Research workbench

Tap-B-associated rat MHC class I molecule

Analyse Tap-B-associated rat MHC class I molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KJV
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mature alpha chain of major histocompatibility complex class I antigen (heavy chain)…
UniProt: Q95565, P07151, Q9JJP9
Ligands: SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mature alpha chain of major histocompatibility complex class I antigen (heavy chain)	protein	276	30% helix, 38% strand	Q95565
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P07151
P	Peptide npr	protein	9	0% helix, 0% strand	Q9JJP9

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	751	0.71	0.78	60	empty
2	80	0.44	0.81	16	SO4
3	121	0.40	0.75	18	empty
4	53	0.35	0.79	17	empty

Interfaces

2 interfaces between chains.

A–B · 1407 Å² buried · 23 hydrogen bonds · protein-protein
A–P · 842 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1KJV · TAP-B-associated rat MHC class I molecule · the same entry in another collection · chain A against A, TM-score 1.00
P07151 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P07151) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q9JJP9 · AlphaFold monomer V2.0 prediction for ubiquilin-1 (Q9JJP9) · a predicted model of the same protein · chain P against A, TM-score 0.40

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 Q95565
Every structure of UniProt P07151
Every structure of UniProt Q9JJP9
Elsewhere: RCSB PDB 1KJV · PDBe 1KJV · UniProt Q95565 · UniProt P07151 · UniProt Q9JJP9

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