MolNFT v1 · #94375 · protein

Crystal structure of H2DB-H155A-np

4HUX · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of H2DB-H155A-np”. X-ray diffraction, 4 pockets (best druggability 0.61). MolNFT v1 #94375 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4HUX
Type: protein
Length: 380 residues
Chains: 3
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; Np peptide
UniProt: P01899, P01887
Pockets: 4 · best druggability 0.61

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	273	26% helix, 39% strand	P01899
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
C	Np peptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B
ACT · Acetate ion · additive · chains 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	518	0.61	0.74	56	empty
2	127	0.47	0.78	26	GOL
3	66	0.45	0.83	16	empty
4	52	0.39	0.81	17	empty

Interfaces

2 interfaces between chains.

A–B · 1146 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 885 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4HUX · Crystal Structure of H2Db-H155A-NP · the same entry in another collection · chain A against A, 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 4HUX · PDBe 4HUX · UniProt P01899 · UniProt P01887

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