Research workbench

Crystal structure of HLA-A*11:01 with GTS1 peptide

Analyse Crystal structure of HLA-A*11:01 with GTS1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WJL
Type: protein
Length: 1,152 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-11 alpha chain; Beta-2-microglobulin; GTS1…
UniProt: P13746, P61769
Ligands: CL
Pockets: 12 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	HLA class I histocompatibility antigen, a-11 alpha chain	protein	274	28% helix, 40% strand	P13746
B, E, H	Beta-2-microglobulin	protein	100	0% helix, 44% strand	P61769
C, F, I	GTS1 peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A, C, D, F, E

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

Pockets

12 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	1086	0.73	0.76	90	empty
2	1165	0.72	0.76	102	empty
3	504	0.69	0.80	60	empty
4	566	0.68	0.78	51	empty
5	150	0.60	0.84	24	empty

Interfaces

12 interfaces between chains.

A–B · 1466 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1448 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 1411 Å² buried · 27 hydrogen bonds · protein-protein
G–I · 826 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 814 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5WJL · Crystal Structure of HLA-A*11:01 with GTS1 peptide · the same entry in another collection · chain I against I, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E 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 P13746
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5WJL · PDBe 5WJL · UniProt P13746 · UniProt P61769

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.