MolNFT v1 · #170272 · protein

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

6Y26 · MHC class I antigen: “Crystal structure of HLA-B2705 complexed with the nona-peptide ma”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.69). MolNFT v1 #170272 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6Y26
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-ala-pro-ile-lys-val
UniProt: A3F718, P61769
Ligands: CL
Pockets: 5 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	26% helix, 40% strand	A3F718
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Gly-arg-leu-asn-ala-pro-ile-lys-val	protein	9	0% helix, 0% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 4 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	644	0.69	0.77	57	GOL
2	82	0.66	0.92	24	empty
3	139	0.48	0.78	18	empty
4	75	0.43	0.80	22	empty
5	63	0.37	0.79	16	empty

Interfaces

2 interfaces between chains.

A–B · 1398 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 819 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6Y26 · Crystal structure of HLA-B2705 complexed with the nona-peptide mA · 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 6Y26 · PDBe 6Y26 · UniProt A3F718 · UniProt P61769

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