MolNFT v1 · #176821 · protein

Phosphorylation of MHC I peptide

7DYN · MHC class I antigen: “Phosphorylation of MHC I peptide”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #176821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DYN
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; Arg-arg-phe-sep-arg-sep-pro-ile-arg-arg
UniProt: A3F718, P61769
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	28% helix, 39% strand	A3F718
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Arg-arg-phe-sep-arg-sep-pro-ile-arg-arg	protein	10	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	110	0.74	0.95	28	empty
2	623	0.69	0.77	56	empty
3	137	0.48	0.79	21	empty
4	73	0.41	0.79	17	empty
5	65	0.37	0.78	16	empty

Interfaces

2 interfaces between chains.

A–B · 1286 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1052 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 modified (disulfide, phosphorylation).

Compared structures

7DYN · Phosphorylation of MHC I peptide · 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 7DYN · PDBe 7DYN · UniProt A3F718 · UniProt P61769

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