MolNFT v1 · #160928 · protein

Crystal structure of HLA-B*2705 in complex with lrn, a self-peptide

6PYJ · HLA class I histocompatibility antigen, B-27 alpha chain: “Crystal structure of HLA-B*2705 in complex with lrn, a self-peptide”. X-ray diffraction, 6 pockets (best druggability 0.73). MolNFT v1 #160928 on GenesisL1: 3D structure…

PDB: 6PYJ
Type: protein
Length: 384 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-27 alpha chain; Beta-2-microglobulin; Lrn…
UniProt: P03989, P61769
Pockets: 6 · best druggability 0.73

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-27 alpha chain	protein	276	27% helix, 39% strand	P03989
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Lrn peptide	protein	9	0% helix, 0% strand	—

Pockets

6 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	92	0.73	0.95	24	empty
2	679	0.70	0.77	59	empty
3	127	0.48	0.79	20	empty
4	80	0.46	0.82	18	empty
5	71	0.38	0.78	15	empty

Interfaces

2 interfaces between chains.

A–B · 1286 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 973 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6PYJ · Crystal Structure of HLA-B*2705 in complex with LRN, a self-peptide · 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 P03989
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6PYJ · PDBe 6PYJ · UniProt P03989 · UniProt P61769

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