Research workbench

Crystal structure of class I MHC H-2KK in complex with a nonapeptide

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

PDB: 1ZT7
Type: protein
Length: 766 residues
Chains: 6
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; SV40…
UniProt: P04223, P01887
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	H-2 class I histocompatibility antigen, K-K alpha chain	protein	275	24% helix, 39% strand	P04223
B, D	Beta-2-microglobulin	protein	99	0% helix, 53% strand	P01887
P, Q	SV40 epitope, sefllekri	protein	9	0% helix, 0% strand	—

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	748	0.73	0.79	71	empty
2	631	0.70	0.78	53	empty
3	202	0.51	0.77	35	empty
4	228	0.50	0.75	39	empty
5	187	0.49	0.77	26	empty

Interfaces

6 interfaces between chains.

C–D · 1253 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1239 Å² buried · 17 hydrogen bonds · protein-protein
A–P · 976 Å² buried · 20 hydrogen bonds · protein-protein
C–Q · 974 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 256 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1ZT7 · crystal structure of class I MHC H-2Kk in complex with a nonapeptide · the same entry in another collection · chain Q against Q, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 1ZT7 · PDBe 1ZT7 · UniProt P04223 · UniProt P01887

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