Research workbench

How TCR-like antibody recognizes MHC-bound peptide

Analyse How TCR-like antibody recognizes MHC-bound peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CVH
Type: protein
Length: 1,603 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; Ovalbumin…
UniProt: P01901, P01887, P01012
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 6 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, M	H-2 class I histocompatibility antigen, K-B alpha chain	protein	274	26% helix, 39% strand	P01901
B, N	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
C, O	Ovalbumin	protein	8	0% helix, 0% strand	P01012
H	25-D1.16 heavy chain	protein	213	7% helix, 50% strand	—
L, R	25-D1.16 light chain	protein	209	6% helix, 52% strand	—
Q	25-D1.16 heavy chain	protein	210	4% helix, 47% strand	—

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	593	0.69	0.78	55	empty
2	432	0.68	0.80	51	empty
3	66	0.67	0.94	23	empty
4	454	0.67	0.79	32	empty
5	327	0.65	0.80	40	empty

Interfaces

17 interfaces between chains.

Q–R · 1718 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1680 Å² buried · 15 hydrogen bonds · protein-protein
M–N · 1283 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1213 Å² buried · 19 hydrogen bonds · protein-protein
M–O · 848 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

3CVH · How TCR-like antibody recognizes MHC-bound peptide · the same entry in another collection · chain R against R, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P01887
Every structure of UniProt P01012
Elsewhere: RCSB PDB 3CVH · PDBe 3CVH · UniProt P01901 · UniProt P01887 · UniProt P01012

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