MolNFT v1 · #2589 · protein

Crystal structure analysis of the GAMMA/DELTA T cell ligand T22

1C16 · MHC-like protein T22: “Crystal structure analysis of the GAMMA/DELTA T cell ligand T22”. X-ray diffraction, 20 pockets (best druggability 0.69). MolNFT v1 #2589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1C16
Type: protein
Length: 1,430 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC-like protein T22; Protein (beta-2-microglobulin)
UniProt: Q31615, P61769
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, G	MHC-like protein T22	protein	260	19% helix, 41% strand	Q31615
B, D, F, H	Protein (beta-2-microglobulin)	protein	99	0% helix, 47% strand	P61769
E	MHC-like protein T22	protein	254	20% helix, 41% strand	Q31615

Pockets

20 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	734	0.69	0.77	62	empty
2	703	0.69	0.77	62	empty
3	704	0.69	0.77	61	empty
4	689	0.69	0.77	63	empty
5	85	0.49	0.83	18	empty

Interfaces

6 interfaces between chains.

G–H · 1248 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1247 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1228 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1227 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 736 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

1C16 · Crystal structure analysis of the GAMMA/DELTA T cell ligand T22 · the same entry in another collection · chain H against H, 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 Q31615
Every structure of UniProt P61769
Elsewhere: RCSB PDB 1C16 · PDBe 1C16 · UniProt Q31615 · UniProt P61769

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