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Crystal structure of ilnamitki peptide bound to HLA-A2

Analyse Crystal structure of ilnamitki peptide bound to HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PTE
Type: protein
Length: 1,536 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Haus…
UniProt: P01892, P61769, Q68CZ6
Ligands: NA
Pockets: 19 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, H, K	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	28% helix, 39% strand	P01892
B, F, I, L	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, D, G, J	Haus augmin-like complex subunit 3	protein	9	0% helix, 0% strand	Q68CZ6

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains B, F, I, L
GOL · Glycerol · additive · 12 copies · chains A, C, E, D, H, G, K, J

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	941	0.76	0.79	95	empty
2	913	0.76	0.79	79	empty
3	1105	0.74	0.77	88	empty
4	1012	0.71	0.76	107	empty
5	610	0.70	0.78	53	empty

Interfaces

16 interfaces between chains.

K–L · 1462 Å² buried · 21 hydrogen bonds · protein-protein
H–I · 1459 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1457 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1452 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 851 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6PTE · Crystal Structure of ILNAMITKI peptide bound to HLA-A2 · the same entry in another collection · chain J against J, 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
Every structure of UniProt P61769
Every structure of UniProt Q68CZ6
Elsewhere: RCSB PDB 6PTE · PDBe 6PTE · UniProt P01892 · UniProt P61769 · UniProt Q68CZ6

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