MolNFT v1 · #71339 · protein

TCR 21.30 in complex with MHC class II I-AG7HEL(11-27)

3MBE · MHC class II H2-IAG7 alpha chain: “TCR 21.30 in complex with MHC class II I-AG7HEL(11-27)”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.71). MolNFT v1 #71339 on GenesisL1: 3D structure, binding sites and…

PDB: 3MBE
Type: protein
Length: 1,614 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class II H2-IAG7 alpha chain; MHC class II H2-IAG7 beta chain; Peptide hel 11-27; TCR…
UniProt: P04228, Q31135, P00698
Ligands: NAG
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	MHC class II H2-IAG7 alpha chain	protein	184	13% helix, 42% strand	P04228
B, F	MHC class II H2-IAG7 beta chain	protein	178	18% helix, 40% strand	Q31135
P, Q	Peptide hel 11-27	protein	17	0% helix, 12% strand	P00698
C, G	TCR 21.3 alpha chain	protein	192	0% helix, 43% strand	—
D, H	TCR 21.3 beta chain	protein	236	6% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains D, H, A, E

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

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	881	0.71	0.76	71	empty
2	906	0.71	0.76	83	empty
3	261	0.53	0.76	40	empty
4	239	0.52	0.76	36	empty
5	64	0.46	0.83	17	empty

Interfaces

20 interfaces between chains.

E–F · 2573 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 2572 Å² buried · 44 hydrogen bonds · protein-protein
C–D · 2068 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 2058 Å² buried · 20 hydrogen bonds · protein-protein
F–Q · 748 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3MBE · TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27) · the same entry in another collection · chain G against G, TM-score 1.00
P04228 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P04228
Every structure of UniProt Q31135
Every structure of UniProt P00698
Elsewhere: RCSB PDB 3MBE · PDBe 3MBE · UniProt P04228 · UniProt Q31135 · UniProt P00698

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