Research workbench

Murine alloreactive scfv TCR-peptide-MHC class I molecule complex

Analyse Murine alloreactive scfv TCR-peptide-MHC class I molecule complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NAM
Type: protein
Length: 612 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BM3.3 T cell receptor alpha-chain; BM3.3 T cell receptor beta-chain; H-2 class I…
UniProt: P01901, P11212, P01887
Ligands: NAG
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BM3.3 T cell receptor alpha-chain	protein	116	5% helix, 50% strand	—
B	BM3.3 T cell receptor beta-chain	protein	113	0% helix, 57% strand	—
H	H-2 class I histocompatibility antigen, K-B alpha chain precursor	protein	275	25% helix, 35% strand	P01901
P	Nucleocapsid	protein	8	0% helix, 0% strand	P11212
L	Beta-2-microglobulin	protein	100	0% helix, 32% strand	P01887

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Pockets

6 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	215	0.72	0.88	38	empty
2	606	0.64	0.75	54	empty
3	237	0.54	0.77	42	empty
4	156	0.52	0.80	29	empty
5	203	0.51	0.77	34	empty

Interfaces

7 interfaces between chains.

H–L · 1263 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 994 Å² buried · 22 hydrogen bonds · protein-protein
H–P · 933 Å² buried · 22 hydrogen bonds · protein-protein
A–H · 490 Å² buried · 5 hydrogen bonds · protein-protein
B–H · 392 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

1NAM · Murine alloreactive scfv TCR-peptide-MHC class I molecule complex · the same entry in another collection · chain A against A, 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 0.90

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 P11212
Every structure of UniProt P01887
Elsewhere: RCSB PDB 1NAM · PDBe 1NAM · UniProt P01901 · UniProt P11212 · UniProt P01887

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