MolNFT v1 · #92832 · protein

A2-MHC complex carrying fatgigiitv

4GKN · MHC class I antigen: “A2-MHC complex carrying fatgigiitv”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.72). MolNFT v1 #92832 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GKN
Type: protein
Length: 772 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Fat cognate peptide
UniProt: A0A5B8RNS7, P61769
Ligands: SO4
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I antigen	protein	276	25% helix, 38% strand	A0A5B8RNS7
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Fat cognate peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, D, E

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

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	1132	0.72	0.76	99	SO4
2	613	0.69	0.77	59	empty
3	74	0.40	0.79	14	empty
4	81	0.39	0.78	17	empty
5	94	0.38	0.76	20	empty

Interfaces

7 interfaces between chains.

D–E · 1455 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1439 Å² buried · 26 hydrogen bonds · protein-protein
D–F · 875 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 859 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 118 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4GKN · A2-MHC Complex carrying FATGIGIITV · the same entry in another collection · chain F against F, 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 A0A5B8RNS7
Every structure of UniProt P61769
Elsewhere: RCSB PDB 4GKN · PDBe 4GKN · UniProt A0A5B8RNS7 · UniProt P61769

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