MolNFT v1 · #181875 · protein

Crystal structure of HLA-A*02:01 in complex with klndlcftnv, an 10-mer epitope from SARS-cov-2 spike (S386-395)

7M8S · HLA class I histocompatibility antigen, a alpha chain: “Crystal structure of HLA-A*02:01 in complex with klndlcftnv, an 10-mer epitope from SARS-cov-2 spike…”. X-ray diffraction, 13 pockets (best druggability 0.71). MolNFT v1…

PDB: 7M8S
Type: protein
Length: 769 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a alpha chain; Beta-2-microglobulin; Spike…
UniProt: Q861F7, P61769, P0DTC2
Pockets: 13 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a alpha chain	protein	276	25% helix, 39% strand	Q861F7
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Spike protein S1 peptide	protein	10	0% helix, 0% strand	P0DTC2
D	HLA class I histocompatibility antigen, a alpha chain	protein	274	25% helix, 40% strand	Q861F7
E	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Ligands and binding sites

GOL · Glycerol · additive · chains A, D

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	428	0.71	0.82	47	empty
2	467	0.69	0.80	65	GOL
3	285	0.64	0.81	34	empty
4	184	0.54	0.79	33	empty
5	59	0.53	0.88	17	empty

Interfaces

5 interfaces between chains.

A–B · 1404 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1340 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 956 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 945 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 807 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7M8S · Crystal Structure of HLA-A*02:01 in complex with KLNDLCFTNV, an 10-mer epitope from… · 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 Q861F7
Every structure of UniProt P61769
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7M8S · PDBe 7M8S · UniProt Q861F7 · UniProt P61769 · UniProt P0DTC2

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