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

Analyse Crystal structure of H2-kb in complex with a DPAGT1 mutant peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JQ3
Type: protein
Length: 372 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; DPAGT1 mutant antigen siivfnll…
UniProt: P01901, P01887
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, K-B alpha chain	protein	274	27% helix, 39% strand	P01901
P	DPAGT1 mutant antigen siivfnll	protein	8	0% helix, 0% strand	—
B	Beta-2-microglobulin	protein	90	0% helix, 38% strand	P01887

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	571	0.63	0.74	47	empty
2	171	0.49	0.77	33	empty
3	178	0.47	0.76	37	empty
4	75	0.35	0.76	14	empty

Interfaces

2 interfaces between chains.

A–B · 1065 Å² buried · 12 hydrogen bonds · protein-protein
A–P · 844 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6JQ3 · Crystal Structure of H2-Kb in complex with a DPAGT1 mutant 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 0.96

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 6JQ3 · PDBe 6JQ3 · UniProt P01901 · UniProt P01887

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