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Structure of NKG2A/CD94 bound to HLA-E

Analyse Structure of NKG2A/CD94 bound to HLA-E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CII
Type: protein
Length: 1,238 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin; HLA class I…
UniProt: P13747, P61769, P17693, Q13241, P26715
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 16% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, alpha chain E	protein	273	23% helix, 37% strand	P13747
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	HLA class I histocompatibility antigen peptide	protein	9	0% helix, 0% strand	P17693
G, I	Natural killer cells antigen CD94	protein	121	14% helix, 30% strand	Q13241
H, J	NKG2-A/NKG2-B type II integral membrane protein	protein	116	15% helix, 30% strand	P26715

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	929	0.81	0.83	86	empty
2	923	0.79	0.82	78	empty
3	1097	0.79	0.81	93	empty
4	854	0.78	0.81	75	empty
5	565	0.76	0.83	39	empty

Interfaces

20 interfaces between chains.

D–E · 1518 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1493 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 963 Å² buried · 2 hydrogen bonds · protein-protein
D–F · 932 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 927 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

3CII · Structure of NKG2A/CD94 bound to HLA-E · the same entry in another collection · chain J against J, 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 P13747
Every structure of UniProt P61769
Every structure of UniProt P17693
Every structure of UniProt Q13241
Every structure of UniProt P26715
Elsewhere: RCSB PDB 3CII · PDBe 3CII · UniProt P13747 · UniProt P61769 · UniProt P17693 · UniProt Q13241 · UniProt P26715

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