MolNFT v1 · #82214 · protein

Crystal structure of HLA B*3508LPEP-P4ALA, peptide mutant P4-ala

3VFR · MHC class I antigen: “Crystal structure of HLA B*3508LPEP-P4ALA, peptide mutant P4-ala”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #82214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VFR
Type: protein
Length: 389 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, P4A, lpealpqgqltay
UniProt: C5MK56, P61769
Pockets: 5 · 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	100	0% helix, 49% strand	P61769
C	Lpep peptide from EBV, P4A, lpealpqgqltay	protein	13	0% helix, 0% strand	—

Pockets

5 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	633	0.69	0.78	55	empty
2	139	0.46	0.77	28	empty
3	58	0.40	0.81	19	empty
4	74	0.36	0.77	17	empty
5	52	0.27	0.74	16	empty

Interfaces

2 interfaces between chains.

A–B · 1415 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 940 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3VFR · crystal structure of HLA B*3508LPEP-P4Ala, peptide mutant P4-ala · 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 3VFR · PDBe 3VFR · UniProt C5MK56 · UniProt P61769

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