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Structure of the 2C/KB/DEV8 complex

Analyse Structure of the 2C/KB/DEV8 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CKB
Type: protein
Length: 1,640 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha, beta T cell receptor; Major histocompatibility complex class I molecule K(B); DEV8…
UniProt: P01901, P01887
Pockets: 18 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Alpha, beta T cell receptor	protein	202	3% helix, 33% strand	—
B, D	Alpha, beta T cell receptor	protein	237	6% helix, 48% strand	—
H, I	Major histocompatibility complex class I molecule K(B)	protein	274	29% helix, 38% strand	P01901
P, Q	DEV8 peptide	protein	8	0% helix, 0% strand	—
L, M	Beta-2 microglobulin	protein	99	0% helix, 38% strand	P01887

Pockets

18 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	1106	0.73	0.77	78	empty
2	1177	0.73	0.76	78	empty
3	582	0.65	0.76	50	empty
4	540	0.64	0.76	45	empty
5	179	0.50	0.77	26	empty

Interfaces

14 interfaces between chains.

A–B · 2208 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2158 Å² buried · 23 hydrogen bonds · protein-protein
H–L · 1371 Å² buried · 19 hydrogen bonds · protein-protein
I–M · 1366 Å² buried · 20 hydrogen bonds · protein-protein
H–P · 901 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2CKB · Structure of the 2C/KB/DEV8 complex · the same entry in another collection · chain M against M, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain L against A, TM-score 0.97

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 P01901
Every structure of UniProt P01887
Elsewhere: RCSB PDB 2CKB · PDBe 2CKB · UniProt P01901 · UniProt P01887

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