MolNFT v1 · #15771 · protein

The crystal structure of a TL/CD8AA complex at 2.1A RESOLUTION:IMPLICATIONS for memory T cell generation, co-receptor preference and affinity

1NEZ · H-2 class I histocompatibility antigen, TLA(C) alpha chain: “The crystal structure of a TL/CD8AA complex at 2.1A RESOLUTION:IMPLICATIONS for memory T cell generation…”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability…

PDB: 1NEZ
Type: protein
Length: 615 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, TLA(C) alpha chain; Beta-2-microglobulin; T-cell…
UniProt: P14433, P01887, P01731
Ligands: NAG
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, TLA(C) alpha chain	protein	274	27% helix, 41% strand	P14433
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
G	T-cell surface glycoprotein CD8 alpha chain	protein	122	5% helix, 51% strand	P01731
H	T-cell surface glycoprotein CD8 alpha chain	protein	120	3% helix, 49% strand	P01731

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G, H

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1115	0.84	0.85	108	empty
2	52	0.70	0.98	23	empty
3	327	0.62	0.79	46	empty
4	98	0.39	0.76	16	empty
5	83	0.34	0.75	21	NAG

Interfaces

5 interfaces between chains.

A–B · 1259 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1118 Å² buried · 6 hydrogen bonds · protein-protein
A–H · 954 Å² buried · 16 hydrogen bonds · protein-protein
A–G · 644 Å² buried · 9 hydrogen bonds · protein-protein
B–H · 285 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 glycan, 3 disulfide (N-glycosylation, disulfide).

Compared structures

1NEZ · The Crystal Structure of a TL/CD8aa Complex at 2.1A resolution:Implications for Memory T… · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
P01731 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD8 alpha chain (P01731) · a predicted model of the same protein · chain G against A, TM-score 0.95

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 P14433
Every structure of UniProt P01887
Every structure of UniProt P01731
Elsewhere: RCSB PDB 1NEZ · PDBe 1NEZ · UniProt P14433 · UniProt P01887 · UniProt P01731

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