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Crystal structure of a complex between the human adenovirus type 4 E3- 19K protein and MHC class molecule HLA-A2/TAX

Analyse Crystal structure of a complex between the human adenovirus type 4 E3- 19K… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IRO
Type: protein
Length: 2,811 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Tax protein…
UniProt: P01892, Q80817, P61769, Q8BEL5
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 11 distinct chains · 20% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	264	23% helix, 23% strand	P01892
B, F, J, N, R, V	Tax protein	protein	9	0% helix, 0% strand	Q80817
C	Beta-2-microglobulin	protein	96	0% helix, 45% strand	P61769
D	E3 19 kda protein	protein	102	11% helix, 34% strand	Q8BEL5
E	HLA class I histocompatibility antigen, a-2 alpha chain	protein	268	23% helix, 24% strand	P01892
G, K, O, S, W	Beta-2-microglobulin	protein	98	0% helix, 46% strand	P61769
H, L, P, T, X	E3 19 kda protein	protein	103	7% helix, 34% strand	Q8BEL5
I	HLA class I histocompatibility antigen, a-2 alpha chain	protein	252	24% helix, 24% strand	P01892
M	HLA class I histocompatibility antigen, a-2 alpha chain	protein	265	25% helix, 25% strand	P01892
Q	HLA class I histocompatibility antigen, a-2 alpha chain	protein	259	25% helix, 23% strand	P01892
U	HLA class I histocompatibility antigen, a-2 alpha chain	protein	246	24% helix, 26% strand	P01892

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1114	0.79	0.81	117	empty
2	861	0.78	0.81	81	empty
3	911	0.76	0.79	92	empty
4	484	0.76	0.84	71	empty
5	479	0.76	0.84	65	empty

Interfaces

48 interfaces between chains.

U–W · 1285 Å² buried · 12 hydrogen bonds · protein-protein
I–K · 1231 Å² buried · 7 hydrogen bonds · protein-protein
M–O · 1202 Å² buried · 10 hydrogen bonds · protein-protein
Q–S · 1200 Å² buried · 6 hydrogen bonds · protein-protein
E–G · 1171 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide (disulfide).

Compared structures

5IRO · Crystal structure of a complex between the Human adenovirus type 4 E3-19K protein and MHC… · the same entry in another collection · chain K against K, TM-score 1.00

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 P01892
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Elsewhere: RCSB PDB 5IRO · PDBe 5IRO · UniProt P01892 · UniProt Q80817 · UniProt P61769 · UniProt Q8BEL5

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