MolNFT v1 · #11226 · protein

HLA-B*2709 bound to deca-peptide S10R

1JGD · Human lymphocyte antigen HLA-B27: “HLA-B*2709 bound to deca-peptide S10R”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #11226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JGD
Type: protein
Length: 386 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human lymphocyte antigen HLA-B27; Beta-2-microglobulin; Peptide S10R
UniProt: P03989, P61769
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Human lymphocyte antigen HLA-B27	protein	276	29% helix, 39% strand	P03989
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Peptide S10R	protein	10	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	139	0.74	0.93	24	empty
2	599	0.68	0.78	60	empty
3	91	0.44	0.79	19	empty
4	75	0.41	0.79	15	empty
5	59	0.30	0.75	17	empty

Interfaces

2 interfaces between chains.

A–B · 1381 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1013 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1JGD · HLA-B*2709 bound to deca-peptide s10R · the same entry in another collection · chain A against A, 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 P03989
Every structure of UniProt P61769
Elsewhere: RCSB PDB 1JGD · PDBe 1JGD · UniProt P03989 · UniProt P61769

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