MolNFT v1 · #76939 · protein

Plasticity of human CD8 binding to peptide-HLA-A*2402

3QZW · HLA class I histocompatibility antigen, a-24 alpha chain: “Plasticity of human CD8 binding to peptide-HLA-A*2402”. X-ray diffraction, 19 pockets (best druggability 0.82). MolNFT v1 #76939 on GenesisL1: 3D structure, binding sites…

PDB: 3QZW
Type: protein
Length: 1,224 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-24 alpha chain; Beta-2-microglobulin; 10-mer…
UniProt: P05534, P61769, Q9YYU8, P01732
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-24 alpha chain	protein	274	27% helix, 39% strand	P05534
B, E	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
C, F	10-mer peptide from protein nef	protein	10	0% helix, 0% strand	Q9YYU8
G, H, I, J	T-cell surface glycoprotein CD8 alpha chain	protein	114	3% helix, 46% strand	P01732

Pockets

19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	877	0.82	0.85	92	empty
2	1195	0.82	0.83	103	empty
3	856	0.72	0.77	89	empty
4	816	0.69	0.75	74	empty
5	50	0.66	0.96	19	empty

Interfaces

18 interfaces between chains.

A–B · 1392 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1369 Å² buried · 22 hydrogen bonds · protein-protein
I–J · 1009 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 1000 Å² buried · 7 hydrogen bonds · protein-protein
D–F · 968 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

3QZW · Plasticity of human CD8 binding to peptide-HLA-A*2402 · the same entry in another collection · chain J against J, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E 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 P05534
Every structure of UniProt P61769
Every structure of UniProt Q9YYU8
Every structure of UniProt P01732
Elsewhere: RCSB PDB 3QZW · PDBe 3QZW · UniProt P05534 · UniProt P61769 · UniProt Q9YYU8 · UniProt P01732

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