MolNFT v1 · #82218 · protein

Crystal structure of HLA B*3508 lpep-P9ALA, peptide mutant P9-ala

3VFV · MHC class I antigen: “Crystal structure of HLA B*3508 lpep-P9ALA, peptide mutant P9-ala”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #82218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VFV
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, P9A, lpeplpqgaltay
UniProt: C5MK56, P61769
Pockets: 3 · 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, P9A, lpeplpqgaltay	protein	13	0% helix, 0% strand	—

Pockets

3 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	615	0.69	0.78	55	empty
2	118	0.43	0.77	25	empty
3	71	0.42	0.80	18	empty

Interfaces

2 interfaces between chains.

A–B · 1397 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 944 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3VFV · crystal structure of HLA B*3508 LPEP-P9Ala, peptide mutant P9-ala · the same entry in another collection · chain B against B, 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 3VFV · PDBe 3VFV · UniProt C5MK56 · UniProt P61769

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