MolNFT v1 · #101130 · protein

The M33 TCR P3M33L/H-2 ld complex

4NHU · 2C M33 alpha vmch chimera: “The M33 TCR P3M33L/H-2 ld complex”. X-ray diffraction, 18 pockets (best druggability 0.74). MolNFT v1 #101130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NHU
Type: protein
Length: 1,243 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2C M33 alpha vmch chimera; 2C M33 beta vmch chimera; H-2 class I histocompatibility…
UniProt: P01897
Pockets: 18 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2C M33 alpha vmch chimera	protein	197	3% helix, 43% strand	—
B, D	2C M33 beta vmch chimera	protein	238	7% helix, 51% strand	—
E	H-2 class I histocompatibility antigen, L-D alpha chain	protein	186	34% helix, 30% strand	P01897
C	2C M33 alpha vmch chimera	protein	199	3% helix, 43% strand	—
G	H-2 class I histocompatibility antigen, L-D alpha chain	protein	185	35% helix, 30% strand	P01897

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1179	0.74	0.77	80	empty
2	622	0.73	0.81	63	empty
3	380	0.65	0.79	49	empty
4	240	0.62	0.81	42	empty
5	58	0.54	0.88	19	empty

Interfaces

8 interfaces between chains.

C–D · 2082 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2079 Å² buried · 24 hydrogen bonds · protein-protein
E–C · 568 Å² buried · 5 hydrogen bonds · protein-protein
A–G · 503 Å² buried · 6 hydrogen bonds · protein-protein
D–G · 441 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4NHU · The M33 TCR p3M33l/H-2 Ld Complex · the same entry in another collection · chain G against G, 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 G against A, TM-score 0.92

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
Elsewhere: RCSB PDB 4NHU · PDBe 4NHU · UniProt P01897

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