockets

4 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	636	0.69	0.77	56	empty
2	178	0.47	0.76	30	empty
3	84	0.42	0.79	22	empty
4	54	0.39	0.81	16	empty

Interfaces

2 interfaces between chains.

A–B · 1362 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 952 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3VFP · crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158 · 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 C5MK56
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3VFP · PDBe 3VFP · UniProt C5MK56 · UniProt P61769

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