Research workbench

HLA-B*2705 bound to nona-peptide M9

Analyse HLA-B*2705 bound to nona-peptide M9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JGE
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-27 B*2705 alpha chain; Beta-2-microglobulin…
UniProt: P03989, P61769
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-27 B*2705 alpha chain	protein	276	27% helix, 39% strand	P03989
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Peptide M9	protein	9	0% helix, 0% strand	—

Pockets

6 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	672	0.69	0.77	55	empty
2	91	0.68	0.92	20	empty
3	124	0.49	0.80	19	empty
4	96	0.41	0.77	23	empty
5	76	0.39	0.78	16	empty

Interfaces

2 interfaces between chains.

A–B · 1339 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 816 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1JGE · HLA-B*2705 bound to nona-peptide m9 · 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 1JGE · PDBe 1JGE · UniProt P03989 · UniProt P61769

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