Research workbench

42F3 TCR PCPE3/H-2LD complex

Analyse 42F3 TCR PCPE3/H-2LD complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N0C
Type: protein
Length: 1,235 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, L-D alpha chain; PCPE3; 42F3 vmch alpha; 42F3…
UniProt: P01897
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, L-D alpha chain	protein	173	38% helix, 33% strand	P01897
B, F	PCPE3	protein	9	0% helix, 0% strand	—
C	42F3 vmch alpha	protein	195	2% helix, 42% strand	—
D, H	42F3 vmch beta	protein	239	8% helix, 52% strand	—
E	H-2 class I histocompatibility antigen, L-D alpha chain	protein	174	37% helix, 32% strand	P01897
G	42F3 vmch alpha	protein	197	2% helix, 42% strand	—

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	393	0.76	0.86	65	empty
2	741	0.76	0.81	72	empty
3	1134	0.72	0.76	80	empty
4	331	0.70	0.83	46	empty
5	289	0.69	0.84	52	empty

Interfaces

18 interfaces between chains.

G–H · 2097 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1999 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 952 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 926 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 557 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4N0C · 42F3 TCR pCPE3/H-2Ld complex · the same entry in another collection · chain H against H, 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 E 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
Elsewhere: RCSB PDB 4N0C · PDBe 4N0C · UniProt P01897

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