MolNFT v1 · #54628 · protein

The structure of hdeb

2XUV: “The structure of hdeb”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.47). MolNFT v1 #54628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XUV
Type: protein
Length: 280 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hdeb
UniProt: P0AET2
Ligands: SO4
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 3 distinct chains · 60% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hdeb	protein	69	61% helix, 7% strand	P0AET2
B	Hdeb	protein	71	59% helix, 7% strand	P0AET2
C, D	Hdeb	protein	70	61% helix, 6% strand	P0AET2

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.47	0.76	30	empty

Interfaces

5 interfaces between chains.

C–D · 1244 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1233 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 229 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 224 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 145 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 32 modified, 4 disulfide (methylation, disulfide).

Compared structures

2XUV · The structure of HdeB · the same entry in another collection · chain A against A, TM-score 1.00
P0AET2 · AlphaFold monomer V2.0 prediction for acid stress chaperone hdeb (P0AET2) · a predicted model of the same protein · chain C against A, TM-score 0.86

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 P0AET2
Elsewhere: RCSB PDB 2XUV · PDBe 2XUV · UniProt P0AET2

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