MolNFT v1 · #105008 · protein

Crystal structure of HLA B*0801 in complex with ELN_YYM, elnrkmiym

4QRT · HLA class I histocompatibility antigen, B-8 alpha chain: “Crystal structure of HLA B*0801 in complex with ELN_YYM, elnrkmiym”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #105008 on GenesisL1: 3D structure…

PDB: 4QRT
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-8 alpha chain; Beta-2-microglobulin; Major…
UniProt: P30460, P61769, Q9YRL8
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-8 alpha chain	protein	276	28% helix, 39% strand	P30460
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Major immediate-early protein	protein	9	0% helix, 0% strand	Q9YRL8

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains A

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

Pockets

5 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	619	0.68	0.77	59	empty
2	84	0.52	0.84	24	empty
3	92	0.44	0.80	23	empty
4	82	0.38	0.77	19	empty
5	61	0.32	0.76	14	empty

Interfaces

2 interfaces between chains.

A–B · 1366 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 984 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4QRT · Crystal Structure of HLA B*0801 in complex with ELN_YYM, ELNRKMIYM · 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 P30460
Every structure of UniProt P61769
Every structure of UniProt Q9YRL8
Elsewhere: RCSB PDB 4QRT · PDBe 4QRT · UniProt P30460 · UniProt P61769 · UniProt Q9YRL8

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