MolNFT v1 · #153798 · protein

Crystal structure of H2-kb in complex with a DPAGT1 self-peptide

6JQ2 · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H2-kb in complex with a DPAGT1 self-peptide”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #153798 on GenesisL1: 3D structure…

PDB: 6JQ2
Type: protein
Length: 367 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, K-B alpha chain; DPATG1 antigen siivfnlv…
UniProt: P01901, P01887
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, K-B alpha chain	protein	274	28% helix, 39% strand	P01901
P	DPATG1 antigen siivfnlv	protein	8	0% helix, 0% strand	—
B	Beta-2-microglobulin	protein	85	0% helix, 51% strand	P01887

Pockets

4 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	564	0.63	0.75	49	empty
2	201	0.52	0.77	36	empty
3	171	0.47	0.76	29	empty
4	88	0.39	0.77	16	empty

Interfaces

2 interfaces between chains.

A–B · 1031 Å² buried · 16 hydrogen bonds · protein-protein
A–P · 840 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6JQ2 · Crystal Structure of H2-Kb in complex with a DPAGT1 self-peptide · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P01901
Every structure of UniProt P01887
Elsewhere: RCSB PDB 6JQ2 · PDBe 6JQ2 · UniProt P01901 · UniProt P01887

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