MolNFT v1 · #170274 · protein

Crystal structure of HLA-B2705 complexed with the nona-peptide me

6Y28 · MHC class I antigen: “Crystal structure of HLA-B2705 complexed with the nona-peptide me”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1 #170274 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y28
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Gly-arg-leu-asn-glu-pro-ile-lys-val
UniProt: A3F718, P61769
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	28% helix, 40% strand	A3F718
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Gly-arg-leu-asn-glu-pro-ile-lys-val	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains A, B, C

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	95	0.71	0.94	24	empty
2	668	0.69	0.77	56	GOL
3	129	0.47	0.78	20	GOL
4	88	0.42	0.79	16	empty
5	78	0.39	0.78	23	empty

Interfaces

2 interfaces between chains.

A–B · 1384 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 855 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6Y28 · Crystal structure of HLA-B2705 complexed with the nona-peptide mE · 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 A3F718
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6Y28 · PDBe 6Y28 · UniProt A3F718 · UniProt P61769

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