MolNFT v1 · #179807 · protein

Crystal structure of HLA-A*0201IN complex with SARS-cov-2 N351-359

7KGO · MHC class I antigen: “Crystal structure of HLA-A*0201IN complex with SARS-cov-2 N351-359”. X-ray diffraction, 3 ligands (3NI, CD, CL), 4 pockets (best druggability 0.70). MolNFT v1 #179807 on GenesisL1: 3D structure, binding sites…

PDB: 7KGO
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Nucleoprotein
UniProt: Q861F7, P61769, P0DTC9
Ligands: 3NI, CD, CL
Pockets: 4 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	275	26% helix, 40% strand	Q861F7
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769
C	Nucleoprotein	protein	9	0% helix, 0% strand	P0DTC9

Ligands and binding sites

3NI · Nickel (III) ion · metal · 3 copies · chains A, B
CD · Cadmium ion · metal · chains A
CL · Chloride ion · ion · 3 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	657	0.70	0.78	55	empty
2	120	0.46	0.78	19	empty
3	50	0.39	0.81	16	empty
4	65	0.35	0.77	15	empty

Interfaces

2 interfaces between chains.

A–B · 1238 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 871 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7KGO · Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N351-359 · 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 0.99

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 Q861F7
Every structure of UniProt P61769
Every structure of UniProt P0DTC9
Elsewhere: RCSB PDB 7KGO · PDBe 7KGO · UniProt Q861F7 · UniProt P61769 · UniProt P0DTC9

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