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Murine class I major histocompatibility complex H-2 db in complex with lcmv-derived GP33 altered peptide V3P and T-cell receptor P14

Analyse Murine class I major histocompatibility complex H-2 db in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TIL
Type: protein
Length: 1,462 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin…
UniProt: P01899, P01887, Q9QDK7
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 7 distinct chains · 10% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	275	27% helix, 40% strand	P01899
B, E	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
C, F	Pre-glycoprotein polyprotein gp complex	protein	9	0% helix, 0% strand	Q9QDK7
G	Alpha chain of P14 T cell receptor	protein	114	3% helix, 54% strand	—
H	Beta chain of murine T cell receptor P14	protein	230	4% helix, 51% strand	—
K	Alpha chain of murine P14 T cell receptor	protein	118	3% helix, 53% strand	—
L	Beta chain of murine T cell receptor P14	protein	236	7% helix, 49% strand	—

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	866	0.73	0.78	90	empty
2	860	0.73	0.78	83	empty
3	629	0.68	0.77	51	empty
4	345	0.67	0.81	52	empty
5	323	0.66	0.81	59	empty

Interfaces

17 interfaces between chains.

D–E · 1258 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1250 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 934 Å² buried · 24 hydrogen bonds · protein-protein
D–F · 933 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 872 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5TIL · Murine class I major histocompatibility complex H-2 Db in complex with LCMV-derived GP33… · the same entry in another collection · chain H against H, 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 P01899
Every structure of UniProt P01887
Every structure of UniProt Q9QDK7
Elsewhere: RCSB PDB 5TIL · PDBe 5TIL · UniProt P01899 · UniProt P01887 · UniProt Q9QDK7

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