MolNFT v1 · #165336 · protein

Crystal structure of HLA A2*01-avydgrehtv

6TRN · MHC class I antigen: “Crystal structure of HLA A2*01-avydgrehtv”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #165336 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6TRN
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Mage-A4 peptide (amino acids 230-239) variant
UniProt: A0A5B8RNS7, P61769
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	274	27% helix, 40% strand	A0A5B8RNS7
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769
C	Mage-A4 peptide (amino acids 230-239) variant	protein	10	0% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains A, C

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

Pockets

6 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	597	0.69	0.78	54	empty
2	67	0.45	0.83	18	empty
3	94	0.43	0.79	17	empty
4	59	0.35	0.78	15	empty
5	87	0.32	0.74	18	empty

Interfaces

2 interfaces between chains.

A–B · 1228 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 890 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6TRN · Crystal structure of HLA A2*01-AVYDGREHTV · 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 A0A5B8RNS7
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6TRN · PDBe 6TRN · UniProt A0A5B8RNS7 · UniProt P61769

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