MolNFT v1 · #58636 · protein

Crystal structure of CD8ALPHA-beta in complex with yts 156.7 Fab

3B9K · Fab light chain: “Crystal structure of CD8ALPHA-beta in complex with yts 156.7 Fab”. X-ray diffraction, 1 ligand (NAG), 18 pockets (best druggability 0.59). MolNFT v1 #58636 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3B9K
Type: protein
Length: 1,324 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain; T-cell surface glycoprotein CD8 alpha chain; T-cell…
UniProt: P01731, P10300
Ligands: NAG
Pockets: 18 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, C	Fab light chain	protein	213	8% helix, 48% strand	—
H, D	Fab heavy chain	protein	214	6% helix, 48% strand	—
A, E	T-cell surface glycoprotein CD8 alpha chain	protein	118	3% helix, 53% strand	P01731
B, F	T-cell surface glycoprotein CD8 beta chain	protein	117	3% helix, 50% strand	P10300

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	70	0.59	0.89	18	empty
2	378	0.57	0.75	57	empty
3	269	0.52	0.75	34	empty
4	249	0.50	0.75	41	empty
5	134	0.47	0.78	22	empty

Interfaces

10 interfaces between chains.

C–D · 1849 Å² buried · 17 hydrogen bonds · protein-protein
L–H · 1829 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1079 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1076 Å² buried · 7 hydrogen bonds · protein-protein
H–B · 631 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3B9K · Crystal structure of CD8alpha-beta in complex with YTS 156.7 FAB · the same entry in another collection · chain F against F, TM-score 1.00
P01731 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD8 alpha chain (P01731) · a predicted model of the same protein · chain E against A, TM-score 0.94
P10300 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD8 beta chain (P10300) · a predicted model of the same protein · chain F against A, TM-score 0.92

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 P01731
Every structure of UniProt P10300
Elsewhere: RCSB PDB 3B9K · PDBe 3B9K · UniProt P01731 · UniProt P10300

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