Research workbench

Human leukocyte antigen class I A02 carrying llwngpmhv

Analyse Human leukocyte antigen class I A02 carrying llwngpmhv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SS9
Type: protein
Length: 770 residues
Chains: 6
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…
UniProt: P01892, P61769
Ligands: SO4
Pockets: 9 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	25% helix, 39% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
C, F	Leu-leu-TRP-asn-gly-pro-met-his-val	protein	9	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, C, D, F
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, D
EDO · 1,2-ethanediol · additive · 2 copies · chains D, E

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	647	0.68	0.77	55	PEG
2	636	0.68	0.77	59	EDO
3	398	0.65	0.79	53	empty
4	66	0.43	0.82	18	empty
5	70	0.41	0.80	20	empty

Interfaces

7 interfaces between chains.

A–B · 1420 Å² buried · 25 hydrogen bonds · protein-protein
D–E · 1402 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 890 Å² buried · 15 hydrogen bonds · protein-protein
D–F · 881 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 301 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6SS9 · Human Leukocyte Antigen Class I A02 Carrying LLWNGPMHV · the same entry in another collection · chain E against E, 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 P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6SS9 · PDBe 6SS9 · UniProt P01892 · UniProt P61769

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