Research workbench

Crystal structure of class I MHC H-2KK in complex with an octapeptide

Analyse Crystal structure of class I MHC H-2KK in complex with an octapeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZT1
Type: protein
Length: 379 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, K-K alpha chain; Beta-2-microglobulin; Influenza…
UniProt: P04223, P01887
Ligands: CL
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, K-K alpha chain	protein	273	25% helix, 39% strand	P04223
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
P	Influenza virus epitope, feangnli	protein	8	0% helix, 0% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	676	0.71	0.78	56	empty
2	144	0.54	0.81	22	empty
3	133	0.52	0.80	24	empty
4	118	0.40	0.75	16	empty
5	50	0.33	0.78	16	CL

Interfaces

2 interfaces between chains.

A–B · 1275 Å² buried · 21 hydrogen bonds · protein-protein
A–P · 829 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1ZT1 · crystal structure of class I MHC H-2Kk in complex with an octapeptide · 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
P04223 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-K alpha… · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P04223
Every structure of UniProt P01887
Elsewhere: RCSB PDB 1ZT1 · PDBe 1ZT1 · UniProt P04223 · UniProt P01887

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