MolNFT v1 · #46898 · protein

Structure of the 2C/LD/QL9 allogeneic complex

2OI9 · Major histocompatibility complex protein: “Structure of the 2C/LD/QL9 allogeneic complex”. X-ray diffraction, 6 pockets (best druggability 0.64). MolNFT v1 #46898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2OI9
Type: protein
Length: 405 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex protein; T cell receptor alpha chain; T cell receptor…
UniProt: P01897, P01738, A2NTY6
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 20% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex protein	protein	175	38% helix, 34% strand	P01897
B	T cell receptor alpha chain	protein	110	8% helix, 51% strand	P01738
C	T cell receptor beta chain	protein	111	3% helix, 52% strand	A2NTY6
Q	Peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP) (leu)	protein	9	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	288	0.64	0.81	40	empty
2	73	0.40	0.79	18	empty
3	76	0.37	0.77	15	empty
4	78	0.34	0.76	18	empty
5	67	0.32	0.75	16	empty

Interfaces

6 interfaces between chains.

A–Q · 922 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 813 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 453 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 312 Å² buried · 1 hydrogen bond · protein-protein
C–Q · 219 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

2OI9 · Structure of the 2C/Ld/QL9 allogeneic complex · the same entry in another collection · chain A against A, TM-score 1.00
P01897 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, L-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
P01738 · AlphaFold monomer V2.0 prediction for T-cell receptor alpha chain V region PHDS58 (P01738) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P01897
Every structure of UniProt P01738
Every structure of UniProt A2NTY6
Elsewhere: RCSB PDB 2OI9 · PDBe 2OI9 · UniProt P01897 · UniProt P01738 · UniProt A2NTY6

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