MolNFT v1 · #59720 · protein

Crystal structure of mouse MHC class II I-AB/3K peptide complexed with mouse TCR 2W20

3C6L · TCR 2W20 alpha chain: “Crystal structure of mouse MHC class II I-AB/3K peptide complexed with mouse TCR 2W20”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.83). MolNFT v1 #59720 on GenesisL1: 3D structure…

PDB: 3C6L
Type: protein
Length: 1,580 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TCR 2W20 alpha chain; TCR 2W20 beta chain; H-2 class II histocompatibility antigen, a-B…
UniProt: P14434, P14483
Ligands: CA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TCR 2W20 alpha chain	protein	185	0% helix, 38% strand	—
B	TCR 2W20 beta chain	protein	227	6% helix, 43% strand	—
C, G	H-2 class II histocompatibility antigen, a-B alpha chain	protein	182	12% helix, 45% strand	P14434
D, H	3K peptide, LINKER,AND H-2 class II histocompatibility antigen (a beta chain)	protein	192	17% helix, 33% strand	P14483
E	TCR 2W20 alpha chain	protein	184	2% helix, 38% strand	—
F	TCR 2W20 beta chain	protein	236	6% helix, 44% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, C, D, E, G, H

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	492	0.83	0.89	34	empty
2	854	0.80	0.83	65	empty
3	925	0.79	0.81	79	empty
4	1063	0.74	0.77	82	empty
5	990	0.72	0.76	88	empty

Interfaces

15 interfaces between chains.

C–D · 2946 Å² buried · 46 hydrogen bonds · protein-protein
G–H · 2938 Å² buried · 43 hydrogen bonds · protein-protein
E–F · 2162 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2153 Å² buried · 22 hydrogen bonds · protein-protein
D–H · 1093 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

3C6L · Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20 · the same entry in another collection · chain H against H, TM-score 1.00
P14434 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-B alpha… · a predicted model of the same protein · chain C against A, TM-score 0.95
P14483 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a beta… · a predicted model of the same protein · chain D against A, TM-score 0.78

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 P14434
Every structure of UniProt P14483
Elsewhere: RCSB PDB 3C6L · PDBe 3C6L · UniProt P14434 · UniProt P14483

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