MolNFT v1 · #82210 · protein

Crystal structure of HLA B*3508LPEP151A, HLA mutant ALA151

3VFN · MHC class I antigen: “Crystal structure of HLA B*3508LPEP151A, HLA mutant ALA151”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #82210 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VFN
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	26% 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	—

Pockets

4 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	618	0.69	0.78	55	empty
2	203	0.50	0.76	35	empty
3	92	0.44	0.79	23	empty
4	56	0.27	0.74	16	empty

Interfaces

2 interfaces between chains.

A–B · 1371 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 938 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3VFN · crystal structure of HLA B*3508LPEP151A, HLA mutant Ala151 · 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 3VFN · PDBe 3VFN · UniProt C5MK56 · UniProt P61769

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