Research workbench

Mch class I H-2KB molecule complexed with PBM1 peptide

Analyse Mch class I H-2KB molecule complexed with PBM1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NAN
Type: protein
Length: 770 residues
Chains: 6
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; PBM1…
UniProt: P01901, P01887
Pockets: 9 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, L	H-2 class I histocompatibility antigen, K-B alpha chain	protein	278	26% helix, 39% strand	P01901
P, I	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
M, Q	PBM1 peptide	protein	8	0% helix, 0% strand	—

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	699	0.67	0.75	60	empty
2	563	0.63	0.75	52	empty
3	173	0.50	0.78	36	empty
4	131	0.47	0.78	29	empty
5	61	0.45	0.83	18	empty

Interfaces

5 interfaces between chains.

H–P · 1292 Å² buried · 22 hydrogen bonds · protein-protein
L–I · 1257 Å² buried · 23 hydrogen bonds · protein-protein
L–Q · 932 Å² buried · 19 hydrogen bonds · protein-protein
H–M · 888 Å² buried · 18 hydrogen bonds · protein-protein
H–L · 180 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1NAN · Mch class I H-2KB molecule complexed with PBM1 peptide · the same entry in another collection · chain Q against Q, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain I 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
Elsewhere: RCSB PDB 1NAN · PDBe 1NAN · UniProt P01901 · UniProt P01887

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