MolNFT v1 · #134924 · protein

Murine class I major histocompatibility complex H-2DB in complex with lcmv-derived GP33 and T cell receptor P14

5TJE · H-2 class I histocompatibility antigen, D-B alpha chain: “Murine class I major histocompatibility complex H-2DB in complex with lcmv-derived GP33 and T cell receptor…”. X-ray diffraction, 19 pockets (best druggability 0.72). MolNFT…

PDB: 5TJE
Type: protein
Length: 1,460 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; Alpha…
UniProt: P01899, P01887
Pockets: 19 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	275	24% helix, 38% strand	P01899
B, D	Beta-2-microglobulin	protein	98	0% helix, 47% strand	P01887
C	H-2 class I histocompatibility antigen, D-B alpha chain	protein	274	24% helix, 38% strand	P01899
G	Alpha chain of murine T cell receptor P14	protein	112	3% helix, 54% strand	—
H	Beta chain of murine T cell receptor P14	protein	232	4% helix, 48% strand	—
E	Alpha chain of murine T cell receptor P14	protein	116	3% helix, 53% strand	—
F	Beta chain of murine T cell receptor P14	protein	237	4% helix, 44% strand	—
I, J	Peptide GP33-41 from lcmv	protein	9	0% helix, 0% strand	—

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	813	0.72	0.77	72	empty
2	742	0.69	0.76	64	empty
3	256	0.69	0.85	52	empty
4	705	0.69	0.76	56	empty
5	193	0.67	0.86	39	empty

Interfaces

17 interfaces between chains.

C–D · 1237 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1235 Å² buried · 18 hydrogen bonds · protein-protein
C–J · 968 Å² buried · 24 hydrogen bonds · protein-protein
A–I · 964 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 882 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5TJE · Murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33… · the same entry in another collection · chain J against J, 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
Elsewhere: RCSB PDB 5TJE · PDBe 5TJE · UniProt P01899 · UniProt P01887

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