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Crystal structure of HLA-A*11:01-GTS3

Analyse Crystal structure of HLA-A*11:01-GTS3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WJN
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; GTS3…
UniProt: P13746, P61769
Ligands: K
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	HLA class I histocompatibility antigen, a-11 alpha chain	protein	274	27% helix, 41% strand	P13746
B, E, H	Beta-2-microglobulin	protein	100	0% helix, 47% strand	P61769
C, F, I	GTS3 peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

K · Potassium ion · metal · chains B

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

Pockets

13 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	972	0.74	0.77	82	empty
2	958	0.74	0.77	90	empty
3	589	0.72	0.80	70	empty
4	533	0.67	0.77	52	empty
5	261	0.57	0.78	40	empty

Interfaces

13 interfaces between chains.

A–B · 1495 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 1457 Å² buried · 28 hydrogen bonds · protein-protein
D–E · 1445 Å² buried · 27 hydrogen bonds · protein-protein
G–I · 847 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 841 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5WJN · Crystal Structure of HLA-A*11:01-GTS3 · 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 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 P13746
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5WJN · PDBe 5WJN · UniProt P13746 · UniProt P61769

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