MolNFT v1 · #145928 · protein

HLA-B*57:01 presenting lsdstardvtw

6D2B · HLA class I histocompatibility antigen, B-57 alpha chain: “HLA-B*57:01 presenting lsdstardvtw”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #145928 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D2B
Type: protein
Length: 386 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-57 alpha chain; Beta-2-microglobulin…
UniProt: P18465, P61769
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-57 alpha chain	protein	276	27% helix, 40% strand	P18465
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Leu-ser-asp-ser-thr-arg-asp-val-thr-TRP	protein	10	0% helix, 0% strand	—

Pockets

4 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	591	0.67	0.77	53	empty
2	112	0.47	0.79	24	empty
3	79	0.42	0.80	22	empty
4	70	0.38	0.78	16	empty

Interfaces

2 interfaces between chains.

A–B · 1390 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 966 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6D2B · HLA-B*57:01 presenting LSDSTARDVTW · 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 P18465
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6D2B · PDBe 6D2B · UniProt P18465 · UniProt P61769

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.