Research workbench

Human CD94/NKG2A in complex with HLA-E

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

PDB: 3CDG
Type: protein
Length: 1,246 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; Natural…
UniProt: P13747, P61769, Q13241, P26715, P17693
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 16% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	HLA class I histocompatibility antigen, alpha chain E	protein	273	25% helix, 37% strand	P13747
B, D	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
J, E	Natural killer cells antigen CD94	protein	123	13% helix, 33% strand	Q13241
K	NKG2-A/NKG2-B type II integral membrane protein	protein	116	16% helix, 34% strand	P26715
F	NKG2-A/NKG2-B type II integral membrane protein	protein	120	15% helix, 33% strand	P26715
P, Q	Leader peptide of HLA class I histocompatibility antigen, alpha chain G	protein	9	0% helix, 0% strand	P17693

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	667	0.80	0.85	72	empty
2	624	0.79	0.85	74	empty
3	934	0.76	0.79	80	empty
4	464	0.74	0.83	44	empty
5	408	0.73	0.84	39	empty

Interfaces

22 interfaces between chains.

C–D · 1388 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1379 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 971 Å² buried · 8 hydrogen bonds · protein-protein
C–Q · 922 Å² buried · 12 hydrogen bonds · protein-protein
A–P · 921 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide (disulfide).

Compared structures

3CDG · Human CD94/NKG2A in complex with HLA-E · the same entry in another collection · chain Q against Q, 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 Q13241
Every structure of UniProt P26715
Every structure of UniProt P17693
Elsewhere: RCSB PDB 3CDG · PDBe 3CDG · UniProt P13747 · UniProt P61769 · UniProt Q13241 · UniProt P26715 · UniProt P17693

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