MolNFT v1 · #12513 · protein

MHC class I H-2KB molecule complexed with PKB1 peptide

1KJ3 · H-2KB MHC class I molecule alpha chain: “MHC class I H-2KB molecule complexed with PKB1 peptide”. X-ray diffraction, 9 pockets (best druggability 0.63). MolNFT v1 #12513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KJ3
Type: protein
Length: 771 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2KB MHC class I molecule alpha chain; Naturally processed octapeptide PKB1; Beta-2…
UniProt: P01901, O08582, P01887
Pockets: 9 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	H-2KB MHC class I molecule alpha chain	protein	279	28% helix, 39% strand	P01901
P, Q	Naturally processed octapeptide PKB1	protein	8	0% helix, 0% strand	O08582
L, M	Beta-2 microglobulin	protein	99	0% helix, 49% strand	P01887
I	H-2KB MHC class I molecule alpha chain	protein	278	27% helix, 39% strand	P01901

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	602	0.63	0.74	53	empty
2	584	0.62	0.74	54	empty
3	138	0.42	0.75	29	empty
4	60	0.42	0.82	16	empty
5	65	0.41	0.81	16	empty

Interfaces

5 interfaces between chains.

I–M · 1281 Å² buried · 24 hydrogen bonds · protein-protein
H–L · 1278 Å² buried · 23 hydrogen bonds · protein-protein
I–Q · 900 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 900 Å² buried · 15 hydrogen bonds · protein-protein
H–I · 170 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1KJ3 · Mhc Class I H-2Kb molecule complexed with pKB1 peptide · the same entry in another collection · chain M against M, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain M against A, TM-score 0.99
P01901 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-B alpha… · a predicted model of the same protein · chain I against A, TM-score 0.95
O08582 · AlphaFold monomer V2.0 prediction for GTP-binding protein 1 (O08582) · a predicted model of the same protein · chain P against A, TM-score 0.57

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 O08582
Every structure of UniProt P01887
Elsewhere: RCSB PDB 1KJ3 · PDBe 1KJ3 · UniProt P01901 · UniProt O08582 · UniProt P01887

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